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1. Enterosignatures define common bacterial guilds in the human gut microbiome

Author: Frioux, Clémence, Ansorge, Rebecca, Özkurt, Ezgi, Ghassemi Nedjad, Chabname, Fritscher, Joachim, Quince, Christopher, Waszak, Sebastian, Hildebrand, Falk, from patterns to models in computational biodiversity and biotechnology (PLEIADE), Laboratoire Bordelais de Recherche en Informatique (LaBRI), Université de Bordeaux (UB)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Centre National de la Recherche Scientifique (CNRS)-Université de Bordeaux (UB)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Centre National de la Recherche Scientifique (CNRS)-Inria Bordeaux - Sud-Ouest, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Biodiversité, Gènes & Communautés (BioGeCo), Université de Bordeaux (UB)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Quadram Institute, Biotechnology and Biological Sciences Research Council (BBSRC), Université de Bordeaux (UB)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Centre National de la Recherche Scientifique (CNRS), Earlham Institute [Norwich], Centre for Molecular Medicine Norway (NCMM), Faculty of Medicine [Oslo], University of Oslo (UiO)-University of Oslo (UiO)-Rigshospitalet [Copenhagen], Copenhagen University Hospital-Copenhagen University Hospital, and European Project: erc-stg-948219,EPYC
Subjects: non-negative matrix factorization, metagenomics, human gut microbiome, [STAT.ML]Statistics [stat]/Machine Learning [stat.ML], dysbiosis, enterotypes, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], enterosignatures
Abstract: International audience; The human gut microbiome composition is generally in a stable dynamic equilibrium, but it can deteriorate into dysbiotic states detrimental to host health. To disentangle the inherent complexity and capture the ecological spectrum of microbiome variability, we used 5,230 gut metagenomes to characterize signatures of bacteria commonly co-occurring, termed enterosignatures (ESs). We find five generalizable ESs dominated by either Bacteroides, Firmicutes, Prevotella, Bifidobacterium, or Escherichia. This model confirms key ecological characteristics known from previous enterotype concepts, while enabling the detection of gradual shifts in community structures.Temporal analysis implies that the Bacteroides-associated ES is “core” in the resilience of westernized gut microbiomes, while combinations with other ESs often complement the functional spectrum. The model reliably detects atypical gut microbiomes correlated with adverse host health conditions and/or the presence of pathobionts. ESs provide an interpretable and generic model that enables an intuitive characterization of gut microbiome composition in health and disease.
Published: 2023

2. Galaxy Training: A Powerful Framework for Teaching!

Author: Hiltemann, Saskia, Rasche, Helena, Gladman, Simon, Hotz, Hans-Rudolf, Larivière, Delphine, Blankenberg, Daniel, Jagtap, Pratik D., Wollmann, Thomas, Bretaudeau, Anthony, Goué, Nadia, Griffin, Timothy J., Royaux, Coline, Le Bras, Yvan, Mehta, Subina, Syme, Anna, Coppens, Frederik, Droesbeke, Bert, Soranzo, Nicola, Bacon, Wendi, Psomopoulos, Fotis, Gallardo-Alba, Cristóbal, Davis, John, Föll, Melanie Christine, Fahrner, Matthias, Doyle, Maria A., Serrano-Solano, Beatriz, Fouilloux, Anne Claire, van Heusden, Peter, Maier, Wolfgang, Clements, Dave, Heyl, Florian, on behalf of the Galaxy Training Network, [ missing ], Grüning, Björn, Batut, Bérénice, Erasmus University Medical Center [Rotterdam] (Erasmus MC), Albert-Ludwigs-Universität Freiburg, University of Melbourne, Friedrich Miescher Institute for Biomedical Research (FMI), Novartis Research Foundation, Pennsylvania State University (Penn State), Penn State System, Department of Genomic Medicine [Lerner Research Institute, Cleveland Clinic], Lerner Research Institute [Cleveland, OH, USA], Cleveland Clinic-Cleveland Clinic, University of Minnesota [Twin Cities] (UMN), University of Minnesota System, Heidelberg University, Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Université de Rennes (UR)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Rennes Angers, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Plateforme bioinformatique GenOuest [Rennes], Université de Rennes (UR)-Plateforme Génomique Santé Biogenouest®-Inria Rennes – Bretagne Atlantique, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-GESTION DES DONNÉES ET DE LA CONNAISSANCE (IRISA-D7), Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT), Université Clermont Auvergne (UCA), Muséum National d' Histoire Naturelle [Concarneau], Universiteit Gent = Ghent University (UGENT), Earlham Institute [Norwich], The Open University [Milton Keynes] (OU), Centre for Research and Technology Hellas (CERTH), Johns Hopkins University (JHU), University of Freiburg [Freiburg], Simula Research Laboratory [Lysaker] (SRL), South African National Bioinformatics Institute (SANBI), University of the Western Cape (UWC), Anaconda, Inc. [Austin], Plateforme Auvergne Bioinformatique (AuBi), Mésocentre Clermont Auvergne, Université Clermont Auvergne (UCA)-Université Clermont Auvergne (UCA), and Pathology
Subjects: Cellular and Molecular Neuroscience, Computational Theory and Mathematics, Ecology, Modeling and Simulation, Genetics, Biology and Life Sciences, ONLINE, STUDENTS, Molecular Biology, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Ecology, Evolution, Behavior and Systematics
Abstract: There is an ongoing explosion of scientific datasets being generated, brought on by recent technological advances in many areas of the natural sciences. As a result, the life sciences have become increasingly computational in nature, and bioinformatics has taken on a central role in research studies. However, basic computational skills, data analysis, and stewardship are still rarely taught in life science educational programs, resulting in a skills gap in many of the researchers tasked with analysing these big datasets. In order to address this skills gap and empower researchers to perform their own data analyses, the Galaxy Training Network (GTN) has previously developed the Galaxy Training Platform (https://training.galaxyproject.org), an open access, community-driven framework for the collection of FAIR (Findable, Accessible, Interoperable, Reusable) training materials for data analysis utilizing the user-friendly Galaxy framework as its primary data analysis platform. Since its inception, this training platform has thrived, with the number of tutorials and contributors growing rapidly, and the range of topics extending beyond life sciences to include topics such as climatology, cheminformatics, and machine learning. While initially aimed at supporting researchers directly, the GTN framework has proven to be an invaluable resource for educators as well. We have focused our efforts in recent years on adding increased support for this growing community of instructors. New features have been added to facilitate the use of the materials in a classroom setting, simplifying the contribution flow for new materials, and have added a set of train-the-trainer lessons. Here, we present the latest developments in the GTN project, aimed at facilitating the use of the Galaxy Training materials by educators, and its usage in different learning environments.
Published: 2023

3. Four functional profiles for fibre and mucin metabolism in the human gut microbiome

Author: Simon Labarthe, Sandra Plancade, Sebastien Raguideau, Florian Plaza Onate, Emmanuelle Le Chatelier, Marion Leclerc, Béatrice Laroche, from patterns to models in computational biodiversity and biotechnology (PLEIADE), Laboratoire Bordelais de Recherche en Informatique (LaBRI), Université de Bordeaux (UB)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Centre National de la Recherche Scientifique (CNRS)-Université de Bordeaux (UB)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Centre National de la Recherche Scientifique (CNRS)-Inria Bordeaux - Sud-Ouest, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Biodiversité, Gènes & Communautés (BioGeCo), Université de Bordeaux (UB)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Biodiversité, Gènes & Communautés (BioGeCo), Université de Bordeaux (UB)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Mathématiques et Informatique Appliquées du Génome à l'Environnement [Jouy-En-Josas] (MaIAGE), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Unité de Mathématiques et Informatique Appliquées de Toulouse (MIAT INRAE), Earlham Institute [Norwich], MetaGenoPolis (MGP (US 1367)), MICrobiologie de l'ALImentation au Service de la Santé (MICALIS), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Pendulum Therapeutics [San Francisco], Dynamiques de populations multi-échelles pour des systèmes physiologiques (MUSCA), Inria Saclay - Ile de France, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Physiologie de la reproduction et des comportements [Nouzilly] (PRC), Institut Français du Cheval et de l'Equitation [Saumur] (IFCE)-Université de Tours (UT)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Français du Cheval et de l'Equitation [Saumur] (IFCE)-Université de Tours (UT)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Mathématiques et Informatique Appliquées du Génome à l'Environnement [Jouy-En-Josas] (MaIAGE), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), ANR-11-DPBS-0001,MGP,MetaGenoPolis(2011), European Project: 609398,EC:FP7:PEOPLE,FP7-PEOPLE-2013-COFUND,AGREENSKILLSPLUS(2014), and Labarthe, Simon
Subjects: [SDV] Life Sciences [q-bio], [SDV]Life Sciences [q-bio], [INFO.INFO-MO] Computer Science [cs]/Modeling and Simulation, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], [INFO.INFO-MO]Computer Science [cs]/Modeling and Simulation, [INFO.INFO-BI] Computer Science [cs]/Bioinformatics [q-bio.QM]
Abstract: Background With the emergence of metagenomic data, multiple links between the gut microbiome and the host health have been shown. Deciphering these complex interactions require evolved analysis methods focusing on the microbial ecosystem functions. Despite the fact that host or diet-derived fibres are the most abundant nutrients available in the gut, the presence of distinct functional traits regarding fibre and mucin hydrolysis, fermentation and hydrogenotrophic processes has never been investigated. Results After manually selecting 91 KEGG orthologies and 33 glycoside hydrolases further aggregated in 101 functional descriptors representative of fibre and mucin degradation pathways in the gut microbiome, we used non-negative matrix factorization to mine metagenomic datasets. Four distinct metabolic profiles were further identified on a training set of 1153 samples and thoroughly validated on a large database of 2571 unseen samples from 5 external metagenomic cohorts. Profiles 1 and 2 are the main contributors to the fibre-degradation-related metagenome: they present contrasted involvement in fibre degradation and sugar metabolism and are differentially linked to dysbiosis, metabolic disease and inflammation. Profile 1 takes over Profile 2 inhealthy samples, and unbalance of these profiles characterize dysbiotic samples. Furthermore, high fibre diet favours a healthy balance between Profiles 1 and Profile 2. Profile 3 takes over Profile 2 during Crohn’s disease, inducing functional reorientations towards unusual metabolism such as fucose and H2S degradation or propionate, acetone and butanediol production. Profile 4 gathers under-represented functions, like methanogenesis. Two taxonomic makes up of the profiles were investigated, using either the covariation of 203 prevalent genomes or metagenomic species, both providing consistent results in line with their functional characteristics. This taxonomic characterization showed that Profiles 1 and 2 were respectively mainly composed of bacteria from the phyla Bacteroidetes and Firmicutes while Profile 3 is representative of Proteobacteria and Profile 4 of methanogens.Conclusions Integrating anaerobic microbiology knowledge with statistical learning can narrow down the metagenomic analysis to investigate functional profiles. Applying this approach to fibre degradation in the gut ended with 4 distinct functional profiles that can be easily monitored as markers of diet, dysbiosis, inflammation and disease.
Published: 2023

4. Democratizing knowledge representation with BioCypher

Author: Lobentanzer, Sebastian, Aloy, Patrick, Baumbach, Jan, Bohar, Balazs, Charoentong, Pornpimol, Danhauser, Katharina, Doğan, Tunca, Dreo, Johann, Dunham, Ian, Fernandez-Torras, Adrià, Gyori, Benjamin, Hartung, Michael, Hoyt, Charles Tapley, Klein, Christoph, Korcsmaros, Tamas, Maier, Andreas, Mann, Matthias, Ochoa, David, Pareja-Lorente, Elena, Preusse, Martin, Probul, Niklas, Schwikowski, Benno, Sen, Bünyamin, Strauss, Maximilian, Turei, Denes, Ulusoy, Erva, Wodke, Judith, Waltemath, Dagmar, Saez-Rodriguez, Julio, Carey, Vincent, Farr, Elias, Popp, Ferdinand, Universität Heidelberg [Heidelberg] = Heidelberg University, Institute for Research in Biomedicine [Barcelona, Spain] (IRB), University of Barcelona-Barcelona Institute of Science and Technology (BIST), University of Hamburg, Earlham Institute [Norwich], Biological Research Centre [Szeged] (BRC), Dr von Hauner Children's Hospital [Munich, Germany], Ludwig-Maximilians-Universität München (LMU), Hacettepe University = Hacettepe Üniversitesi, Biomédecine computationelle des systèmes / Computational systems biomedicine, Institut Pasteur [Paris] (IP)-Université Paris Cité (UPCité), Hub Bioinformatique et Biostatistique - Bioinformatics and Biostatistics HUB, European Bioinformatics Institute [Hinxton] (EMBL-EBI), EMBL Heidelberg, Harvard Medical School [Boston] (HMS), Dr Von Hauner Children's Hospital, Partenaires INRAE, Quadram Institute Bioscience [Norwich, U.K.] (QIB), Biotechnology and Biological Sciences Research Council (BBSRC), Imperial College London, Universität zu Köln = University of Cologne, Max-Planck-Institut für Biochemie = Max Planck Institute of Biochemistry (MPIB), Max-Planck-Gesellschaft, German Center for Diabetes Research - Deutsches Zentrum für Diabetesforschung [Neuherberg] (DZD), University of Medicine Greifswald, Brigham & Women’s Hospital [Boston] (BWH), German Cancer Research Center - Deutsches Krebsforschungszentrum [Heidelberg] (DKFZ), European Project: 965193, H2020-EU.3.1. - SOCIETAL CHALLENGES - Health, demographic change and well-being H2020-EU.3.1.5. - Methods and data ,DECIDER(2021), European Project: 066490,WT::(2003), European Project: 031L0181B,LaMarck, European Project: 031L0212A,SMART-CARE, European Project: W911NF-20-1-0255, and European Project: 01ZZ2019,MIRACUM
Subjects: prior knowledge, knowledge graph, federated learning, harmonisation, FAIRness, ontology, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], database
Abstract: International audience; Standardising the representation of biomedical knowledge among allresearchers is an insurmountable task, hindering the effectiveness of manycomputational methods. To facilitate harmonisation and interoperability despitethis fundamental challenge, we propose to standardise the framework ofknowledge graph creation instead. We implement this standardisation inBioCypher, a FAIR (findable, accessible, interoperable, reusable) framework totransparently build biomedical knowledge graphs while preserving provenances ofthe source data. Mapping the knowledge onto biomedical ontologies helps tobalance the needs for harmonisation, human and machine readability, and ease ofuse and accessibility to non-specialist researchers. We demonstrate the usefulnessof the framework on a variety of use cases, from maintenance of task-specificknowledge stores, to interoperability between biomedical domains, to on-demandbuilding of task-specific knowledge graphs for federated learning. BioCypher(https://biocypher.org) thus facilitates automating knowledge-based biomedicalresearch, and we encourage the community to further develop and use it.
Published: 2023

5. From bag-of-genes to bag-of-genomes: metabolic modelling of communities in the era of metagenome-assembled genomes

Author: Falk Hildebrand, Tamas Korcsmaros, Clémence Frioux, Dipali Singh, from patterns to models in computational biodiversity and biotechnology (PLEIADE), Laboratoire Bordelais de Recherche en Informatique (LaBRI), Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Inria Bordeaux - Sud-Ouest, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Biodiversité, Gènes & Communautés (BioGeCo), Université de Bordeaux (UB)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Quadram Institute, Earlham Institute [Norwich], FH’s salary is funded by the BBSRC Institute Strategic Programme Gut Microbes and Health BB/r012490/1, its constituent project BBS/ e/F/000Pr10355. TK is funded through the BBSRC Core Strategic Programme Grant (Genomes to Food Security) BB/CSP17270/1 and its constituent work package BBS/E/T/000PR9817. DS is funded by the BBSRC Institute Strategic Programme Microbes in the Food Chain BB/R012504/1 and its constituent project 'Microbial Survival in the Food Chain' BBS/E/F/000PR10349., Université de Bordeaux (UB)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Centre National de la Recherche Scientifique (CNRS)-Université de Bordeaux (UB)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Centre National de la Recherche Scientifique (CNRS)-Inria Bordeaux - Sud-Ouest, and Biotechnology and Biological Sciences Research Council (BBSRC)
Subjects: Bioinformatics, lcsh:Biotechnology, Systems biology, Biophysics, Context (language use), Review Article, Computational biology, Biology, Gene Functions, Biochemistry, Genome, 03 medical and health sciences, Taxonomic composition, 0302 clinical medicine, Single species, Models, Structural Biology, lcsh:TP248.13-248.65, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Genetics, Gene, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, Metabolic modelling, 0303 health sciences, Microbiota, Metagenomics Metagenomic assembled genomes, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Computer Science Applications, Metabolism, Metagenomics, 030220 oncology & carcinogenesis, Metagenomic-assembled genomes, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], Biotechnology
Abstract: Metagenomic sequencing of complete microbial communities has greatly enhanced our understanding of the taxonomic composition of microbiotas. This has led to breakthrough developments in bioinformatic disciplines such as assembly, gene clustering, metagenomic binning of species genomes and the discovery of an incredible, so far undiscovered, taxonomic diversity. However, functional annotations and estimating metabolic processes from single species – or communities – is still challenging. Earlier approaches relied mostly on inferring the presence of key enzymes for metabolic pathways in the whole metagenome, ignoring the genomic context of such enzymes, resulting in the ‘bag-of-genes’ approach to estimate functional capacities of microbiotas. Here, we review recent developments in metagenomic bioinformatics, with a special focus on emerging technologies to simulate and estimate metabolic information, that can be derived from metagenomic assembled genomes. Genome-scale metabolic models can be used to model the emergent properties of microbial consortia and whole communities, and the progress in this area is reviewed. While this subfield of metagenomics is still in its infancy, it is becoming evident that there is a dire need for further bioinformatic tools to address the complex combinatorial problems in modelling the metabolism of large communities as a ‘bag-of-genomes’.
Published: 2020

6. Strainberry: automated strain separation in low-complexity metagenomes using long reads

Author: Vicedomini, Riccardo, Quince, Christopher, Darling, Aaron E., Chikhi, Rayan, Algorithmes pour les séquences biologiques - Sequence Bioinformatics, Institut Pasteur [Paris] (IP)-Université Paris Cité (UPCité), Warwick Medical School, University of Warwick [Coventry], Earlham Institute [Norwich], Quadram Institute, Biotechnology and Biological Sciences Research Council (BBSRC), iThree Institute, University of Technology Sydney (UTS), R.V. and R.C. are funded by ANR INCEPTION (PIA/ANR-16-CONV-0005) and R.C. by ANR PRAIRIE (ANR-19-P3IA-0001) and ANR SeqDigger (ANR-19-CE45-0008). C.Q. is funded through 'Strain resolved metagenomics for medical microbiology' MRC MR/S037195/1 and the 'CLIMB-BIG-DATA' consortium MR/T030062/1. A.E.D.’s contributions to this research were supported in part by the Australian Government through the Australian Research Council Discovery Projects funding scheme (project DP180101506)., ANR-16-CONV-0005,INCEPTION,Institut Convergences pour l'étude de l'Emergence des Pathologies au Travers des Individus et des populatiONs(2016), ANR-19-P3IA-0001,PRAIRIE,PaRis Artificial Intelligence Research InstitutE(2019), ANR-19-CE45-0008,SeqDigger,Moteur de recherche de donne´es de se´quenc¸age en ge´nomique environnementale(2019), and Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS)
Subjects: Bacteria, Bioinformatics, Science, MESH: Genomics, Computational Biology, High-Throughput Nucleotide Sequencing, Genomics, MESH: Metagenome, MESH: Genome, Bacterial, Article, MESH: Bacteria, Species Specificity, Genome assembly algorithms, Metagenome, MESH: Species Specificity, Metagenomics, MESH: Metagenomics, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], MESH: High-Throughput Nucleotide Sequencing, Software, Genome, Bacterial, MESH: Computational Biology
Abstract: High-throughput short-read metagenomics has enabled large-scale species-level analysis and functional characterization of microbial communities. Microbiomes often contain multiple strains of the same species, and different strains have been shown to have important differences in their functional roles. Recent advances on long-read based methods enabled accurate assembly of bacterial genomes from complex microbiomes and an as-yet-unrealized opportunity to resolve strains. Here we present Strainberry, a metagenome assembly pipeline that performs strain separation in single-sample low-complexity metagenomes and that relies uniquely on long-read data. We benchmarked Strainberry on mock communities for which it produces strain-resolved assemblies with near-complete reference coverage and 99.9% base accuracy. We also applied Strainberry on real datasets for which it improved assemblies generating 20-118% additional genomic material than conventional metagenome assemblies on individual strain genomes. We show that Strainberry is also able to refine microbial diversity in a complex microbiome, with complete separation of strain genomes. We anticipate this work to be a starting point for further methodological improvements on strain-resolved metagenome assembly in environments of higher complexities., Existing long-read de novo assembly methods can partially, but not completely, separate strains. Here, the authors develop Strainberry, a metagenome assembly bioinformatic pipeline that exclusively uses longread data to accurately separate and reconstruct strain genomes from single-sample low-complexity microbiomes.
Published: 2021

7. Describing variability in pig genes involved in coronavirus infections for a One Health perspective in conservation of animal genetic resources

Author: Giuseppina Schiavo, Valeria Taurisano, Raquel Quintanilla, Anisa Ribani, Juan García-Casco, Rui Charneca, Valerio Joe Utzeri, Marie-José Mercat, Estefania Alves, Fabián García, Graham J Etherington, Samuele Bovo, Juliette Riquet, Danijel Karolyi, Christoph Zimmer, Ivona Djurkin Kušec, Federica Di Palma, Ana Isabel Fernández, G. Usai, Violeta Razmaite, María Muñoz, Yolanda Núñez, José Pedro Araújo, Martin Škrlep, Radomir Savić, J.M. Martins, Maurizio Gallo, Luca Fontanesi, Čedomir Radović, Mohamad Ballan, Cristina Óvilo, Riccardo Bozzi, University of Bologna, Instituto Nacional de Investigación Agropecuaria (INIA), Centro de Investigação de Montanha [Bragança, Portugal] (CIMO), Instituto Politécnico de Bragança, Department of Agriculture, Food, Environment and Forestry (DAGRI), Università degli Studi di Firenze = University of Florence [Firenze] (UNIFI), Universidade de Évora, University of East Anglia [Norwich] (UEA), Josip Juraj Strossmayer University of Osijek, Earlham Institute [Norwich], University of Zagreb, Associazione Nazionale Allevatori Suini, Institut du Porc (IFIP), Institute of Agrifood Research and Technology (IRTA), Institute for Animal Husbandry, Lithuanian University of Health Sciences [Kaunas, Lithuania], Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), University of Belgrade [Belgrade], Kmetijski Inštitut Slovenije (KIS), AGRIS sardegna, Bäuerliche Erzeugergemeinschaft Schwäbisch Hall (BESH), European Cooperation in Science and Technology (COST)Ministry of Foreign Affairs of ItalyUniversity of Bologna RFO 2016-2019 programmesItalian MIUR 2017 PigPhenomics projectEuropean Commission634476European Open Science Cloud (EOSC) Secretariat, project 'Application of animal genomics and data mining to predict and monitor novel coronavirus potential infections (VirAnimalOne)'EGI call for COVID-19 research projects (AnGen1H project)Por Fesr Emilia-Romagna 2014-2020 (actions 1.1.4 and 1.2.2-Bando per sostenere progetti di ricerca ed innovazione per lo sviluppo di soluzioni finalizzate al contrasto dell'epidemia da COVID-19-Project LIVESTOCK-STOP-COVI), European Project: 634476,H2020,H2020-SFS-2014-2,TREASURE(2015), Producció Animal, Genètica i Millora Animal, University of Bologna/Università di Bologna, Università degli Studi di Firenze = University of Florence (UniFI), Institut de Recerca i Tecnologia Agroalimentàries = Institute of Agrifood Research and Technology (IRTA), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-École nationale supérieure agronomique de Toulouse (ENSAT), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Università di Bologna, European Commission, Bovo, Samuele, Schiavo, Giuseppina, Ribani, Anisa, Utzeri, Valerio J, Taurisano, Valeria, Araujo, Jose P, Bozzi, Riccardo, Charneca, Rui, Di Palma, Federica, Djurkin Kušec, Ivona, Etherington, Graham, Fernandez, Ana I, Suárez García, Fabián, García-Casco, Juan, Karolyi, D 0000-003-0409-9071], Martins, José Manuel, Mercat, Marie-José, Núñez, Yolanda, Radović, Čedomir, Razmaite, Violeta, Riquet, Juliette, Savić, Radomir, Škrlep, Martin, Usai, Graziano, Ovilo, Cristina, Bovo S., Schiavo G., Ribani A., Utzeri V.J., Taurisano V., Ballan M., Munoz M., Alves E., Araujo J.P., Bozzi R., Charneca R., Di Palma F., Djurkin Kusec I., Etherington G., Fernandez A.I., Garcia F., Garcia-Casco J., Karolyi D., Gallo M., Martins J.M., Mercat M.-J., Nunez Y., Quintanilla R., Radovic C., Razmaite V., Riquet J., Savic R., Skrlep M., Usai G., Zimmer C., Ovilo C., and Fontanesi L.
Subjects: 0301 basic medicine, Candidate gene, Population genetics, Swine, MESH: Coronavirus Infections, Sus scrofa, MESH: Angiotensin-Converting Enzyme 2, MESH: One Health, Breeding, MESH: INDEL Mutation, 0302 clinical medicine, Gene Frequency, INDEL Mutation, Receptors, Receptors, Viru, MESH: Animals, MESH: Serine Endopeptidases, MESH: Genetic Variation, MESH: High-Throughput Nucleotide Sequencing, MESH: Swine, 2. Zero hunger, Genetics, education.field_of_study, Multidisciplinary, MESH: Polymorphism, Single Nucleotide, Serine Endopeptidases, High-Throughput Nucleotide Sequencing, Single Nucleotide, Genomics, Virus, Serine Endopeptidase, One Health, 030220 oncology & carcinogenesis, Microsomal aminopeptidase, Medicine, Infectious diseases, Receptors, Virus, Angiotensin-Converting Enzyme 2, Coronavirus Infections, MESH: Whole Genome Sequencing, Human, Agricultural genetics, pig, local breed, whole genome sequencing, coronavirus, Science, Dipeptidyl Peptidase 4, Population, MESH: Genetics, Population, Context (language use), MESH: Breeding, CD13 Antigens, Biology, Polymorphism, Single Nucleotide, Article, 03 medical and health sciences, Animals, Genetics, Population, Humans, Whole Genome Sequencing, Genetic Variation, Genetic variation, MESH: Gene Frequency, Polymorphism, education, Data mining, Gene, CD13 Antigen, Animal breeding, Whole genome sequencing, MESH: Humans, Animal, Coronavirus Infection, Host (biology), Virus receptor, MESH: CD13 Antigens, MESH: Dipeptidyl Peptidase 4, MESH: Receptors, Virus, MESH: Sus scrofa, [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, 030104 developmental biology, Dipeptidyl peptidase IV, Next-generation sequencing, Genetic markers, Serine proteinase
Abstract: 14 Pág. Departamento de Mejora Genética Animal, Coronaviruses silently circulate in human and animal populations, causing mild to severe diseases. Therefore, livestock are important components of a "One Health" perspective aimed to control these viral infections. However, at present there is no example that considers pig genetic resources in this context. In this study, we investigated the variability of four genes (ACE2, ANPEP and DPP4 encoding for host receptors of the viral spike proteins and TMPRSS2 encoding for a host proteinase) in 23 European (19 autochthonous and three commercial breeds and one wild boar population) and two Asian Sus scrofa populations. A total of 2229 variants were identified in the four candidate genes: 26% of them were not previously described; 29 variants affected the protein sequence and might potentially interact with the infection mechanisms. The results coming from this work are a first step towards a "One Health" perspective that should consider conservation programs of pig genetic resources with twofold objectives: (i) genetic resources could be reservoirs of host gene variability useful to design selection programs to increase resistance to coronaviruses; (ii) the described variability in genes involved in coronavirus infections across many different pig populations might be part of a risk assessment including pig genetic resources., This work has received funding from the University of Bologna RFO 2016-2019 programmes, the Italian MIUR 2017 PigPhenomics project, from the European Union’s Horizon 2020 research and innovation programme under grant agreement No. 634476 for the project with acronym TREASURE, from the European Open Science Cloud (EOSC) Secretariat, project “Application of animal genomics and data mining to predict and monitor novel coronavirus potential infections (VirAnimalOne)”, the EGI call for COVID-19 research projects (AnGen1H project) and from the Por Fesr Emilia-Romagna 2014-2020 (actions 1.1.4 and 1.2.2—Bando per sostenere progetti di ricerca ed innovazione per lo sviluppo di soluzioni finalizzate al contrasto dell’epidemia da COVID-19—Project LIVESTOCK-STOP-COVI). The content of this article reflects only the authors' view and the European Union Agency is not responsible for any use that may be made of the information it contains.
Published: 2021

8. Disentangling the complexity of low complexity proteins

Author: Mier, Pablo, Bernadó, Pau, Gáspári, Zoltán, Ouzounis, Christos A., Promponas, Vasilis J., Kajava, Andrey V., Hancock, John M., Tosatto, Silvio C. E., Dosztanyi, Zsuzsanna, Andrade-Navarro, Miguel A., Paladin, Lisanna, Tamana, Stella, Petrosian, Sophia, Hajdu-Soltész, Borbála, Urbanek, Annika, Gruca, Aleksandra, Plewczynski, Dariusz, Grynberg, Marcin, Promponas, Vasilis J. [0000-0003-3352-4831], University Medical Center of the Johannes Gutenberg-University Mainz, Azienda Ospedaliera di Padova, University of Cyprus [Nicosia], Eötvös Loránd University (ELTE), Centre de Biochimie Structurale [Montpellier] (CBS), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut National de la Santé et de la Recherche Médicale (INSERM), Silesian University of Technology, Warsaw University of Technology [Warsaw], Pázmány Péter Catholic University, Centre de recherche en Biologie Cellulaire (CRBM), Université Montpellier 2 - Sciences et Techniques (UM2)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Université Montpellier 1 (UM1), National Research University of Information Technologies, Mechanics and Optics [St. Petersburg] (ITMO), Earlham Institute [Norwich], and Department of Chemical Sciences University of Padova and Institute on Membrane Technology, Unit of Padova, via F. Marzolo 1, Padova, 35131
Subjects: Protein Conformation, Computer science, Review Article, Computational biology, Measure (mathematics), Evolution, Molecular, Low complexity, 03 medical and health sciences, Protein Domains, Amino Acid Sequence, structure, [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biochemistry [q-bio.BM], Databases, Protein, Molecular Biology, 030304 developmental biology, Structure (mathematical logic), 0303 health sciences, Sequence, [SCCO.NEUR]Cognitive science/Neuroscience, composition bias, 030302 biochemistry & molecular biology, Proteins, disorder, low complexity regions, Structure and function, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], Algorithms, Information Systems
Abstract: There are multiple definitions for low complexity regions (LCRs) in protein sequences, with all of them broadly considering LCRs as regions with fewer amino acid types compared to an average composition. Following this view, LCRs can also be defined as regions showing composition bias. In this critical review, we focus on the definition of sequence complexity of LCRs and their connection with structure. We present statistics and methodological approaches that measure low complexity (LC) and related sequence properties. Composition bias is often associated with LC and disorder, but repeats, while compositionally biased, might also induce ordered structures. We illustrate this dichotomy, and more generally the overlaps between different properties related to LCRs, using examples. We argue that statistical measures alone cannot capture all structural aspects of LCRs and recommend the combined usage of a variety of predictive tools and measurements. While the methodologies available to study LCRs are already very advanced, we foresee that a more comprehensive annotation of sequences in the databases will enable the improvement of predictions and a better understanding of the evolution and the connection between structure and function of LCRs. This will require the use of standards for the generation and exchange of data describing all aspects of LCRs. Short abstract There are multiple definitions for low complexity regions (LCRs) in protein sequences. In this critical review, we focus on the definition of sequence complexity of LCRs and their connection with structure. We present statistics and methodological approaches that measure low complexity (LC) and related sequence properties. Composition bias is often associated with LC and disorder, but repeats, while compositionally biased, might also induce ordered structures. We illustrate this dichotomy, plus overlaps between different properties related to LCRs, using examples.
Published: 2019

9. Swarm v3: towards tera-scale amplicon clustering

Author: Mahé, Frédéric, Czech, Lucas, Stamatakis, Alexandros, Quince, Christopher, de Vargas, Colomban, Dunthorn, Micah, Rognes, Torbjørn, Plant Health Institute of Montpellier (UMR PHIM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Heidelberg Institute for Theoretical Studies (HITS ), Carnegie Institution for Science [Washington], Karlsruhe Institute of Technology (KIT), Earlham Institute [Norwich], Quadram Institute, University of Warwick [Coventry], ECOlogy of MArine Plankton (ECOMAP), Adaptation et diversité en milieu marin (AD2M), Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), University of Oslo (UiO), University of Duisburg-Essen, Gordon and Betty Moore Foundation through the UniEuk grant GBMF5275, the Klaus Tschira Foundation, and the Deutsche Forschungsgemeinschaft (#DU1319/5-1)., Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Montpellier (UM), Carnegie Institution for Science, Biotechnology and Biological Sciences Research Council (BBSRC), Adaptation et diversité en milieu marin (ADMM), Institut national des sciences de l'Univers (INSU - CNRS)-Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Station biologique de Roscoff (SBR), Universität Duisburg-Essen = University of Duisburg-Essen [Essen], the Klaus Tschira Foundation, and Deutsche Forschungsgemeinschaft (#DU1319/5-1).
Subjects: Open Source, AcademicSubjects/SCI01060, U10 - Informatique, mathématiques et statistiques, amplicon clustering, Taxonomie, Logiciel, Applications Notes, operational taxonomic units, F30 - Génétique et amélioration des plantes, Séquence d'ADN, Échantillonnage, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], Sequence Analysis, Technique analytique, Biologie
Abstract: Motivation Previously we presented swarm, an open-source amplicon clustering programme that produces fine-scale molecular operational taxonomic units (OTUs) that are free of arbitrary global clustering thresholds. Here, we present swarm v3 to address issues of contemporary datasets that are growing towards tera-byte sizes. Results When compared with previous swarm versions, swarm v3 has modernized C++ source code, reduced memory footprint by up to 50%, optimized CPU-usage and multithreading (more than 7 times faster with default parameters), and it has been extensively tested for its robustness and logic. Availability and implementation Source code and binaries are available at https://github.com/torognes/swarm. Supplementary information Supplementary data are available at Bioinformatics online.
Published: 2021

10. Metagenomic assessment of the global distribution of bacteria and fungi

Author: BAHRAM, Mohammad, NETHERWAY, Tarquin, FRIOUX, Clémence, FERRETTI, Pamela, COELHO, Luis Pedro, GEISEN, Stefan, BORK, Peer, HILDEBRAND, Falk, Swedish University of Agricultural Sciences (SLU), from patterns to models in computational biodiversity and biotechnology (PLEIADE), Laboratoire Bordelais de Recherche en Informatique (LaBRI), Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Inria Bordeaux - Sud-Ouest, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Biodiversité, Gènes & Communautés (BioGeCo), Université de Bordeaux (UB)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Earlham Institute [Norwich], Quadram Institute, European Molecular Biology Laboratory [Heidelberg] (EMBL), Netherlands Institute of Ecology - NIOO-KNAW (NETHERLANDS), Max Delbrück Center for Molecular Medicine [Berlin] (MDC), Helmholtz-Gemeinschaft = Helmholtz Association, Funding was provided by Swedish Research Council (Vetenskapsrådet grant no: 2017‐05019 and Biotechnology and Biological Sciences research Council (Institute Strategic Programme Gut Microbes and Health BB/r012490/1 and its constituent project BBS/E/F/000Pr10355)., Université de Bordeaux (UB)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Centre National de la Recherche Scientifique (CNRS)-Université de Bordeaux (UB)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Centre National de la Recherche Scientifique (CNRS)-Inria Bordeaux - Sud-Ouest, and Biotechnology and Biological Sciences Research Council (BBSRC)
Subjects: Microbiology (Microbiology in the medical area to be 30109), Ecology, fungi, Biochemistry and Molecular Biology, Life Science, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Laboratory of Nematology, PE&RC, Laboratorium voor Nematologie
Abstract: International audience; Bacteria and fungi are of uttermost importance in determining environmental and host functioning. Despite close interactions between animals, plants, their associated microbiomes,and the environment they inhabit, the distribution and role of bacteria and especially fungi across host and environments as well as the cross-habitat determinants of their community compositions remain little investigated. Using a uniquely broad global dataset of 13,483 metagenomes, we analyzed the microbiome structure and function of 25 host-associated and environmental habitats, focusing on potential interactions between bacteria and fungi. We found that themetagenomic relative abundance ratio of bacteria-to-fungi is a distinctive microbial feature of habitats. Compared to fungi, the cross-habitat distribution pattern of bacteria was more strongly driven by habitat type. Fungal diversity was depleted in host-associated communities compared with those in the environment, particularly terrestrial habitats, whereas this diversity pattern was less pronounced for bacteria. The relative gene functional potential of bacteria or fungi reflectedtheir diversity patterns and appeared to depend on a balance between substrate availability and biotic interactions. Alongside helping to identify hotspots and sources of microbial diversity, our study provides support for differences in assembly patterns and processes between bacterial and fungal communities across different habitats.
Published: 2021

11. Metage2Metabo, microbiota-scale metabolic complementarity for the identification of key species

Author: Arnaud Belcour, Clémence Frioux, Méziane Aite, Anthony Bretaudeau, Falk Hildebrand, Anne Siegel, Dynamics, Logics and Inference for biological Systems and Sequences (Dyliss), Inria Rennes – Bretagne Atlantique, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-GESTION DES DONNÉES ET DE LA CONNAISSANCE (IRISA-D7), Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Université de Bretagne Sud (UBS)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National de Recherche en Informatique et en Automatique (Inria)-École normale supérieure - Rennes (ENS Rennes)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-CentraleSupélec-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Bretagne Sud (UBS)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-École normale supérieure - Rennes (ENS Rennes)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT), Quadram Institute, from patterns to models in computational biodiversity and biotechnology (PLEIADE), Laboratoire Bordelais de Recherche en Informatique (LaBRI), Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Inria Bordeaux - Sud-Ouest, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Biodiversité, Gènes & Communautés (BioGeCo), Université de Bordeaux (UB)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Plateforme bioinformatique GenOuest [Rennes], Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Plateforme Génomique Santé Biogenouest®-GESTION DES DONNÉES ET DE LA CONNAISSANCE (IRISA-D7), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-École normale supérieure - Rennes (ENS Rennes)-Centre National de la Recherche Scientifique (CNRS)-CentraleSupélec-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Earlham Institute [Norwich], This research was supported in part by the NBI Computing infrastructure for Science (CiS) group. FH and CF’s salaries have been funded by the BBSRC Institute Strategic Programme Gut Microbes and Health BB/r012490/1, its constituent project BBS/e/F/000Pr10355. AB’s, CF,and MA’s salaries have been funded by the ANR project IDEALG (ANR-10-BTBR-04) 'Investissements d’Avenir, Biotechnologies-Bioressources'., ANR-10-BTBR-0004,IDEALG,Biotechnologies pour la valorisation des macroalgues(2010), Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Biotechnology and Biological Sciences Research Council (BBSRC), Université de Bordeaux (UB)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Centre National de la Recherche Scientifique (CNRS)-Université de Bordeaux (UB)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Centre National de la Recherche Scientifique (CNRS)-Inria Bordeaux - Sud-Ouest, Université de Rennes (UR)-Plateforme Génomique Santé Biogenouest®-Inria Rennes – Bretagne Atlantique, Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Université de Rennes (UR)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-INSTITUT AGRO Agrocampus Ouest, and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)
Subjects: Databases, Factual, QH301-705.5, Science, computational biology, Species Specificity, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], microbiota, Animals, human, Biology (General), metabolic modelling, metagenomics, Bacteria, systems biology, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Tools and Resources, Gastrointestinal Microbiome, metabolic complementarity, Medicine, Cattle, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], Genome, Bacterial, Software, Computational and Systems Biology, keystone species
Abstract: To capture the functional diversity of microbiota, one must identify metabolic functions and species of interest within hundreds or thousands of microorganisms. We present Metage2Metabo (M2M) a resource that meets the need for de novo functional screening of genome-scale metabolic networks (GSMNs) at the scale of a metagenome, and the identification of critical species with respect to metabolic cooperation. M2M comprises a flexible pipeline for the characterisation of individual metabolisms and collective metabolic complementarity. In addition, M2M identifies key species, that are meaningful members of the community for functions of interest. We demonstrate that M2M is applicable to collections of genomes as well as metagenome-assembled genomes, permits an efficient GSMN reconstruction with Pathway Tools, and assesses the cooperation potential between species. M2M identifies key organisms by reducing the complexity of a large-scale microbiota into minimal communities with equivalent properties, suitable for further analyses., eLife digest All the microbes that live in a specific environment, for example an organ, are collectively called the microbiota. In humans, the microbiota of the gut has been extensively studied by sequencing the DNA of the different microbes to identify them and determine the roles they play in health and disease. The DNA sequences of all the members of the microbiota is called the metagenome. The chemical reactions that the gut microbiota perform to produce energy and make the biomolecules they need to survive are collectively referred to as the metabolism of these microbes. Studying the metabolism of the gut microbiota can help researchers understand the roles of the different microbes. However, the large variety of species in the gut microbiota and gaps in the information about them render these studies difficult, despite technology improving quickly. To tackle this issue, Belcour, Frioux et al developed a new piece of software called Metage2Metabo (M2M) that simulates the metabolism of the gut microbiota and describes the metabolic relationships between the different microbes. Metage2Metabo analyses the roles of the metabolic genes of a large number of microbe species to establish how they complement each other metabolically. Then, it can calculate the minimum number of species needed to perform a metabolic role of interest within that microbiota, and which key species are associated with that role. To test the new software, Belcour, Frioux et al. used Metage2Metabo to analyse genomes from the human gut microbiota and from the cow rumen (one of the cow’s stomachs). They showed that even if the metagenome was incomplete, the software was able to make stable predictions of key species involved in metabolic complementarity. Additionally, they also illustrated how the method can be used to study the gut microbiota of individuals. This work presents a new method for determining the metabolic relationships between species within a microbiota. The software is highly flexible and could be adapted to identify key members within different communities. In the context of the gut microbiota, the predictions of Metage2Metabo could shed lights on the interactions between the host and the microbes and contribute to a better understanding of microbe environments.
Published: 2020

12. A single-cell RNA-sequencing training and analysis suite using the Galaxy framework

Author: Rolf Backofen, Nicola Soranzo, Dave Clements, Jelle Scholtalbers, Christophe Antoniewski, Graham J Etherington, James Taylor, Léa Bellenger, Stefan Mautner, Hans Rudolf Hotz, Anton Nekrutenko, Irene Papatheodorou, Mohammad Heydarian, Bérénice Batut, Daniel Blankenberg, Alexander Ostrovsky, Björn Grüning, Jonathan R. Manning, Mehmet Tekman, Ni Huang, Maria A. Doyle, Pablo Moreno, Fidel Ramirez, Institut de Biologie Paris Seine (IBPS), Sorbonne Université (SU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), University of Freiburg [Freiburg], Johns Hopkins University (JHU), Unité Mixte de Service Production et Analyse de données en Sciences de la vie et en Santé (PASS), Sorbonne Université (SU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Bioinformatique [IBPS] (IBPS-Artbio), Sorbonne Université (SU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Boehringer Ingelheim International GmbH, Earlham Institute [Norwich], Friedrich Miescher Institute for Biomedical Research (FMI), Novartis Research Foundation, Swiss Institute of Bioinformatics - Basel, Swiss Institute of Bioinformatics [Lausanne] (SIB), Université de Lausanne (UNIL)-Université de Lausanne (UNIL)-University of Basel (Unibas), European Molecular Biology Laboratory [Heidelberg] (EMBL), European Bioinformatics Institute [Hinxton] (EMBL-EBI), EMBL Heidelberg, Peter MacCallum Cancer Centre [Melbourne, Australie], University of Melbourne, Wellcome Trust Sanger Institute [Hinxton, UK], Pennsylvania State University (Penn State), Penn State System, Lerner Research Institute [Cleveland, OH, USA], Antoniewski, Christophe, Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU), Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), University of Basel (Unibas)-Swiss Institute of Bioinformatics [Lausanne] (SIB), Université de Lausanne = University of Lausanne (UNIL)-Université de Lausanne = University of Lausanne (UNIL), and Cleveland Clinic
Subjects: AcademicSubjects/SCI02254, Interoperability, Health Informatics, 03 medical and health sciences, 0302 clinical medicine, Software, Technical Note, Preprocessor, Cluster analysis, Ecosystem, 030304 developmental biology, 0303 health sciences, [SDV.BIBS] Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], training, business.industry, Sequence Analysis, RNA, Suite, Computational Biology, high-performance computing, single-cell, File format, Supercomputer, Data science, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Web, Computer Science Applications, Galaxy, Workflow, 10x, RNA, AcademicSubjects/SCI00960, business, resources, scRNA, 030217 neurology & neurosurgery
Abstract: BackgroundThe vast ecosystem of single-cell RNA-sequencing tools has until recently been plagued by an excess of diverging analysis strategies, inconsistent file formats, and compatibility issues between different software suites. The uptake of 10x Genomics datasets has begun to calm this diversity, and the bioinformatics community leans once more towards the large computing requirements and the statistically driven methods needed to process and understand these ever-growing datasets.ResultsHere we outline several Galaxy workflows and learning resources for single-cell RNA-sequencing, with the aim of providing a comprehensive analysis environment paired with a thorough user learning experience that bridges the knowledge gap between the computational methods and the underlying cell biology. The Galaxy reproducible bioinformatics framework provides tools, workflows, and trainings that not only enable users to perform 1-click 10x preprocessing but also empower them to demultiplex raw sequencing from custom tagged and full-length sequencing protocols. The downstream analysis supports a range of high-quality interoperable suites separated into common stages of analysis: inspection, filtering, normalization, confounder removal, and clustering. The teaching resources cover concepts from computer science to cell biology. Access to all resources is provided at the singlecell.usegalaxy.eu portal.ConclusionsThe reproducible and training-oriented Galaxy framework provides a sustainable high-performance computing environment for users to run flexible analyses on both 10x and alternative platforms. The tutorials from the Galaxy Training Network along with the frequent training workshops hosted by the Galaxy community provide a means for users to learn, publish, and teach single-cell RNA-sequencing analysis.
Published: 2020

13. Assessment of genetically modified maize MZIR098 for food and feed uses, under Regulation (EC) No 1829/2003 (application EFSA‐GMO‐DE‐2017‐142)

Author: EFSA Panel on Genetically Modified Organisms (GMO), Naegeli, H, Bresson, J, Dalmay, T, Dewhurst, IC, Epstein, MM, Firbank, LG, Guerche, P, Hejatko, J, Moreno, FJ, Mullins, E, Nogué, F, Rostoks, N, Sánchez Serrano, JJ, Savoini, G, Veromann, E, Veronesi, F, Álvarez, F, Ardizzone, M, De Sanctis, G, Devos, Y, Dumont, AF, Gennaro, A, Gómez Ruiz, JÁ, Lanzoni, A, Neri, FM, Papadopoulou, N, Paraskevopoulos, K, Raffaello, T, University of Zurich, Orthopaedic Surgery Department, Sant Rafael Hospital, European Food Safety Authority (EFSA), Tuscia University, Center for Nanotechnology Innovation, @NEST (CNI), National Enterprise for nanoScience and nanoTechnology (NEST), Scuola Normale Superiore di Pisa (SNS)-Scuola Universitaria Superiore Sant'Anna [Pisa] (SSSUP)-Istituto Italiano di Tecnologia (IIT)-Consiglio Nazionale delle Ricerche [Pisa] (CNR PISA)-Scuola Normale Superiore di Pisa (SNS)-Scuola Universitaria Superiore Sant'Anna [Pisa] (SSSUP)-Istituto Italiano di Tecnologia (IIT)-Consiglio Nazionale delle Ricerche [Pisa] (CNR PISA), Universität Zürich [Zürich] = University of Zurich (UZH), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Earlham Institute [Norwich], Centre for Ecology and Hydrology [Bangor] (CEH), Natural Environment Research Council (NERC), Institut Jean-Pierre Bourgin (IJPB), and AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
Subjects: MZIR098, [SDV.BIO]Life Sciences [q-bio]/Biotechnology, 040301 veterinary sciences, Veterinary (miscellaneous), [SDV]Life Sciences [q-bio], 2405 Parasitology, Context (language use), mCry3A, Plant Science, TP1-1185, 010501 environmental sciences, Biology, 01 natural sciences, Microbiology, 0403 veterinary science, Environmental safety, 1110 Plant Science, TX341-641, maize (Zea mays), 1106 Food Science, 0105 earth and related environmental sciences, 2. Zero hunger, Maize (Zea mays), Genetically modified maize, PAT Proteins, Animal health, business.industry, Nutrition. Foods and food supply, GMO, Chemical technology, 2404 Microbiology, Regulation (EC) No 1829/2003, 04 agricultural and veterinary sciences, 10079 Institute of Veterinary Pharmacology and Toxicology, eCry3.1Ab, Biotechnology, 3401 Veterinary (miscellaneous), Scientific Opinion, PAT Requestor: Competent Authority of Germany, 570 Life sciences, biology, Animal Science and Zoology, Parasitology, 1103 Animal Science and Zoology, business, PAT, Food Science, eCry31Ab
Abstract: © 2020 European Food Safety Authority., Maize MZIR098 was developed to confer tolerance to glufosinate‐ammonium‐containing herbicides and resistance to certain coleopteran pests. The molecular characterisation data and bioinformatic analyses do not identify issues requiring food/feed safety assessment. None of the identified differences in the agronomic/phenotypic and compositional characteristics tested between maize MZIR098 and its conventional counterpart needs further assessment, except for neutral detergent fibre (NDF) in grains, which does not raise nutritional and safety concerns. The GMO Panel does not identify safety concerns regarding the toxicity and allergenicity of the eCry3.1Ab, mCry3A and PAT proteins as expressed in maize MZIR098, and finds no evidence that the genetic modification would change the overall allergenicity of maize MZIR098. In the context of this application, the consumption of food and feed from maize MZIR098 does not represent a nutritional concern in humans and animals. The GMO Panel concludes that maize MZIR098 is as safe as the conventional counterpart and non‐GM maize reference varieties tested, and no post‐market monitoring of food/feed is considered necessary. In the case of accidental release of viable maize MZIR098 grains into the environment, maize MZIR098 would not raise environmental safety concerns. The post‐market environmental monitoring plan and reporting intervals are in line with the intended uses of maize MZIR098. In conclusion, the GMO Panel considers that maize MZIR098, as described in this application, is as safe as its conventional counterpart and the non‐GM maize reference varieties tested with respect to potential effects on human and animal health and the environment.
Published: 2020

14. Whole-genome sequencing of European autochthonous and commercial pig breeds allows the detection of signatures of selection for adaptation of genetic resources to different breeding and production systems

Author: Valerio Joe Utzeri, Ana Isabel Fernández, G. Usai, Marjeta Čandek-Potokar, María Muñoz, José Pedro Araújo, Maurizio Gallo, Riccardo Bozzi, Čedomir Radović, Fabián García, Giuseppina Schiavo, Federica Di Palma, Cristina Óvilo, Marie J. Mercat, Juan García-Casco, Christoph Zimmer, Anisa Ribani, Juliette Riquet, Danijel Karolyi, Vladimir Margeta, Samuele Bovo, Luca Fontanesi, Giulia Moscatelli, Radomir Savić, Violeta Razmaite, Estefania Alves, Rui Charneca, J.M. Martins, Raquel Quintanilla, Yolanda Núñez, Graham J Etherington, University of Bologna/Università di Bologna, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria = National Institute for Agricultural and Food Research and Technology (INIA), Instituto Politécnico de Viana do Castelo = Polytechnic Institute of Viana do Castelo (IPVC), Università degli Studi di Firenze = University of Florence (UniFI), Kmetijski Institut Slovenije, Partenaires INRAE, Universidade de Évora, Earlham Institute [Norwich], University of Zagreb, Associazione Nazionale Allevatori Suini, Josip Juraj Strossmayer University of Osijek, Institut du Porc (IFIP), Institut de Recerca i Tecnologia Agroalimentàries = Institute of Agrifood Research and Technology (IRTA), Institute for Animal Husbandry, Lithuanian University of Health Sciences [Kaunas, Lithuania], Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-École nationale supérieure agronomique de Toulouse (ENSAT), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), University of Belgrade [Belgrade], AGRIS sardegna, Bäuerliche Erzeugergemeinschaft Schwäbisch Hall (BESH), Europe-FAANG COST Action, University of Bologna RFO 2016–2019 programme, European Project: 634476,H2020,H2020-SFS-2014-2,TREASURE(2015), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Producció Animal, Genètica i Millora Animal, University of Bologna, Instituto Politécnico de Viana do Castelo, Università degli Studi di Firenze = University of Florence [Firenze] (UNIFI), Institute of Agrifood Research and Technology (IRTA), Bovo S., Ribani A., Munoz M., Alves E., Araujo J.P., Bozzi R., Candek-Potokar M., Charneca R., Di Palma F., Etherington G., Fernandez A.I., Garcia F., Garcia-Casco J., Karolyi D., Gallo M., Margeta V., Martins J.M., Mercat M.J., Moscatelli G., Nunez Y., Quintanilla R., Radovic C., Razmaite V., Riquet J., Savic R., Schiavo G., Usai G., Utzeri V.J., Zimmer C., Ovilo C., and Fontanesi L.
Subjects: Male, Genotyping Techniques, Swine, Acclimatization, [SDV]Life Sciences [q-bio], Breeding, Fixation index, Domestication, Chromosome regions, local pig breeds, WGS, genome variability, ComputingMilieux_MISCELLANEOUS, lcsh:SF1-1100, 2. Zero hunger, 0303 health sciences, Genome, biology, Genomics, 04 agricultural and veterinary sciences, General Medicine, Adaptation, Physiological, Alentejana, Algorithm, Europe, Phenotype, Pigs, Female, Algorithms, SNPs, Research Article, lcsh:QH426-470, Genotype, Whole-genome sequencing, pig, autochthonous breeds, selection, adaptation, Polymorphism, Single Nucleotide, Crossbreed, 03 medical and health sciences, Genetics, Animals, Selection, Genetic, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, Whole genome sequencing, Genetic diversity, Models, Genetic, Whole Genome Sequencing, Animal, Directional selection, 0402 animal and dairy science, biology.organism_classification, 040201 dairy & animal science, Bísaro pig, Alentejano pig, European local breeds, lcsh:Genetics, Evolutionary biology, Genomic, Animal Science and Zoology, lcsh:Animal culture, Genotyping Technique
Abstract: Background Natural and artificial directional selection in cosmopolitan and autochthonous pig breeds and wild boars have shaped their genomes and resulted in a reservoir of animal genetic diversity. Signatures of selection are the result of these selection events that have contributed to the adaptation of breeds to different environments and production systems. In this study, we analysed the genome variability of 19 European autochthonous pig breeds (Alentejana, Bísara, Majorcan Black, Basque, Gascon, Apulo-Calabrese, Casertana, Cinta Senese, Mora Romagnola, Nero Siciliano, Sarda, Krškopolje pig, Black Slavonian, Turopolje, Moravka, Swallow-Bellied Mangalitsa, Schwäbisch-Hällisches Schwein, Lithuanian indigenous wattle and Lithuanian White old type) from nine countries, three European commercial breeds (Italian Large White, Italian Landrace and Italian Duroc), and European wild boars, by mining whole-genome sequencing data obtained by using a DNA-pool sequencing approach. Signatures of selection were identified by using a single-breed approach with two statistics [within-breed pooled heterozygosity (HP) and fixation index (FST)] and group-based FST approaches, which compare groups of breeds defined according to external traits and use/specialization/type. Results We detected more than 22 million single nucleotide polymorphisms (SNPs) across the 23 compared populations and identified 359 chromosome regions showing signatures of selection. These regions harbour genes that are already known or new genes that are under selection and relevant for the domestication process in this species, and that affect several morphological and physiological traits (e.g. coat colours and patterns, body size, number of vertebrae and teats, ear size and conformation, reproductive traits, growth and fat deposition traits). Wild boar related signatures of selection were detected across all the genome of several autochthonous breeds, which suggests that crossbreeding (accidental or deliberate) occurred with wild boars. Conclusions Our findings provide a catalogue of genetic variants of many European pig populations and identify genome regions that can explain, at least in part, the phenotypic diversity of these genetic resources.
Published: 2020

15. Assessment of genetically modified oilseed rape GT73 for renewal authorisation under Regulation (EC) No 1829/2003 (application EFSA-GMO-RX-002) EFSA Panel on Genetically Modified Organisms (GMO), Panel members: Scientific Opinion

Author: EFSA Panel on Genetically Modified Organisms (GMO), ., Alvarez, Fernando, Ardizzone, Michele, Raffaello, Tommaso, Naegeli, Hanspeter, Bresson, Jean-Louis, Dalmay, Tamas, Dewhurst, Ian, Epstein, Michelle, Firbank, Leslie, Guerche, Philippe, Hejatko, Jan, Moreno, Francisco, Mullins, Ewen, Nogu, Fabien, Rostoks, Nils, Juan S Anchez Serrano, Jose, Savoini, Giovanni, Veromann, Eve, VERONESI, Fabio, Orthopaedic Surgery Department, Sant Rafael Hospital, Department of Forest Sciences [Helsinki], Faculty of Agriculture and Forestry [Helsinki], University of Helsinki-University of Helsinki, Universität Zürich [Zürich] = University of Zurich (UZH), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Earlham Institute [Norwich], Centre for Ecology and Hydrology [Bangor] (CEH), Natural Environment Research Council (NERC), Institut Jean-Pierre Bourgin (IJPB), and AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
Subjects: renewal, GT73, [SDV.BIO]Life Sciences [q-bio]/Biotechnology, [SDV]Life Sciences [q-bio], Regulation (EC) No 1829/2003, Oilseed rape
Abstract: International audience; Following the submission of application EFSA-GMO-RX-002 under Regulation (EC) No 1829/2003 from Monsanto Company, the Panel on Genetically Modified Organisms of EFSA (GMO) was asked to deliver a scientific risk assessment on the data submitted in the context of the renewal of authorisation application for the herbicide-tolerant genetically modified oilseed rape GT73. The data received in the context of this renewal application contained post-market environmental monitoring reports, a systematic search and evaluation of literature, updated bioinformatic analyses and additional documents or studies performed by or on behalf of the applicant. The GMO Panel assessed these data for possible new hazards, modified exposure or new scientific uncertainties identified during the authorisation period and not previously assessed in the context of the original application. Under the assumption that the DNA sequence of the event in oilseed rape GT73 considered for renewal of authorisation is identical to the sequence of the originally assessed event, the GMO Panel concludes that there is no evidence in renewal application EFSA-GMO-RX-002 for new hazards, modified exposure or scientific uncertainties that would change the conclusions of the original risk assessment on oilseed rape GT73.
Published: 2020

16. Genome-wide detection of copy number variants in European autochthonous and commercial pig breeds by whole-genome sequencing of DNA pools identified breed-characterising copy number states

Author: Čedomir Radović, Valerio Joe Utzeri, Rui Charneca, Juan García-Casco, Christoph Zimmer, Raquel Quintanilla, Samuele Bovo, Danijel Karolyi, E. Alves, Angeles Fernandez, Luca Fontanesi, João P. Araújo, J.M. Martins, Martin Škrlep, F. Di Palma, Radomir Savić, Marie-José Mercat, Ricardo Bozzi, María Muñoz, Violeta Razmaite, Graham J Etherington, Kristina Gvozdanović, Giuseppina Schiavo, Anisa Ribani, Yolanda Núñez, Maurizio Gallo, G. Usai, Cristina Óvilo, Felisa Laíz García, Juliette Riquet, Bovo S., Ribani A., Munoz M., Alves E., Araujo J.P., Bozzi R., Charneca R., Di Palma F., Etherington G., Fernandez A.I., Garcia F., Garcia-Casco J., Karolyi D., Gallo M., Gvozdanovic K., Martins J.M., Mercat M.J., Nunez Y., Quintanilla R., Radovic C., Razmaite V., Riquet J., Savic R., Schiavo G., Skrlep M., Usai G., Utzeri V.J., Zimmer C., Ovilo C., Fontanesi L., University of Bologna/Università di Bologna, Alma Mater Studiorum Università di Bologna [Bologna] (UNIBO), Instituto Nacional de Investigación Agropecuaria (INIA), Instituto Politécnico de Viana do Castelo = Polytechnic Institute of Viana do Castelo (IPVC), UNIVERSITY OF FIRENZE (UNIVERSITY OF FIRENZE), Università degli Studi di Firenze = University of Florence (UniFI), Universidade de Évora, Earlham Institute [Norwich], University of Zagreb, Assoc Nazl Allevatori Suini, University of Osijek, Institut du Porc (IFIP), Institut de Recerca i Tecnologia Agroalimentàries = Institute of Agrifood Research and Technology (IRTA), Lithuanian University of health Sciences, Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-École nationale supérieure agronomique de Toulouse (ENSAT), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), University of Belgrade [Belgrade], Agricultural Institute of Slovenia, Agenzia della Regione Sardegna per la Ricerca Scientifica (AGRIS), Bäuerliche Erzeugergemeinschaft Schwäbisch Hall, Institute of animal husbandry, Slovenian Agency of Research / P4-0133, European Project: 634476,H2020,H2020-SFS-2014-2,TREASURE(2015), University of Bologna, Instituto Politécnico de Viana do Castelo, Università degli Studi di Firenze = University of Florence [Firenze] (UNIFI), Institute of Agrifood Research and Technology (IRTA), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Producció Animal, and Genètica i Millora Animal
Subjects: 0301 basic medicine, Male, [SDV.OT]Life Sciences [q-bio]/Other [q-bio.OT], DNA Copy Number Variations, Sus scrofa, Breeding, Genome, DNA sequencing, 03 medical and health sciences, Species Specificity, copy number variant, ELOVL6, genetic resource, KIT, MSRB3, next-generation sequencing, ZNF622, Genetics, Animals, Copy-number variation, Gene, 2. Zero hunger, Whole genome sequencing, Genetic diversity, biology, Genetic ressource, Whole Genome Sequencing, Animal, 0402 animal and dairy science, Turopolje pig, 04 agricultural and veterinary sciences, General Medicine, DNA, biology.organism_classification, 040201 dairy & animal science, Breed, 030104 developmental biology, Phenotype, Italy, Evolutionary biology, Animal Science and Zoology, Female
Abstract: In this study, we identified copy number variants (CNVs) in 19 European autochthonous pig breeds and in two commercial breeds (Italian Large White and Italian Duroc) that represent important genetic resources for this species. The genome of 725 pigs was sequenced using a breed‐specific DNA pooling approach (30–35 animals per pool) obtaining an average depth per pool of 42×. This approach maximised CNV discovery as well as the related copy number states characterising, on average, the analysed breeds. By mining more than 17.5 billion reads, we identified a total of 9592 CNVs (~683 CNVs per breed) and 3710 CNV regions (CNVRs; 1.15% of the reference pig genome), with an average of 77 CNVRs per breed that were considered as private. A few CNVRs were analysed in more detail, together with other information derived from sequencing data. For example, the CNVR encompassing the KIT gene was associated with coat colour phenotypes in the analysed breeds, confirming the role of the multiple copies in determining breed‐specific coat colours. The CNVR covering the MSRB3 gene was associated with ear size in most breeds. The CNVRs affecting the ELOVL6 and ZNF622 genes were private features observed in the Lithuanian Indigenous Wattle and in the Turopolje pig breeds respectively. Overall, the genome variability unravelled here can explain part of the genetic diversity among breeds and might contribute to explain their origin, history and adaptation to a variety of production systems. info:eu-repo/semantics/acceptedVersion
Published: 2020

17. Assessment of genetically modified soybean MON 87705 3 MON 87708 3 MON 89788, for food and feed uses, under Regulation (EC) No 1829/2003 (application EFSA-GMO-NL-2015-126)

Author: EFSA Panel on Genetically Modified Organisms (GMO), ., Naegeli, Hanspeter, Bresson, Jean-Louis, Dalmay, Tamas, Dewhurst, Ian, Epstein, Michelle, Firbank, Leslie, Guerche, Philippe, Hejatko, Jan, Moreno, Francisco, Mullins, Ewen, Nogu, Fabien, Rostoks, Nils, Juan S Anchez Serrano, Jose, Savoini, Giovanni, Veromann, Eve, VERONESI, Fabio, Alvarez, Fernando, Ardizzone, Michele, De Sanctis, Giacomo, Dumont, Antonio, Devos, Yann, Gennaro, Andrea, Angel G Omez Ruiz, Jose, Lanzoni, Anna, Franco, Maria, Neri, Nikoletta, Papadopoulou, Konstantinos, Paraskevopoulos, Tommaso, Universität Zürich [Zürich] = University of Zurich (UZH), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Earlham Institute [Norwich], Centre for Ecology and Hydrology [Bangor] (CEH), Natural Environment Research Council (NERC), Institut Jean-Pierre Bourgin (IJPB), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Orthopaedic Surgery Department, Sant Rafael Hospital, European Food Safety Authority (EFSA), Tuscia University, Center for Nanotechnology Innovation, @NEST (CNI), National Enterprise for nanoScience and nanoTechnology (NEST), and Scuola Normale Superiore di Pisa (SNS)-Scuola Universitaria Superiore Sant'Anna [Pisa] (SSSUP)-Istituto Italiano di Tecnologia (IIT)-Consiglio Nazionale delle Ricerche [Pisa] (CNR PISA)-Scuola Normale Superiore di Pisa (SNS)-Scuola Universitaria Superiore Sant'Anna [Pisa] (SSSUP)-Istituto Italiano di Tecnologia (IIT)-Consiglio Nazionale delle Ricerche [Pisa] (CNR PISA)
Subjects: [SDV.BIO]Life Sciences [q-bio]/Biotechnology, fungi, food and beverages
Abstract: International audience; Soybean MON 87705 9 MON 87708 9 MON 89788 (three-event stack soybean) was produced by conventional crossing to combine three single soybean events: MON 87705, MON 87708 and MON 89788. This combination is intended to alter the fatty acid profile in the seed (in particular increasing the levels of oleic acid) and tolerance to glyphosate-based and dicamba herbicides. The Genetically Modified Organisms Panel previously assessed the three single soybean events and did not identify safety concerns. No new data on the single soybean events, leading to modification of the original conclusions on their safety have been identified. The molecular characterisation, comparative analysis (agronomic, phenotypic and compositional characteristics) and the outcome of the toxicological, allergenicity and nutritional assessment indicate that the combination of the single soybean events and of the newly expressed proteins in the three-event stack soybean does not give rise to food and feed safety and nutritional concerns. In the case of accidental release of viable three-event stack soybean seeds into the environment, this would not raise environmental safety concerns. The post-market environmental monitoring plan and the reporting intervals are in line with the intended uses of soybean MON 87705 9 MON 87708 9 MON 89788. Considering the altered fatty acid profile of the three-event stack soybean, a proposal for post-market monitoring needs to be provided by the applicant. The GMO Panel notes that in the context of this application EFSA-GMO-NL-2015-126 the applicant did not provide a 90-day study on MON 87705 soybean in line with the applicable legal requirements. Therefore, the GMO Panel is not in the position to finalise the risk assessment of soybean MON 87705 9 MON 87708 9 MON 89788 under the current regulatory frame.
Published: 2020

18. Assessment of genetically modified maize MON 88017 for renewal authorisation under Regulation (EC) No 1829/2003 (application EFSA-GMO-RX-014) EFSA Panel on Genetically Modified Organisms (GMO), Panel members: Scientific Opinion

Author: EFSA Panel on Genetically Modified Organisms (GMO), ., VERONESI, Fabio, Alvarez, Fernando, Ardizzone, Michele, Raffaello, Tommaso, Naegeli, Hanspeter, Bresson, Jean-Louis, Dalmay, Tamas, Dewhurst, Ian, Epstein, Michelle, Firbank, Leslie, Guerche, Philippe, Hejatko, Jan, Moreno, Francisco, Mullins, Ewen, Nogu, Fabien, Rostoks, Nils, Juan S Anchez Serrano, Jose, Savoini, Giovanni, Veromann, Eve, Gastroenterology, Hepatology and Nutrition Division, CHU Sainte Justine [Montréal], Department of Forest Sciences [Helsinki], Faculty of Agriculture and Forestry [Helsinki], University of Helsinki-University of Helsinki, Universität Zürich [Zürich] = University of Zurich (UZH), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Earlham Institute [Norwich], Centre for Ecology and Hydrology [Bangor] (CEH), Natural Environment Research Council (NERC), Institut Jean-Pierre Bourgin (IJPB), and AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
Subjects: renewal, [SDV.BIO]Life Sciences [q-bio]/Biotechnology, Regulation (EC) No 1829/2003, Articles 11 and 23, Maize, MON 88017
Abstract: International audience; Following the submission of application EFSA-GMO-RX-014 under Regulation (EC) No 1829/2003 from Monsanto Company the Panel on Genetically Modified Organisms of the European Food Safety Authority was asked to deliver a scientific risk assessment on the data submitted in the context of the renewal of authorisation application for the insect-resistant and herbicide-tolerant genetically modified maize MON 88017, for food and feed uses, excluding cultivation within the EU. The data received in the context of this renewal application contained post-market environmental monitoring reports, a systematic search and evaluation of literature, updated bioinformatic analyses, and additional documents or studies performed by or on behalf of the applicant. The GMO Panel assessed these data for possible new hazards, modified exposure or new scientific uncertainties identified during the authorisation period and not previously assessed in the context of the original application. Under the assumption that the DNA sequence of the event in maize MON 88017 considered for renewal is identical to the sequence of the originally assessed event, the GMO Panel concludes that there is no evidence in renewal application EFSA-GMO-RX-014 for new hazards, modified exposure or scientific uncertainties that would change the conclusions of the original risk assessment on maize MON 88017.
Published: 2020

19. Assessment of genetically modified soybean SYHT0H2 for food and feed uses, import and processing, under Regulation (EC) No 1829/2003 (application EFSA-GMO-DE- 2012-111)

Author: EFSA Panel on Genetically Modified Organisms (GMO), Naegeli, H, Bresson, J, Dalmay, T, Dewhurst, IC, Epstein, MM, Firbank, LG, Guerche, P, Hejatko, J, Moreno, FJ, Mullins, E, Nogué, F, Rostoks, N, Sánchez Serrano, JJ, Savoini, G, Veromann, E, Veronesi, F, Álvarez, F, Ardizzone, M, Dumont, AF, Devos, Y, Gennaro, A, Gómez Ruiz, JÁ, Lanzoni, A, Neri, FM, Paraskevopoulos, K, Gastroenterology, Hepatology and Nutrition Division, CHU Sainte Justine [Montréal], European Food Safety Authority (EFSA), Tuscia University, Center for Nanotechnology Innovation, @NEST (CNI), National Enterprise for nanoScience and nanoTechnology (NEST), Scuola Normale Superiore di Pisa (SNS)-Scuola Universitaria Superiore Sant'Anna [Pisa] (SSSUP)-Istituto Italiano di Tecnologia (IIT)-Consiglio Nazionale delle Ricerche [Pisa] (CNR PISA)-Scuola Normale Superiore di Pisa (SNS)-Scuola Universitaria Superiore Sant'Anna [Pisa] (SSSUP)-Istituto Italiano di Tecnologia (IIT)-Consiglio Nazionale delle Ricerche [Pisa] (CNR PISA), Universität Zürich [Zürich] = University of Zurich (UZH), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Earlham Institute [Norwich], Centre for Ecology and Hydrology [Bangor] (CEH), Natural Environment Research Council (NERC), Institut Jean-Pierre Bourgin (IJPB), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), and University of Zurich
Subjects: 0106 biological sciences, [SDV.BIO]Life Sciences [q-bio]/Biotechnology, 2405 Parasitology, Plant Science, 01 natural sciences, Genetically modified soybean, Mesotrione, chemistry.chemical_compound, 1110 Plant Science, AvHPPD‐03, TX341-641, media_common, 2. Zero hunger, 0303 health sciences, Animal health, GMO, 2404 Microbiology, Regulation (EC) No 1829/2003, food and beverages, Genetically modified organism, 3401 Veterinary (miscellaneous), soybean (Glycine max), Veterinary (miscellaneous), TP1-1185, Biology, SYHT0H2, Microbiology, 03 medical and health sciences, Environmental safety, Glufosinate-ammonium, media_common.cataloged_instance, European union, 1106 Food Science, 030304 developmental biology, PAT Proteins, business.industry, Nutrition. Foods and food supply, Chemical technology, fungi, 10079 Institute of Veterinary Pharmacology and Toxicology, Biotechnology, Scientific Opinion, chemistry, Soybean (Glycine max), 570 Life sciences, biology, Animal Science and Zoology, Parasitology, 1103 Animal Science and Zoology, business, PAT, 010606 plant biology & botany, Food Science, AvHPPD-03, PAT Requestor: Competent Authority of Germany Question number: EFSA-Q-2012-00753
Abstract: © 2020 European Food Safety Authority., The scope of application EFSA‐GMO‐DE‐2012‐111 is for food and feed uses, import and processing of genetically modified (GM) soybean SYHT0H2 in the European Union. Soybean SYHT0H2 was developed to confer tolerance to the herbicidal active substances mesotrione and other p‐hydroxyphenylpyruvate dioxygenase (HPPD)‐inhibiting herbicides and glufosinate ammonium. The molecular characterisation data and bioinformatic analyses do not identify issues except for sequence similarity of AvHPPD‐03 to bacterial haemolysins that was considered in food/feed safety assessment. The outcome of the comparative analysis (agronomic/phenotypic and compositional characteristics) did not need further assessment except for the changes in seed levels of α‐tocopherol and γ‐tocopherol that were assessed for food and feed relevance. The GMO Panel does not identify toxicological and allergenicity concerns for the AvHPPD‐03 and PAT proteins expressed in soybean SYHT0H2 and finds no evidence that the genetic modification would change the overall allergenicity of soybean SYHT0H2. The nutritional impact of food/feed from soybean SYHT0H2 is expected to be the same as that of food/feed from the conventional counterpart and commercial non‐GM soybean reference varieties. The GMO Panel concludes that soybean SYHT0H2 is as safe as and nutritionally equivalent to the conventional counterpart and the tested non‐GM soybean reference varieties, and no post‐market monitoring of food/feed is considered necessary. In the case of accidental release of viable soybean SYHT0H2 grains into the environment, soybean SYHT0H2 would not raise environmental safety concerns. The post‐market environmental monitoring plan and reporting intervals are in line with the intended uses of soybean SYHT0H2. In conclusion, the GMO Panel considers that soybean SYHT0H2, as described in this application, is as safe as its conventional counterpart and the tested non‐GM soybean reference varieties with respect to potential effects on human and animal health and the environment.
Published: 2020

20. Current status of the multinational Arabidopsis community

Author: Parry, Geraint, Provart, Nicholas J., Brady, Siobhan M., Uzilday, Baris, Adams, K., Araújo, W., Aubourg, S., Baginsky, S., Bakker, E., Bärenfaller, K., Batley, J., Beale, M., Beilstein, M., Belkhadir, Y., Berardini, T., Bergelson, J., Blanco-Herrera, F., Brady, S., Braun, Hans-Peter, Briggs, S., Brownfield, L., Cardarelli, M., Castellanos-Uribe, M., Coruzzi, G., Dassanayake, M., Jaeger, G.D., Dilkes, B., Doherty, C., Ecker, J., Edger, P., Edwards, D., Kasmi, F.E., Eriksson, M., Exposito-Alonso, M., Falter-Braun, P., Fernie, A., Ferro, M., Fiehn, O., Friesner, J., Greenham, K., Guo, Y., Hamann, T., Hancock, A., Hauser, M.-T., Heazlewood, J., Ho, C.-H., Hõrak, H., Huala, E., Hwang, I., Iuchi, S., Jaiswal, P., Jakobson, L., Jiang, Y., Jiao, Y., Jones, A., Kadota, Y., Khurana, J., Kliebenstein, D., Knee, E., Kobayashi, M., Koch, M., Krouk, G., Larson, T., Last, R., Lepiniec, L., Li, S., Lurin, C., Lysak, M., Maere, S., Malinowski, R., Maumus, F., May, S., Mayer, K., Mendoza-Cozatl, D., Mendoza-Poudereux, I., Meyers, B., Micol, J.L., Millar, H., Mock, H.-P., Mukhtar, K., Mukhtar, S., Murcha, M., Nakagami, H., Nakamura, Y., Nicolov, L., Nikolau, B., Nowack, M., Nunes-Nesi, A., Palmgren, M., Parry, G., Patron, N., Peck, S., Pedmale, U., Perrot-Rechenmann, C., Pieruschka, R., Pío-Beltrán, J., Pires, J.C., Provart, N., Rajjou, L., Reiser, L., Reumann, S., Rhee, S., Rigas, S., Rolland, N., Romanowski, A., Santoni, V., Savaldi-Goldstein, S., Schmitz, R., Schulze, W., Seki, M., Shimizu, K.K., Slotkin, K., Small, I., Somers, D., Sozzani, R., Spillane, C., Srinivasan, R., Taylor, N., Tello-Ruiz, M.-K., Thelen, J., Tohge, T., Town, C., Toyoda, T., Uzilday, B., Peer, Y.V.D., Wijk, K., Gillhaussen, P.V., Walley, J., Ware, D., Weckwerth, W., Whitelegge, J., Wienkoop, S., Wright, C., Wrzaczek, M., Yamazaki, M., Yanovsky, M., Žárský, V., Zhong, X., Biological Systems Engineering, Organisms and Environment Research Division, Cardiff School of Biosciences, Cardiff University, University of Toronto, University of California [Davis] (UC Davis), University of California, Institut de Recherche en Horticulture et Semences (IRHS), Université d'Angers (UA)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, 06099 Halle, Germany, Department of Ecology and Evolution [Chicago], University of Chicago, Biochimie et Physiologie Moléculaire des Plantes (BPMP), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Unité de recherche en génomique végétale (URGV), Institut National de la Recherche Agronomique (INRA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), Rothamsted Research, Biotechnology and Biological Sciences Research Council (BBSRC), University of Arizona, Gregor Mendel Institute (GMI) - Vienna Biocenter (VBC), Austrian Academy of Sciences (OeAW), University of California (UC), Center for Genomics and Systems Biology, Department of Biology [New York], New York University [New York] (NYU), NYU System (NYU)-NYU System (NYU)-New York University [New York] (NYU), NYU System (NYU)-NYU System (NYU), Flanders Institute for Biotechnology, National Center for Atmospheric Research [Boulder] (NCAR), Max Planck Institute of Molecular Plant Physiology (MPI-MP), Max-Planck-Gesellschaft, Laboratoire de Biologie à Grande Échelle (BGE - UMR S1038), Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Grenoble Alpes (UGA), Agricultural Sustainability Institute and Department of Neurobiology, Physiology, and Behavior, Norwegian University of Science and Technology (NTNU), University of Melbourne, King Abdullah University of Science and Technology (KAUST), University of Chinese Academy of Sciences [Beijing] (UCAS), The Sainsbury Laboratory [Norwich] (TSL), IBM Research – Tokyo, University Medical Center Groningen [Groningen] (UMCG), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Centre for Novel Agricultural Products, Department of Biology, University of York [York, UK], Biologie des Semences (LBS), Institut National de la Recherche Agronomique (INRA)-Institut National Agronomique Paris-Grignon (INA P-G), Sichuan University [Chengdu] (SCU), Institut des Sciences des Plantes de Paris-Saclay (IPS2 (UMR_9213 / UMR_1403)), Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Department of Plant Systems Biology, Unité de Recherche Génomique Info (URGI), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), University of Nottingham, UK (UON), Institute of Bioinformatics and System Biology (IBIS), Helmholtz Zentrum München = German Research Center for Environmental Health, Saint Mary's University [Halifax], Max Planck Institute for Plant Breeding Research (MPIPZ), National Institute of Genetics (NIG), University of Copenhagen = Københavns Universitet (UCPH), Division of Biology [La Jolla], University of California [San Diego] (UC San Diego), University of California (UC)-University of California (UC), Earlham Institute [Norwich], Forschungszentrum Jülich GmbH | Centre de recherche de Juliers, Helmholtz-Gemeinschaft = Helmholtz Association, University of Missouri [Columbia] (Mizzou), University of Missouri System, Institut Jean-Pierre Bourgin (IJPB), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Department of Plant Biology, Carnegie Institution for Science, Dynamique du protéome et biogenèse du chloroplaste (ChloroGenesis), Physiologie cellulaire et végétale (LPCV), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Grenoble Alpes (UGA)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Grenoble Alpes (UGA), Plateforme de Spectrométrie de Masse Protéomique - Mass Spectrometry Proteomics Platform (MSPP), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Plant Systems Biology, Institute of Physiology and Biotechnology of plants, RIKEN Center for Sustainable Resource Science [Yokohama] (RIKEN CSRS), RIKEN - Institute of Physical and Chemical Research [Japon] (RIKEN), Unité de recherche Génétique et amélioration des plantes (GAP), Institut National de la Recherche Agronomique (INRA), Department of Biology, Duke University, Genetics and Biotechnology Lab, Plant & AgriBiosciences Research Centre (PABC), School of Natural Sciences, National University of Ireland [Galway] (NUI Galway), Universidade Federal de São Paulo, RIKEN Plant Science Center and RIKEN Bioinformatics and Systems Engineering Division, Cold Spring Harbor Laboratory (CSHL), University of Vienna [Vienna], University of California [Los Angeles] (UCLA), Department of Plant Molecular Biology, Université de Lausanne = University of Lausanne (UNIL), UKRI-BBSRC grant BB/M004376/1, HHMI Faculty Scholar Fellowship, Turkiye Bilimsel ve Teknolojik Arastirma Kurumu (TUBITAK) 118Z137, UK Research & Innovation (UKRI) Biotechnology and Biological Sciences Research Council (BBSRC) BB/M004376/1, Sainsbury Lab, Norwich Research Park, Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Helmholtz-Zentrum München (HZM), University of Copenhagen = Københavns Universitet (KU), University of California-University of California, Carnegie Institution for Science [Washington], Université de Lausanne (UNIL), Ege Üniversitesi, Organismal and Evolutionary Biology Research Programme, Plant Biology, Viikki Plant Science Centre (ViPS), Receptor-Ligand Signaling Group, University of Zurich, Parry, Geraint, Provart, Nicholas J, and Brady, Siobhan M
Subjects: 0106 biological sciences, Arabidopsis thaliana, [SDV]Life Sciences [q-bio], White Paper, Genetics and Molecular Biology (miscellaneous), Plant Science, Biochemistry, 01 natural sciences, Dewey Decimal Classification::500 | Naturwissenschaften::580 | Pflanzen (Botanik), Research community, Arabidopsis, 1110 Plant Science, 0303 health sciences, Ecology, biology, 1184 Genetics, developmental biology, physiology, ddc:580, Multinational corporation, MAP, 590 Animals (Zoology), Life Sciences & Biomedicine, Arabidopsis research community, Evolution, Steering committee, Multinational Arabidopsis Steering Committee, Library science, 1301 Biochemistry, Genetics and Molecular Biology (miscellaneous), Biochemistry, Genetics and Molecular Biology (miscellaneous), Business and Economics, 10127 Institute of Evolutionary Biology and Environmental Studies, 03 medical and health sciences, Behavior and Systematics, Political science, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, MASC, roadmap, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, [SDV.GEN]Life Sciences [q-bio]/Genetics, Plant Sciences, Botany, 15. Life on land, 11831 Plant biology, biology.organism_classification, White Papers, collaboration, 1105 Ecology, Evolution, Behavior and Systematics, QK1-989, Arabidopsis Thaliana, Collaboration, Research Network, Roadmap, 570 Life sciences, 1182 Biochemistry, cell and molecular biology, 2303 Ecology, 010606 plant biology & botany
Abstract: The multinational Arabidopsis research community is highly collaborative and over the past thirty years these activities have been documented by the Multinational Arabidopsis Steering Committee (MASC). Here, we (a) highlight recent research advances made with the reference plantArabidopsis thaliana; (b) provide summaries from recent reports submitted by MASC subcommittees, projects and resources associated with MASC and from MASC country representatives; and (c) initiate a call for ideas and foci for the "fourth decadal roadmap," which will advise and coordinate the global activities of the Arabidopsis research community., UKRI-BBSRC grant [BB/M004376/1]; HHMI Faculty Scholar Fellowship; Scientific and Technological Research Council of TurkeyTurkiye Bilimsel ve Teknolojik Arastirma Kurumu (TUBITAK) [118Z137], UKRI-BBSRC grant, Grant/Award Number: BB/M004376/1; HHMI Faculty Scholar Fellowship; the Scientific and Technological Research Council of Turkey, Grant/Award Number: 118Z137
Published: 2020

21. Wheat chromatin architecture is organized in genome territories and transcription factories

Author: Susan Duncan, Soon-Kap Kim, Chang Liu, Anthony Hall, Thomas Blein, Ying Huang, Alaguraj Veluchamy, Magali Perez, Azahara Martin-Ramirez, Deborah Manza-Mianza, Martin Crespi, Abdelhafid Bendahmane, Catherine Bergounioux, Etienne Paux, Cécile Raynaud, Graham Moore, Moussa Benhamed, Clement Pichot, Heribert Hirt, Natalia Y. Rodriguez Granados, Lorenzo Concia, David Latrasse, Caroline Juery, Magdy M. Mahfouz, Juan S. Ramirez-Prado, Séverine Domenichini, Institut des Sciences des Plantes de Paris-Saclay (IPS2 (UMR_9213 / UMR_1403)), Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), King Abdullah University of Science and Technology (KAUST), John Innes Centre [Norwich], Biotechnology and Biological Sciences Research Council (BBSRC), Earlham Institute [Norwich], Génétique Diversité et Ecophysiologie des Céréales (GDEC), Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Zentrum für Molekularbiologie der Pflanzen (ZMBP), Eberhard Karls Universität Tübingen = Eberhard Karls University of Tuebingen, Institut Universitaire de France (IUF), Ministère de l'Education nationale, de l’Enseignement supérieur et de la Recherche (M.E.N.E.S.R.), ANR-19-CE20-0001,3DWheat,Une approche tridimensionnelle de génomique fonctionnelle pour identifier les cibles contrôlant la réponse au stress thermique chez le blé(2019), and Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
Subjects: 0106 biological sciences, Transcription factories, lcsh:QH426-470, Euchromatin, Transcription, Genetic, RNA polymerase II, 01 natural sciences, Genome, DNA loops, [SDV.GEN.GPL]Life Sciences [q-bio]/Genetics/Plants genetics, Polyploidy, 03 medical and health sciences, Hi-C, Constitutive heterochromatin, lcsh:QH301-705.5, Gene, Triticum, Genome territories, 030304 developmental biology, 0303 health sciences, biology, Research, Chromosome, Chromatin, Histone Code, lcsh:Genetics, lcsh:Biology (General), Evolutionary biology, Hi-ChIP, biology.protein, RNA Polymerase II, Genome, Plant, 010606 plant biology & botany
Abstract: Background Polyploidy is ubiquitous in eukaryotic plant and fungal lineages, and it leads to the co-existence of several copies of similar or related genomes in one nucleus. In plants, polyploidy is considered a major factor in successful domestication. However, polyploidy challenges chromosome folding architecture in the nucleus to establish functional structures. Results We examine the hexaploid wheat nuclear architecture by integrating RNA-seq, ChIP-seq, ATAC-seq, Hi-C, and Hi-ChIP data. Our results highlight the presence of three levels of large-scale spatial organization: the arrangement into genome territories, the diametrical separation between facultative and constitutive heterochromatin, and the organization of RNA polymerase II around transcription factories. We demonstrate the micro-compartmentalization of transcriptionally active genes determined by physical interactions between genes with specific euchromatic histone modifications. Both intra- and interchromosomal RNA polymerase-associated contacts involve multiple genes displaying similar expression levels. Conclusions Our results provide new insights into the physical chromosome organization of a polyploid genome, as well as on the relationship between epigenetic marks and chromosome conformation to determine a 3D spatial organization of gene expression, a key factor governing gene transcription in polyploids.
Published: 2019

22. Unraveling the subtleties of β-(1→3)-glucan phosphorylase specificity in the GH94, GH149, and GH161 glycoside hydrolase families

Author: Nicola J. Patron, Sakonwan Kuhaudomlarp, Bernard Henrissat, Giulia Pergolizzi, Robert A. Field, Norwich Research Park, Earlham Institute [Norwich], Architecture et fonction des macromolécules biologiques (AFMB), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), and Department of Engineering Science
Subjects: 0301 basic medicine, Glycan, orthologs, CAZy, Euglena gracilis, beta-Glucans, enzyme evolution, Glycoside Hydrolases, [SDV]Life Sciences [q-bio], ved/biology.organism_classification_rank.species, phosphorylase, Oligosaccharides, medicine.disease_cause, glycobiology phosphorylase, Biochemistry, Ochromonas, enzyme evolution heterokont, 03 medical and health sciences, glycobiology, Bacterial Proteins, Manchester Institute of Biotechnology, β-1,3-glucan, medicine, Glycoside hydrolase, carbohydrate metabolism, glycoside hydrolase, heterokont, carbohydrate utilization loci, β-1, Molecular Biology, Escherichia coli, Phosphorolysis, 030102 biochemistry & molecular biology, biology, Chemistry, ved/biology, Cell Biology, Gram-positive bacteria, ResearchInstitutes_Networks_Beacons/manchester_institute_of_biotechnology, biology.organism_classification, 030104 developmental biology, 3-glucan, biology.protein, Enzymology, Paenibacillus polymyxa, Bacteria
Abstract: International audience; Glycoside phosphorylases (GPs) catalyze the phosphorolysis of glycans into the corresponding sugar 1-phosphates and shortened glycan chains. Given the diversity of natural β-(1→3)-glucans and their wide range of biotechnological applications, the identification of enzymatic tools that can act on β-(1→3)-glucooligosaccharides is an attractive area of research. GP activities acting on β-(1→3)-glucooligosaccharides have been described in bacteria, the photosynthetic excavate Euglena gracilis, and the heterokont Ochromonas spp. Previously, we characterized β-(1→3)-glucan GPs from bacteria and E. gracilis, leading to their classification in glycoside hydrolase family GH149. Here, we characterized GPs from Gram-positive bacteria and heterokont algae acting on β-(1→3)-glucooligosaccharides. We identified a phosphorylase sequence from Ochromonas spp. (OcP1) together with its orthologs from other species, leading us to propose the establishment of a new GH family, designated GH161. To establish the activity of GH161 members, we recombinantly expressed a bacterial GH161 gene sequence (PapP) from the Gram-positive bacterium Paenibacillus polymyxa ATCC 842 in Escherichia coli. We found that PapP acts on β-(1→3)-glucooligosaccharide acceptors with a degree of polymerization (DP) ≥ 2. This activity was distinct from that of characterized GH149 β-(1→3)-glucan phosphorylases, which operate on acceptors with DP ≥ 1. We also found that bacterial GH161 genes co-localize with genes encoding β-glucosidases and ATP-binding cassette transporters, highlighting a probable involvement of GH161 enzymes in carbohydrate degradation. Importantly, in some species, GH161 and GH94 genes were present in tandem, providing evidence that GPs from different CAZy families may work sequentially to degrade oligosaccharides.
Published: 2019

23. Assessment of genetically modified maize MON 89034 for renewal authorisation under Regulation (EC) No 1829/2003 (application EFSA-GMO-RX-015) EFSA Panel on Genetically Modified Organisms (GMO), Panel members

Author: EFSA Panel on Genetically Modified Organisms (GMO), ., VERONESI, Fabio, Alvarez, Fernando, Ardizzone, Michele, Raffaello, Tommaso, Naegeli, Hanspeter, Bresson, Jean-Louis, Dalmay, Tamas, Dewhurst, Ian, Epstein, Michelle, Firbank, Leslie, Guerche, Philippe, Hejatko, Jan, Moreno, Francisco, Mullins, Ewen, Nogu, Fabien, Rostoks, Nils, Juan S Anchez Serrano, Jose, Savoini, Giovanni, Veromann, Eve, Gastroenterology, Hepatology and Nutrition Division, CHU Sainte Justine [Montréal], Department of Forest Sciences [Helsinki], Faculty of Agriculture and Forestry [Helsinki], University of Helsinki-University of Helsinki, Universität Zürich [Zürich] = University of Zurich (UZH), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Earlham Institute [Norwich], Centre for Ecology and Hydrology [Bangor] (CEH), Natural Environment Research Council (NERC), Institut Jean-Pierre Bourgin (IJPB), and Institut National de la Recherche Agronomique (INRA)-AgroParisTech
Subjects: renewal, [SDV.BIO]Life Sciences [q-bio]/Biotechnology, MON 89034, Articles 11 and 23, Regulation (EC) No 1829/2003 Requestor: European Commission (DG SANTE) Question number: EFSA-Q-2018-00673, Maize
Abstract: International audience; Following the submission of application EFSA-GMO-RX-015 under Regulation (EC) No 1829/2003 from Bayer Agriculture BVBA, the EFSA Panel on Genetically Modified Organisms (GMO Panel) was asked to deliver a scientific risk assessment on the data submitted in the context of the renewal of authorisation application for the insect-resistant genetically modified maize MON 89034, for food and feed uses, excluding cultivation within the EU. The data received in the context of this renewal application contained post-market environmental monitoring reports, a systematic search and evaluation of literature, updated bioinformatic analyses and additional documents or studies performed by or on behalf of the applicant. The GMO Panel assessed these data for possible new hazards, modified exposure or new scientific uncertainties identified during the authorisation period and not previously assessed in the context of the original application. Under the assumption that the DNA sequence of the event in maize MON 89034 considered for renewal is identical to the sequence of the originally assessed event, the GMO Panel concludes that there is no evidence in renewal application EFSA-GMO-RX-015 for new hazards, modified exposure or scientific uncertainties that would change the conclusions of the original risk assessment on maize MON 89034.
Published: 2019

24. Statement complementing the EFSA Scientific Opinion on application (EFSA-GMO-UK-2006-34) for authorisation of food and feed containing, consisting of and produced from genetically modified maize 3272 EFSA Panel on Genetically Modified Organisms (GMO)

Author: EFSA Panel on Genetically Modified Organisms (GMO), ., VERONESI, Fabio, Alvarez, Fernando, Ardizzone, Michele, Lanzoni, Anna, Angel G Omez Ruiz, Jose, De Sanctis, Giacomo, Fern Andez Dumont, Antonio, Gennaro, Andrea, Neri, Franco, Bresson, Jean-Louis, Dalmay, Tamas, Dewhurst, Ian, Epstein, Michelle, Firbank, Leslie, Guerche, Philippe, Hejatko, Jan, Moreno, Francisco, Mullins, Ewen, Naegeli, Hanspeter, Nogu, Fabien, Rostoks, Nils, Juan S Anchez Serrano, Jose, Savoini, Giovanni, Veromann, Eve, Gastroenterology, Hepatology and Nutrition Division, CHU Sainte Justine [Montréal], Center for Nanotechnology Innovation, @NEST (CNI), National Enterprise for nanoScience and nanoTechnology (NEST), Scuola Normale Superiore di Pisa (SNS)-Scuola Universitaria Superiore Sant'Anna [Pisa] (SSSUP)-Istituto Italiano di Tecnologia (IIT)-Consiglio Nazionale delle Ricerche [Pisa] (CNR PISA)-Scuola Normale Superiore di Pisa (SNS)-Scuola Universitaria Superiore Sant'Anna [Pisa] (SSSUP)-Istituto Italiano di Tecnologia (IIT)-Consiglio Nazionale delle Ricerche [Pisa] (CNR PISA), Tuscia University, University of Cambridge [UK] (CAM), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Earlham Institute [Norwich], Centre for Ecology and Hydrology [Bangor] (CEH), Natural Environment Research Council (NERC), Institut Jean-Pierre Bourgin (IJPB), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, and Universität Zürich [Zürich] = University of Zurich (UZH)
Subjects: [SDV.BIO]Life Sciences [q-bio]/Biotechnology, GMO, food and feed safety Requestor: European Commission Question number: EFSA-Q-2017-00341, maize (Zea mays), thermotolerant alpha-amylase
Abstract: International audience; Following a request from the European Commission, the GMO Panel assessed additional information related to the application for authorisation of food and feed containing, consisting of and produced from genetically modified (GM) maize 3272 (EFSA-GMO-UK-2006-34). The applicant conducted new agronomic, phenotypic and compositional analysis studies on maize 3272 and assessed the allergenic potential of AMY797E protein, addressing elements that remained inconclusive from previous EFSA opinion issued in 2013. The GMO Panel is of the opinion that the agronomic and phenotypic characteristics as well as forage and grain composition of maize 3272 do not give rise to food and feed safety, and nutritional concerns when compared to non-GM maize. Considering the scope of this application and the characteristics of the trait introduced in this GM maize, the effect of processing and potential safety implications of specific food or feed products remain to be further investigated. Regarding the allergenic potential of AMY797E protein and considering all possible food and feed uses of maize 3272, the Panel concludes that the information provided does not fully address the concerns previously raised by the Panel in 2013. Owing to the nature and the knowledge available on this protein family, it is still unclear whether under specific circumstances the alpha-amylase AMY797E has the capacity to sensitise certain individuals and to cause adverse effects. To further support the safety of specific products of maize 3272, the applicant provided thorough information relevant for the allergenicity assessment of dried distiller grains with solubles (DDGS), which is the main product of interest for importation into the EU. Having considered the information provided on this product, the Panel is of the opinion that under the specific conditions of use described by the applicant, DDGS produced from maize 3272 does not raise concerns when compared to DDGS from non-GM maize.
Published: 2019

25. EFSA Panel on Genetically Modified Organisms (GMO)

Author: EFSA Panel on Genetically Modified Organisms (GMO), ., VERONESI, Fabio, Alvarez, Fernando, Ardizzone, Michele, De Sanctis, Giacomo, Devos, Yann, Fernandez Dumont, Antonio, Gennaro, Andrea, Angel G Omez Ruiz, Jose, Lanzoni, Anna, Franco, Maria, Neri, Nikoletta, Papadopoulou, Konstantinos, Paraskevopoulos, Tommaso, Bresson, Jean-Louis, Dalmay, Tamas, Dewhurst, Ian, Epstein, Michelle, Firbank, Leslie, Guerche, Philippe, Hejatko, Jan, Moreno, Francisco, Mullins, Ewen, Naegeli, Hanspeter, Nogu, Fabien, Rostoks, Nils, Juan S Anchez Serrano, Jose, Savoini, Giovanni, Veromann, Eve, Orthopaedic Surgery Department, Sant Rafael Hospital, European Food Safety Authority (EFSA), Tuscia University, Center for Nanotechnology Innovation, @NEST (CNI), National Enterprise for nanoScience and nanoTechnology (NEST), Scuola Normale Superiore di Pisa (SNS)-Scuola Universitaria Superiore Sant'Anna [Pisa] (SSSUP)-Istituto Italiano di Tecnologia (IIT)-Consiglio Nazionale delle Ricerche [Pisa] (CNR PISA)-Scuola Normale Superiore di Pisa (SNS)-Scuola Universitaria Superiore Sant'Anna [Pisa] (SSSUP)-Istituto Italiano di Tecnologia (IIT)-Consiglio Nazionale delle Ricerche [Pisa] (CNR PISA), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Earlham Institute [Norwich], Centre for Ecology and Hydrology [Bangor] (CEH), Natural Environment Research Council (NERC), Institut Jean-Pierre Bourgin (IJPB), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, and Universität Zürich [Zürich] = University of Zurich (UZH)
Subjects: soybean (Glycine max), MON 87751, [SDV.BIO]Life Sciences [q-bio]/Biotechnology, fungi, MON 87708, insect resistant Requestor: Competent Authority of the Netherlands, food and beverages, MON 87701, genetically modified organism (GMO), MON 89788, herbicide tolerant
Abstract: International audience; Soybean MON 87751 9 MON 87701 9 MON 87708 9 MON 89788 (four-event stack soybean) was produced by conventional crossing to combine four single events: MON 87751, MON 87701, MON 87708 and MON 89788. The GMO Panel previously assessed the four single events and did not identify safety concerns. No new data on the single events have been identified that would lead to modification of the original conclusions on their safety. The molecular characterisation, comparative analysis (agronomic, phenotypic and compositional characteristics) and the outcome of the toxicological and allergenicity assessment indicate that the combination of the single soybean events and of the newly expressed proteins in the four-event stack soybean does not give rise to food and feed safety and nutritional concerns. The GMO Panel concludes that the four-event stack soybean, as described in this application, is as safe as and nutritionally equivalent to the non-GM comparator and the non-GM reference varieties tested. In the case of accidental release of viable seeds of the four-event stack soybean into the environment, this would not raise environmental safety concerns. The post-market environmental monitoring plan and reporting intervals are in line with the intended uses of the four-event stack soybean. Post-market monitoring of food/feed is not considered necessary. The GMO Panel concludes that the four-event stack soybean is as safe as the non-GM comparator and the tested non-GM reference varieties with respect to potential effects on human and animal health and the environment.
Published: 2019

26. Assessment of genetically modified soybean MON 87708 × MON 89788 × A5547-127, for food and feed uses, under Regulation (EC) No 1829/2003 (application EFSA-GMO-NL-2016-135)

Author: EFSA Panel on Genetically Modified Organisms (GMO), Naegeli, Hanspeter, Bresson, Jean-Louis, Dalmay, Tamas, Dewhurst, Ian Crawford, Epstein, Michelle M., Firbank, Leslie George, Guerche, Philippe, Hejatko, Jan, Moreno, F. Javier, Mullins, Ewen, Nogué, Fabien, Rostoks, Nils, Sánchez Serrano, Jose Juan, Savoini, Giovanni, Veromann, Eve, Veronesi, Fabio, Álvarez, Fernando, Fernandez Dumont, Antonio, Papadopoulou, Nikoletta, Ardizzone, Michele, Devos, Yann, Gennaro, Andrea, Ruiz Gómez, Jose Ángel, Lanzoni, Anna, Neri, Franco Maria, Paraskevopoulos, Konstantinos, Raffaello, Tommaso, De Sanctis, Giacomo, Institut Jean-Pierre Bourgin (IJPB), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, UAR 1171 Soutien aux Projets Européens, Institut National de la Recherche Agronomique (INRA), UAS 0621 Gip Geves Cavaillon, Institut National de la Recherche Agronomique (INRA)-Groupe d'étude et de controle des variétés et des semences (GEVES), European Food Safety Authority = Autorité européenne de sécurité des aliments, Earlham Institute [Norwich], Gembloux Agro-BioTech, Université de Liège, Unité de Recherche Génomique Info (URGI), Middlesex University [London], Luminy Génétique et Biophysique des Plantes (LGBP), Institut de Biosciences et Biotechnologies d'Aix-Marseille (ex-IBEB) (BIAM), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)
Subjects: MON 87708 9 MON 89788 9 A5547-127, Regulation (EC) 1829/2003, DMO, 040301 veterinary sciences, Veterinary (miscellaneous), [SDV]Life Sciences [q-bio], Plant Science, TP1-1185, 010501 environmental sciences, Biology, MON 87708 × MON 89788 × A5547‐127, 01 natural sciences, Microbiology, Genetically modified soybean, oybean (Glycine max), 0403 veterinary science, import and processing, Import and processing, Environmental safety, Regulation (EC)1829/2003, TX341-641, DMO, 0105 earth and related environmental sciences, 2. Zero hunger, CP4 EPSPS, Animal health, business.industry, Nutrition. Foods and food supply, GMO, Chemical technology, fungi, Regulation (EC) 1829/2003, food and beverages, 04 agricultural and veterinary sciences, Biotechnology, Scientific Opinion, soybean (Glycine max), MON 877089MON 897889A5547-127, Soybean (Glycine max), 13. Climate action, Animal Science and Zoology, Parasitology, business, PAT, Food Science
Abstract: Soybean MON 87708 × MON 89788 × A5547‐127 (three‐event stack soybean) was produced by conventional crossing to combine three single events: MON 87708, MON 89788 and A5547‐127. The GMO Panel previously assessed the three single events and did not identify safety concerns. No new data on the single events, leading to modification of the original conclusions on their safety have been identified. The molecular characterisation, comparative analysis (agronomic, phenotypic and compositional characteristics) and the outcome of the toxicological, allergenicity and nutritional assessment indicate that the combination of the single soybean events and of the newly expressed proteins in the three‐event stack soybean does not give rise to food and feed safety and nutritional concerns. The GMO Panel concludes that the three‐event stack soybean, as described in this application, is as safe as and nutritionally equivalent to its conventional counterpart and the non‐GM reference varieties tested. The nutritional impact of food/feed derived from the three‐event stack soybean is expected to be the same as that of food/feed derived from the conventional counterpart and non‐GM reference varieties. In the case of accidental release of viable seeds of the three‐event stack soybean into the environment, this would not raise environmental safety concerns. The post‐market environmental monitoring plan and reporting intervals are in line with the intended uses of the three‐event stack soybean. Post‐market monitoring of food/feed is not considered necessary. The GMO Panel concludes that the three‐event stack soybean is as safe as its conventional counterpart and the tested non‐GM reference varieties with respect to potential effects on human and animal health and the environment.
Published: 2019

27. Assessment of genetically modified maize MIR604 for renewal authorisation under Regulation (EC) No 1829/2003 (application EFSA-GMO-RX-013) EFSA Panel on Genetically Modified Organisms (GMO), Panel members

Author: EFSA Panel on Genetically Modified Organisms (GMO), ., VERONESI, Fabio, Alvarez, Fernando, Ardizzone, Michele, Raffaello, Tommaso, Naegeli, Hanspeter, Bresson, Jean-Louis, Dalmay, Tamas, Dewhurst, Ian, Epstein, Michelle, Firbank, Leslie, Guerche, Philippe, Hejatko, Jan, Moreno, Francisco, Mullins, Ewen, Nogu, Fabien, Rostoks, Nils, Juan S Anchez Serrano, Jose, Savoini, Giovanni, Veromann, Eve, Orthopaedic Surgery Department, Sant Rafael Hospital, Department of Forest Sciences [Helsinki], Faculty of Agriculture and Forestry [Helsinki], University of Helsinki-University of Helsinki, Universität Zürich [Zürich] = University of Zurich (UZH), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Earlham Institute [Norwich], Centre for Ecology and Hydrology [Bangor] (CEH), Natural Environment Research Council (NERC), Institut Jean-Pierre Bourgin (IJPB), and Institut National de la Recherche Agronomique (INRA)-AgroParisTech
Subjects: renewal, [SDV.BIO]Life Sciences [q-bio]/Biotechnology, [SDV]Life Sciences [q-bio], fungi, Regulation (EC) No 1829/2003, Articles 11 and 23, MIR604, Maize
Abstract: International audience; Following the submission of application EFSA-GMO-RX-013 under Regulation (EC) No 1829/2003 from Syngenta Crop Protection NV/SA, the EFSA Panel on Genetically Modified Organisms (GMO) was asked to deliver a scientific risk assessment on the data submitted in the context of the renewal of authorisation application for the insect-resistant genetically modified maize MIR604, for food and feed uses, excluding cultivation within the EU. The data received in the context of this renewal application contained post-market environmental monitoring reports, a systematic search and evaluation of literature, updated bioinformatic analyses, and additional documents or studies performed by or on behalf of the applicant. The GMO Panel assessed these data for possible new hazards, modified exposure or new scientific uncertainties identified during the authorisation period and not previously assessed in the context of the original application. Under the assumption that the DNA sequence of the event in maize MIR604 considered for renewal is identical to the corrected sequence of the originally assessed event, the GMO Panel concludes that there is no evidence in renewal application EFSA-GMO-RX-013 for new hazards, modified exposure or scientific uncertainties that would change the conclusions of the original risk assessment on maize MIR604.
Published: 2019

28. Scientific Opinion

Author: EFSA Panel on Genetically Modified Organisms (GMO), ., VERONESI, Fabio, Alvarez, Fernando, Ardizzone, Michele, Fernandez Dumont, Antonio, Gennaro, Andrea, Angel G Omez Ruiz, Jose, Lanzoni, Anna, Franco, Maria, Neri, Nikoletta, Papadopoulou, Matthew, Bresson, Jean-Louis, Dalmay, Tamas, Dewhurst, Ian, Epstein, Michelle, Firbank, Leslie, Guerche, Philippe, Hejatko, Jan, Moreno, Francisco, Mullins, Ewen, Naegeli, Hanspeter, Nogu, Fabien, Rostoks, Nils, Juan S Anchez Serrano, Jose, Savoini, Giovanni, Veromann, Eve, Gastroenterology, Hepatology and Nutrition Division, CHU Sainte Justine [Montréal], Tuscia University, Center for Nanotechnology Innovation, @NEST (CNI), National Enterprise for nanoScience and nanoTechnology (NEST), Scuola Normale Superiore di Pisa (SNS)-Scuola Universitaria Superiore Sant'Anna [Pisa] (SSSUP)-Istituto Italiano di Tecnologia (IIT)-Consiglio Nazionale delle Ricerche [Pisa] (CNR PISA)-Scuola Normale Superiore di Pisa (SNS)-Scuola Universitaria Superiore Sant'Anna [Pisa] (SSSUP)-Istituto Italiano di Tecnologia (IIT)-Consiglio Nazionale delle Ricerche [Pisa] (CNR PISA), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Earlham Institute [Norwich], Centre for Ecology and Hydrology [Bangor] (CEH), Natural Environment Research Council (NERC), Institut Jean-Pierre Bourgin (IJPB), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, and Universität Zürich [Zürich] = University of Zurich (UZH)
Subjects: [SDV.BIO]Life Sciences [q-bio]/Biotechnology, GMO, DAS-40278-9, herbicide tolerance, MON 89034, [SDV]Life Sciences [q-bio], Regulation (EC) No 1829/2003 Requestor: Competent Authority of the Netherlands, insect resistance, maize (Zea mays), NK603
Abstract: International audience; Maize MON 89034 9 1507 9 NK603 9 DAS-40278-9 (four-event stack maize) was produced by conventional crossing to combine four single events: MON 89034, 1507, NK603 and DAS-40278-9. The GMO Panel previously assessed the four single events and four of their subcombinations and did not identify safety concerns. No new data on the maize single events or their four subcombinations that could lead to modification of the original conclusions on their safety have been identified. The molecular characterisation, comparative analysis (agronomic, phenotypic and compositional characteristics) and the outcome of the toxicological, allergenicity and nutritional assessment indicates that the combination of the single maize events and of the newly expressed proteins in the four-event stack maize does not give rise to food/feed safety and nutritional concerns. The GMO Panel concludes that the four-event stack maize, as described in this application, is as safe as and nutritionally equivalent to its non-GM comparator and the non-GM reference varieties tested. In the case of accidental release of viable grains of the four-event stack maize into the environment, this would not raise environmental safety concerns. The GMO Panel assessed the likelihood of interactions among the single events in the six maize subcombinations for which no experimental data were provided, and concludes that these are expected to be as safe as and nutritionally equivalent to the single events, the previously assessed subcombinations and the four-event stack maize. The post-market environmental monitoring plan and reporting intervals are in line with the intended uses of the four-event stack maize. No post-market monitoring for food/feed is necessary. The GMO Panel concludes that the four-event stack maize and its subcombinations are as safe as its non-GM comparator and the tested non-GM reference varieties with respect to potential effects on human and animal health and the environment.
Published: 2019

29. Assessment of genetically modified maize MON 87427 3 MON 87460 3 MON 89034 3 MIR162 3 NK603 and subcombinations, for food and feed uses, under Regulation (EC) No 1829/2003 (application EFSA-GMO-NL-2016-134): Scientific Opinion

Author: EFSA Panel on Genetically Modified Organisms (GMO), ., Epstein, Michelle, VERONESI, Fabio, Alvarez, Fernando, Ardizzone, Michele, De Sanctis, Giacomo, Fernandez Dumont, Antonio, Gennaro, Andrea, Angel G Omez Ruiz, Jose, Lanzoni, Anna, Papadopoulou, Nikoletta, Paraskevopoulos, Konstantinos, Bresson, Jean-Louis, Dalmay, Tamas, Dewhurst, Ian, Epstein, Michele, Firbank, Leslie, Guerche, Philippe, Hejatko, Jan, Moreno, Francisco, Mullins, Ewen, Naegeli, Hanspeter, Nogu, Fabien, Rostoks, Nils, Juan S Anchez Serrano, Jose, Savoini, Giovanni, Veromann, Eve, Gastroenterology, Hepatology and Nutrition Division, CHU Sainte Justine [Montréal], Tuscia University, Center for Nanotechnology Innovation, @NEST (CNI), National Enterprise for nanoScience and nanoTechnology (NEST), Scuola Normale Superiore di Pisa (SNS)-Scuola Universitaria Superiore Sant'Anna [Pisa] (SSSUP)-Istituto Italiano di Tecnologia (IIT)-Consiglio Nazionale delle Ricerche [Pisa] (CNR PISA)-Scuola Normale Superiore di Pisa (SNS)-Scuola Universitaria Superiore Sant'Anna [Pisa] (SSSUP)-Istituto Italiano di Tecnologia (IIT)-Consiglio Nazionale delle Ricerche [Pisa] (CNR PISA), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Earlham Institute [Norwich], Centre for Ecology and Hydrology [Bangor] (CEH), Natural Environment Research Council (NERC), Institut Jean-Pierre Bourgin (IJPB), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, and Universität Zürich [Zürich] = University of Zurich (UZH)
Subjects: [SDV.BIO]Life Sciences [q-bio]/Biotechnology, GMO, MON, maize (Zea mays)
Abstract: International audience; Maize MON 87427 9MON 87460 9 MON 89034 9 MIR162 9 NK603 (five-event stack maize) was produced by conventional crossing to combine five single events: MON 87427, MON 87460, MON 89034, MIR162 and NK603. The GMO Panel previously assessed the five single maize events and eleven of the subcombinations and did not identify safety concerns. No new data on the single maize events or the 11 subcombinations that could lead to modification of the original conclusions on their safety were identified. The molecular characterisation, comparative analysis (agronomic, phenotypic and compositional characteristics) and the outcome of the toxicological, allergenicity and nutritional assessment indicate that the combination of the single maize events and of the newly expressed proteins in the five-event stack maize does not give rise to food and feed safety and nutritional concerns. The GMO Panel concludes that the five-event stack maize, as described in this application, is as safe as and nutritionally equivalent to its non-GM comparator and the non-GM reference varieties tested. In the case of accidental release of viable grains of the five-event stack maize into the environment, this would not raise environmental safety concerns. The GMO Panel assessed the likelihood of interactions among the single events in the 14 maize subcombinations not previously assessed and concludes that these are expected to be as safe as and nutritionally equivalent to the single events, the previously assessed subcombinations and the five-event stack maize. The post-market environmental monitoring plan and reporting intervals are in line with the intended uses of the five-event stack maize. Post-market monitoring of food/feed is not considered necessary. The GMO Panel concludes that the five-event stack maize and its subcombinations are as safe as its non-GM comparator and the tested non-GM reference varieties with respect to potential effects on human and animal health and the environment.
Published: 2019

30. Identification of Euglena gracilis β-1,3-glucan phosphorylase and establishment of a new glycoside hydrolase (GH) family GH149

Author: Sakonwan Kuhaudomlarp, Nicola J. Patron, Martin Rejzek, Bernard Henrissat, Robert A. Field, Gerhard Saalbach, Norwich Research Park, John Innes Centre [Norwich], Earlham Institute [Norwich], Architecture et fonction des macromolécules biologiques (AFMB), Institut National de la Recherche Agronomique (INRA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Department of Engineering Science, Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU)-Institut National de la Recherche Agronomique (INRA), and Biotechnology and Biological Sciences Research Council (BBSRC)
Subjects: 0301 basic medicine, orthologs, Euglena gracilis, phosphorylase, ved/biology.organism_classification_rank.species, Sequence alignment, beta-1, medicine.disease_cause, Biochemistry, Conserved sequence, 03 medical and health sciences, Glycogen phosphorylase, glycobiology, Manchester Institute of Biotechnology, medicine, glycoside hydrolase, Glycoside hydrolase, Sugar transporter, [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biochemistry [q-bio.BM], gene transfer, Molecular Biology, Escherichia coli, Peptide sequence, algae, 2. Zero hunger, 030102 biochemistry & molecular biology, molecular evolution, ved/biology, Chemistry, polysaccharide utilization loci, Cell Biology, ResearchInstitutes_Networks_Beacons/manchester_institute_of_biotechnology, gram-negative bacteria, [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biomolecules [q-bio.BM], phylogenetics, 3-glucan, 030104 developmental biology, polysaccharide
Abstract: International audience; Glycoside phosphorylases (EC 2.4.x.x) carry out the reversible phosphorolysis of glucan polymers, producing the corresponding sugar 1-phosphate and a shortened glycan chain. β-1,3-Glucan phosphorylase activities have been reported in the photosynthetic euglenozoan Euglena gracilis, but the cognate protein sequences have not been identified to date. Continuing our efforts to understand the glycobiology of E. gracilis, we identified a candidate phosphorylase sequence, designated EgP1, by proteomic analysis of an enriched cellular protein lysate. We expressed recombinant EgP1 in Escherichia coli and characterized it in vitro as a β-1,3-glucan phosphorylase. BLASTP identified several hundred EgP1 orthologs, most of which were from Gram-negative bacteria and had 37-91% sequence identity to EgP1. We heterologously expressed a bacterial metagenomic sequence, Pro_7066 in E. coli and confirmed it as a β-1,3-glucan phosphorylase, albeit with kinetics parameters distinct from those of EgP1. EgP1, Pro_7066, and their orthologs are classified as a new glycoside hydrolase (GH) family, designated GH149. Comparisons between GH94, EgP1, and Pro_7066 sequences revealed conservation of key amino acids required for the phosphorylase activity, suggesting a phosphorylase mechanism that is conserved between GH94 and GH149. We found bacterial GH149 genes in gene clusters containing sugar transporter and several other GH family genes, suggesting that bacterial GH149 proteins have roles in the degradation of complex carbohydrates. The Bacteroidetes GH149 genes located to previously identified polysaccharide utilization loci, implicated in the degradation of complex carbohydrates. In summary, we have identified a eukaryotic and a bacterial β-1,3-glucan phosphorylase and uncovered a new family of phosphorylases that we name GH149.
Published: 2018

31. Assessment of genetically modified soybean MON 89788 for renewal of authorisation under Regulation (EC) No 1829/2003 (application EFSA-GMO-RX-011) EFSA Panel on Genetically Modified Organisms (GMO), Panel members

Author: EFSA Panel on Genetically Modified Organisms (GMO), ., Epstein, Michelle, VERONESI, Fabio, Alvarez, Fernando, Ardizzone, Michele, Paraskevopoulos, Konstantinos, Naegeli, Hanspeter, Bresson, Jean-Louis, Dalmay, Tamas, Dewhurst, Ian, Epstein, Michele, Firbank, Leslie, Guerche, Philippe, Hejatko, Jan, Moreno, Francisco, Mullins, Ewen, Nogu, Fabien, Rostoks, Nils, Juan S Anchez Serrano, Jose, Savoini, Giovanni, Veromann, Eve, Orthopaedic Surgery Department, Sant Rafael Hospital, Institute of Pharmacology and Toxicology [Zurich], Universität Zürich [Zürich] = University of Zurich (UZH), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Earlham Institute [Norwich], Centre for Ecology and Hydrology [Bangor] (CEH), Natural Environment Research Council (NERC), Institut Jean-Pierre Bourgin (IJPB), and Institut National de la Recherche Agronomique (INRA)-AgroParisTech
Subjects: renewal, [SDV.BIO]Life Sciences [q-bio]/Biotechnology, [SDV]Life Sciences [q-bio], fungi, Regulation (EC) No 1829/2003, Articles 11 and 23, Soybean, MON 89788
Abstract: International audience; Following the submission of application EFSA-GMO-RX-011 under Regulation (EC) No 1829/2003 from Monsanto Europe, the Panel on Genetically Modified Organisms of the European Food Safety Authority (GMO Panel) was asked to deliver a scientific risk assessment on the data submitted in the context of the renewal of authorisation application for the herbicide-tolerant genetically modified soybean MON 89788, for food and feed uses, excluding cultivation within the European Union. The data received in the context of this renewal application contained post-market environmental monitoring reports, a systematic search and evaluation of literature, updated bioinformatic analyses and additional documents or studies performed by or on behalf of the applicant. The GMO Panel assessed these data for possible new hazards, modified exposure or new scientific uncertainties identified during the authorisation period and not previously assessed in the context of the original application. Under the assumption that the DNA sequence of the event in soybean MON 89788 considered for renewal is identical to the sequence of the originally assessed event, the GMO Panel concludes that there is no evidence in renewal application EFSA-GMO-RX-011 for new hazards, modified exposure or scientific uncertainties that would change the conclusions of the original risk assessment on soybean MON 89788.
Published: 2018

32. Preliminary insights into the genetics of bank vole tolerance to Puumala hantavirus in Sweden : XXXX

Author: Sophie O. Vanwambeke, Nathalie Charbonnel, Renaud Vitalis, Audrey Rohfritsch, Karim Gharbi, Caroline B Zeimes, Mathieu Gautier, Bernhard Gschloessl, Gert E. Olsson, Maxime Galan, UCL - SST/ELI/ELIC - Earth & Climate, Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Earlham Institute [Norwich], Department of Wildlife, Fish and Environmental Studies, Swedish University of Agricultural Sciences (SLU), Centre Georges Lemaître for Earth and Climate Research [Louvain] (TECLIM), Earth and Life Institute [Louvain-La-Neuve] (ELI), Université Catholique de Louvain (UCL)-Université Catholique de Louvain (UCL), Charbonnel, Nathalie, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Université Catholique de Louvain = Catholic University of Louvain (UCL)-Université Catholique de Louvain = Catholic University of Louvain (UCL), and European Project: 261504,EC:FP7:HEALTH,FP7-HEALTH-2010-single-stage,EDENEXT(2011)
Subjects: 0106 biological sciences, 0301 basic medicine, Candidate gene, Evolution, selection, adaptation, RAD sequencing, 010603 evolutionary biology, 01 natural sciences, molecular epidemiology, hantavirus, Population genomics, 03 medical and health sciences, Behavior and Systematics, Biologie animale, Nephropathia epidemica, medicine, Gene, Ecology, Evolution, Behavior and Systematics, Original Research, Hantavirus, Nature and Landscape Conservation, Genetics, Animal biology, tolerance, [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], Molecular epidemiology, biology, Ecology, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], immunity, voles, biology.organism_classification, medicine.disease, Bank vole, 030104 developmental biology, Adaptation, [SDE.BE]Environmental Sciences/Biodiversity and Ecology
Abstract: International audience; Natural reservoirs of zoonotic pathogens generally seem to be capable of tolerating infections. Tolerance and its underlying mechanisms remain difficult to assess using experiments or wildlife surveys. High-throughput sequencing technologies give the opportunity to investigate the genetic bases of tolerance, and the variability of its mechanisms in natural populations. In particular, population genomics may provide preliminary insights into the genes shaping tolerance and potentially influencing epidemiological dynamics. Here, we addressed these questions in the bank vole Myodes glareolus, the specific asymptomatic reservoir host of Puumala hantavirus (PUUV), which causes nephropathia epidemica (NE) in humans. Despite the continuous spatial distribution of M. glareolus in Sweden, NE is endemic to the northern part of the country. Northern bank vole populations in Sweden might exhibit tolerance strategies as a result of coadaptation with PUUV. This may favor the circulation and maintenance of PUUV and lead to high spatial risk of NE in northern Sweden. We performed a genome-scan study to detect signatures of selection potentially correlated with spatial variations in tolerance to PUUV. We analyzed six bank vole populations from Sweden, sampled from northern NE-endemic to southern NE-free areas. We combined candidate gene analyses (Tlr4, Tlr7, and Mx2 genes) and high-through-put sequencing of restriction site-associated DNA (RAD) markers. Outlier loci showed high levels of genetic differentiation and significant associations with environmental data including variations in the regional number of NE human cases. Among the 108 outliers that matched to mouse protein-coding genes, 14 corresponded to immune-related genes. The main biological pathways found to be significantly enriched corresponded to immune processes and responses to hantavirus, including the regulation of cytokine productions, TLR cascades, and IL-7, VEGF, and JAK-STAT signaling. In the future, genome-scan replicates and functional experimentations should enable to assess the role of these biological pathways in M. glareolus tolerance to PUUV.
Published: 2018

33. The ash dieback invasion of Europe was founded by two genetically divergent individuals

Author: Adam Vivian-Smith, Kentaro Yoshida, Halvor Solheim, Christine Fosker, Ari M. Hietala, Bernardo J. Clavijo, David Swarbreck, Gemy Kaithakottil, Lawrence Percival-Alwyn, Mark McMullan, Philip Jennings, James K. M. Brown, Diane G. O. Saunders, Matthew D. Clark, Walter Verweij, Louisa Williamson, Jonathan M. Wright, Lorelei Bilham, J. Allan Downie, Elizabeth S. Orton, Renaud Ioos, Dan MacLean, Maryam Rafiqi, Mark Blaxter, Georgios Koutsovoulos, Gonzalo Garcia Accinelli, Tsuyoshi Hosoya, Ben J. Ward, Anne Edwards, Neil Hall, Claude Husson, McMullan, Mark, Earlham Institute [Norwich], Kew Botanical Garden, John Innes Centre [Norwich], Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, The Sainsbury Laboratory, Department of Agrobioscience - Graduate School of Agricultural Science, Kobe University, National Museum of Nature and Science, Fera Science Limited, Laboratoire de la Santé des Végétaux, Unité de Mycologie (LSV Nancy), Laboratoire de la Santé des Végétaux, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Interactions Arbres-Microorganismes (IAM), Université de Lorraine (UL)-Institut National de la Recherche Agronomique (INRA), Norwegian Institute of Bioeconomy Research (NIBIO), Edinburgh Genomics, The Natural History Museum [London] (NHM), Biotechnology and Biological Sciences Research Council (BBSRC) BB/L024055/1, CyVerse UK of the Earlham Institute National Capability in e-Infrastructure, BBSRC BBS/E/J/000CA523, Department of Environment Food and Rural Affairs (Defra) BBS/E/J/000CA523, Economic and Social Research Council, Forestry Commission, Natural Environment Research Council (NERC), Scottish Government under Tree Health and Plant Biosecurity Initiative BB/L01291X/1, French National Research Agency (ANR) of the Investissements d'Avenir programme ANR-11-LABX-0002-01, BBSRC National Capability in Genomics grant BB/J010375/1, BBSRC Institute Strategic Programme Grant for Bioinformatics BB/ J004669/1, The Sainsbury Laboratory [Norwich] (TSL), Konan University [Kobe, Japan], Unité de Mycologie, and Institut National de la Recherche Agronomique (INRA)-Université de Lorraine (UL)
Subjects: 0301 basic medicine, safety, Population genetics, [SDV]Life Sciences [q-bio], DIVERSITY, sécurité, Introgression, Biology, Fraxinus, Article, cinder, 03 medical and health sciences, Ascomycota, DNA POLYMORPHISM, medicine, PATHOGEN HYMENOSCYPHUS PSEUDOALBIDUS, REVEALS INSIGHTS, POPULATION-STRUCTURE, cendre, Ecology, Evolution, Behavior and Systematics, Plant Diseases, FUNGAL, Genetic diversity, GENOME EVOLUTION, PLANT-PATHOGENS, Ecology, Host (biology), Haplotype, Hymenoscyphus fraxineus, Ecological genetics, biology.organism_classification, frêne, medicine.drug_formulation_ingredient, FRAXINUS-EXCELSIOR, RESISTANCE, haploïde, 030104 developmental biology, Haplotypes, 13. Climate action, Evolutionary biology, Genome, Fungal, europe
Abstract: Accelerating international trade and climate change make pathogen spread an increasing concern. Hymenoscyphus fraxineus, the causal agent of ash dieback, is a fungal pathogen that has been moving across continents and hosts from Asian to European ash. Most European common ash trees (Fraxinus excelsior) are highly susceptible to H. fraxineus, although a minority (~5%) have partial resistance to dieback. Here, we assemble and annotate a H. fraxineus draft genome, which approaches chromosome scale. Pathogen genetic diversity across Europe and in Japan, reveals a strong bottleneck in Europe, though a signal of adaptive diversity remains in key host interaction genes. We find that the European population was founded by two divergent haploid individuals. Divergence between these haplotypes represents the ancestral polymorphism within a large source population. Subsequent introduction from this source would greatly increase adaptive potential of the pathogen. Thus, further introgression of H. fraxineus into Europe represents a potential threat and Europe-wide biological security measures are needed to manage this disease.
Published: 2018

34. ReGaTE: Registration of Galaxy Tools in Elixir

Author: Doppelt-Azeroual, Olivia, Mareuil, Fabien, Deveaud, Eric, Kalaš, Matúš, Soranzo, Nicola, van den Beek, Marius, Grüning, Bjorn, Ison, Jon, Ménager, Hervé, Centre de Bioinformatique, Biostatistique et Biologie Intégrative (C3BI), Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Computational Biology Unit [Bergen] (CBU), University of Bergen (UiB), Department of Informatics [Bergen] (UiB), Earlham Institute [Norwich], Institut de Biologie Paris Seine (IBPS), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Center for Biological Systems Analysis - Zentrum für Biosystemanalyse [Freiburg] (ZBSA), Albert-Ludwigs-Universität Freiburg, Department of Computer Science [Freiburg], Center for Biological Sequence Analysis [Lyngby], Technical University of Denmark [Lyngby] (DTU), ELIXIR-EXCELERATE is funded by the European Commission within the Research Infrastructures Programme of Horizon 2020 (676559)., The authors wish to thank the developers of the bio.tools registry, especially Emil Rydza and Piotr Chmura for the technical support they provided during the development of this tool. They also thank Bertrand Néron for the contribution of his technical expertise in Python., European Project: 676559,H2020,H2020-INFRADEV-1-2015-1,ELIXIR-EXCELERATE(2015), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Danmarks Tekniske Universitet = Technical University of Denmark (DTU), Mareuil, Fabien, and ELIXIR-EXCELERATE: Fast-track ELIXIR implementation and drive early user exploitation across the life-sciences. - ELIXIR-EXCELERATE - - H20202015-09-01 - 2019-08-31 - 676559 - VALID
Subjects: Internet, bioinformatics services, bio.tools, Computational Biology, Reproducibility of Results, Workflow, Bioinformatics services, Automation, User-Computer Interface, Galaxy, Computer Systems, Bio.Tools, Technical Note, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], Software, [INFO.INFO-BI] Computer Science [cs]/Bioinformatics [q-bio.QM]
Abstract: Background:Bioinformaticians routinely use multiple software tools and data sources in their day-to-day work, and have been guided in their choices by a number of cataloguing initiatives. The ELIXIR Tools and Data Services Registry ( bio.tools ) aims to provide a central information point, independent of any specific scientific scope within bioinformatics or technological implementation. Meanwhile, efforts to integrate bioinformatics software in workbench and workflow environments have accelerated, to enable the design, automation, and reproducibility of bioinformatics experiments. One such popular environment is the Galaxy framework, with currently more than 80 publicly available Galaxy servers around the world. In the context of a generic registry for bioinformatics software, such as bio.tools , Galaxy instances constitute a major source of valuable content. Yet there has been, to date, no convenient mechanism to register such services en masse . Findings:We present ReGaTE (Registration of Galaxy Tools in Elixir), a software utility that automates the process of registering the services available in a Galaxy instance. This utility uses the BioBlend API to extract service metadata from a Galaxy server, enhance the metadata with the scientific information required by bio.tools, and push it to the registry. Conclusion:ReGaTE provides a fast and convenient way to publish Galaxy services in bio.tools. By doing so, service providers may increase the visibility of their services, whilst enriching the software discovery function that bio.tools provides for its users. The source code of ReGaTE is freely available on Github, at https://github.com/C3BI-pasteur-fr/ReGaTE .
Published: 2017

35. Rapid transcriptional plasticity of duplicated gene clusters enables a clonally reproducing aphid to colonise diverse plant species

Author: Daniel Mapleson, Daniel R. G. Price, Bernardo J. Clavijo, Honglin Feng, Alex C.C. Wilson, Yazhou Chen, Simon Moxon, Georg Jander, Graeme J. Kettles, Sam T. Mugford, Cock van Oosterhout, Sara Lopez-Gomollon, Thomas Derrien, Tamas Dalmay, Paolo Lenzi, Stefano Colella, Manuella van Munster, Krissana Kowitwanich, Damian Loska, Fabrice Legeai, Akiko Sugio, Darren Waite, Saskia A. Hogenhout, Irene Julca, Anna Jordan, Denis Tagu, Toni Gabaldón, Olivier Collin, Gemy Kaithakottil, Patrice Baa-Puyoulet, David Swarbreck, Dominique Lavenier, Marilyne Uzest, Anthony Bretaudeau, Florian Maumus, Thomas C. Mathers, Norwich Research Park, International Aphid Genomics Consortium (IAGC), Plateforme bioinformatique GenOuest [Rennes], Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Plateforme Génomique Santé Biogenouest®-Inria Rennes – Bretagne Atlantique, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT), Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Institut National de la Recherche Agronomique (INRA)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, Biologie Fonctionnelle, Insectes et Interactions (BF2I), Institut National de la Recherche Agronomique (INRA)-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA), Institut de Génétique et Développement de Rennes (IGDR), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Centre National de la Recherche Scientifique (CNRS)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), University of Miami [Coral Gables], Universitat Pompeu Fabra [Barcelona], Institució Catalana de Recerca i Estudis Avançats (ICREA), Centre for Genomic Regulation (CRG), Scalable, Optimized and Parallel Algorithms for Genomics (GenScale), Inria Rennes – Bretagne Atlantique, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-GESTION DES DONNÉES ET DE LA CONNAISSANCE (IRISA-D7), Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Rennes 1 (UR1), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Unité de Recherche Génomique Info (URGI), Institut National de la Recherche Agronomique (INRA), Biologie et Génétique des Interactions Plante-Parasite (UMR BGPI), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Boyce Thompson Institute [Ithaca], University of East Anglia [Norwich] (UEA), Biotechnology and Biological Sciences Research Council (BBSRC), Institute Strategic Program Grant at the Earlham Institute, Norwich [BB/J004669/1, CCC-15], BBSRC - Industrial Partnership Award (IPA), Syngenta Ltd [BB/L002108/1], BBSRC - Institute Strategic Program Grant (ISPG) Biotic Interactions for Crop Productivity (BIO) [BB/J004553/1], United States Department of Agriculture (USDA) National Institute for Food and Agriculture (NIFA) [2010-65105-20558], Université de Rennes (UR)-Plateforme Génomique Santé Biogenouest®-Inria Rennes – Bretagne Atlantique, Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Institut National de la Recherche Agronomique (INRA)-Université de Rennes (UR)-AGROCAMPUS OUEST, Université de Rennes (UR)-Centre National de la Recherche Scientifique (CNRS)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), Universitat Pompeu Fabra [Barcelona] (UPF), Université de Bretagne Sud (UBS)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National de Recherche en Informatique et en Automatique (Inria)-École normale supérieure - Rennes (ENS Rennes)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-CentraleSupélec-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Bretagne Sud (UBS)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-École normale supérieure - Rennes (ENS Rennes)-Centre National de la Recherche Scientifique (CNRS)-CentraleSupélec-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université de Lyon, Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-École normale supérieure - Rennes (ENS Rennes)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Plateforme Génomique Santé Biogenouest®-GESTION DES DONNÉES ET DE LA CONNAISSANCE (IRISA-D7), AGROCAMPUS OUEST-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National de la Recherche Agronomique (INRA), and Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)
Subjects: 0106 biological sciences, 0301 basic medicine, sap-feeding insects, Gene duplication, Plasticity, Lineage (evolution), [SDV]Life Sciences [q-bio], hemiptera, genome sequence, Myzus persicae, Rna interference (rnai), Biology, 010603 evolutionary biology, 01 natural sciences, Genome, Hemiptera, 03 medical and health sciences, Gene family, Gene, ComputingMilieux_MISCELLANEOUS, amélioration génétique, 2. Zero hunger, Genetics, Aphid, Phenotypic plasticity, myzus persicae, [SDV.GEN]Life Sciences [q-bio]/Genetics, Host (biology), Research, génome, rna interference (rnai), Microbiology and Parasitology, gene duplication, food and beverages, biology.organism_classification, Microbiologie et Parasitologie, Parasite, 030104 developmental biology, plasticity, Sap-feeding insects, parasite, Genome sequence, transcriptome, RNA interference (RNAi), Erratum, Transcriptome
Abstract: Background The prevailing paradigm of host-parasite evolution is that arms races lead to increasing specialisation via genetic adaptation. Insect herbivores are no exception and the majority have evolved to colonise a small number of closely related host species. Remarkably, the green peach aphid, Myzus persicae, colonises plant species across 40 families and single M. persicae clonal lineages can colonise distantly related plants. This remarkable ability makes M. persicae a highly destructive pest of many important crop species. Results To investigate the exceptional phenotypic plasticity of M. persicae, we sequenced the M. persicae genome and assessed how one clonal lineage responds to host plant species of different families. We show that genetically identical individuals are able to colonise distantly related host species through the differential regulation of genes belonging to aphid-expanded gene families. Multigene clusters collectively upregulate in single aphids within two days upon host switch. Furthermore, we demonstrate the functional significance of this rapid transcriptional change using RNA interference (RNAi)-mediated knock-down of genes belonging to the cathepsin B gene family. Knock-down of cathepsin B genes reduced aphid fitness, but only on the host that induced upregulation of these genes. Conclusions Previous research has focused on the role of genetic adaptation of parasites to their hosts. Here we show that the generalist aphid pest M. persicae is able to colonise diverse host plant species in the absence of genetic specialisation. This is achieved through rapid transcriptional plasticity of genes that have duplicated during aphid evolution. Electronic supplementary material The online version of this article (doi:10.1186/s13059-016-1145-3) contains supplementary material, which is available to authorized users.
Published: 2017

36. Erratum to: Rapid transcriptional plasticity of duplicated gene clusters enables a clonally reproducing aphid to colonise diverse plant species

Author: Fabrice Legeai, Darren Waite, Daniel R. G. Price, Bernardo J. Clavijo, Saskia A. Hogenhout, Sara Lopez-Gomollon, David Swarbreck, Damian Loska, Sam T. Mugford, Simon Moxon, Yazhou Chen, Irene Julca, Thomas Derrien, Krissana Kowitwanich, Thomas C. Mathers, Honglin Feng, Paolo Lenzi, Cock van Oosterhout, Daniel Mapleson, Denis Tagu, Patrice Baa-Puyoulet, Florian Maumus, Anna Jordan, Dominique Lavenier, Marilyne Uzest, Manuella van Munster, Stefano Colella, Anthony Bretaudeau, Akiko Sugio, Alex C.C. Wilson, Georg Jander, Gemy Kaithakottil, Graeme J. Kettles, Toni Gabaldón, Tamas Dalmay, Olivier Collin, International Aphid Genomics Consortium (IAGC), Earlham Institute [Norwich], Institut de Génétique, Environnement et Protection des Plantes (IGEPP), AGROCAMPUS OUEST-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National de la Recherche Agronomique (INRA), Biologie Fonctionnelle, Insectes et Interactions (BF2I), Institut National de la Recherche Agronomique (INRA)-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA), Plateforme bioinformatique GenOuest [Rennes], Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Plateforme Génomique Santé Biogenouest®-Inria Rennes – Bretagne Atlantique, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT), Institut de Génétique et Développement de Rennes (IGDR), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Centre National de la Recherche Scientifique (CNRS)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), University of Miami [Coral Gables], Universitat Pompeu Fabra [Barcelona], Institució Catalana de Recerca i Estudis Avançats (ICREA), Centre for Genomic Regulation [Barcelona] (CRG), Universitat Pompeu Fabra [Barcelona]-Centro Nacional de Analisis Genomico [Barcelona] (CNAG), Unité de Recherche Génomique Info (URGI), Institut National de la Recherche Agronomique (INRA), Biologie et Génétique des Interactions Plante-Parasite (UMR BGPI), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA), Boyce Thompson Institute [Ithaca], University of East Anglia [Norwich] (UEA), Institut National de la Recherche Agronomique (INRA)-Université de Rennes (UR)-AGROCAMPUS OUEST, Université de Rennes (UR)-Plateforme Génomique Santé Biogenouest®-Inria Rennes – Bretagne Atlantique, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-GESTION DES DONNÉES ET DE LA CONNAISSANCE (IRISA-D7), Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Université de Rennes (UR)-Centre National de la Recherche Scientifique (CNRS)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), Universitat Pompeu Fabra [Barcelona] (UPF), Universitat Pompeu Fabra [Barcelona] (UPF)-Centro Nacional de Analisis Genomico [Barcelona] (CNAG), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut National de la Recherche Agronomique (INRA)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université de Lyon, Université de Bretagne Sud (UBS)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National de Recherche en Informatique et en Automatique (Inria)-École normale supérieure - Rennes (ENS Rennes)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-CentraleSupélec-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Bretagne Sud (UBS)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-École normale supérieure - Rennes (ENS Rennes)-Centre National de la Recherche Scientifique (CNRS)-CentraleSupélec-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro), Inria Rennes – Bretagne Atlantique, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Rennes 1 (UR1), and Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Plateforme Génomique Santé Biogenouest®-GESTION DES DONNÉES ET DE LA CONNAISSANCE (IRISA-D7)
Subjects: 0301 basic medicine, Genetics, amélioration génétique, Aphid, [SDV.GEN]Life Sciences [q-bio]/Genetics, lcsh:QH426-470, génome, Microbiology and Parasitology, 15. Life on land, Biology, biology.organism_classification, Genome, Microbiologie et Parasitologie, lcsh:Genetics, 03 medical and health sciences, 030104 developmental biology, lcsh:Biology (General), Plant species, lcsh:QH301-705.5, Gene, ComputingMilieux_MISCELLANEOUS
Abstract: After publication of this article [1] we noticed that reference 50 was incorrect. The correct reference 50 is as follows: Santamaría S, Gonzalez-Cabrera J, Martinez M, Grbic V, Castanera P, Diaz L, Ortego F. Digestive proteases in bodies and faeces of the two-spotted spider mite, Tetranychus urticae. J Insect Physiol. 2015; 78:69–77 http://www.sciencedirect.com/science/article/pii/S0022191015001018
Published: 2017

37. Developing data interoperability using standards : a wheat community use case

Author: Sophie Aubin, Hanna Ćwiek-Kupczyńska, Alex Whan, Michael Alaux, Aravind Venkatesan, Patrice Buche, Laurel Cooper, Clement Jonquet, Marie-Angélique Laporte, Elizabeth Arnaud, Rosemary Shrestha, Richard Fulss, Pierre Larmande, Vassilis Protonotarios, Robert P. Davey, Cyril Pommier, Imma Subirats, Ute Baumann, Esther Dzale Yeumo, Hadi Quesneville, Carmen Reverte, Institut National de la Recherche Agronomique (INRA), Unité de Recherche Génomique Info (URGI), Bioversity International [Montpellier], Bioversity International [Rome], Consultative Group on International Agricultural Research [CGIAR] (CGIAR)-Consultative Group on International Agricultural Research [CGIAR] (CGIAR), School of Agriculture, Food and Wine, University of Adelaide, Ingénierie des Agro-polymères et Technologies Émergentes (UMR IATE), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Université Montpellier 2 - Sciences et Techniques (UM2)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Graphs for Inferences on Knowledge (GRAPHIK), Laboratoire d'Informatique de Robotique et de Microélectronique de Montpellier (LIRMM), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Inria Sophia Antipolis - Méditerranée (CRISAM), Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria), Department of Botany and Plant Pathology, Oregon State University (OSU), Earlham Institute [Norwich], International Maize and Wheat Improvement Center (CIMMYT), Consultative Group on International Agricultural Research [CGIAR] (CGIAR), Stanford Center for BioMedical Informatics Research (BMIR), Stanford University, Système Multi-agent, Interaction, Langage, Evolution (SMILE), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Neuropublic S.a., Institut de Recerca i Tecnologia Agroalimentàries = Institute of Agrifood Research and Technology (IRTA), Food and Agriculture Organization of the United Nations [Rome, Italie] (FAO), Institut de Biologie Computationnelle (IBC), Institut National de la Recherche Agronomique (INRA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Commonwealth Scientific and Industrial Research Organisation [Canberra] (CSIRO), ANR-12-JS02-0010,SIFR,Indexation sémantique de ressources biomédicales francophones(2012), European Project: 701771,H2020,H2020-MSCA-IF-2015,SIFRm(2016), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université Montpellier 2 - Sciences et Techniques (UM2)-Université de Montpellier (UM)-Institut National de la Recherche Agronomique (INRA), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Inria Sophia Antipolis - Méditerranée (CRISAM), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Institute of Agrifood Research and Technology (IRTA), Université de Montpellier (UM)-Institut National de la Recherche Agronomique (INRA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS), Bioversity International, Consultative Group on International Agricultural Research [CGIAR], Department of Biometry and Bioinformatics, Institute of Plant Genetics (IPG), Polish Academy of Sciences (PAN)-Polish Academy of Sciences (PAN), Stanford University [Stanford], Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro), Food and Agricultural Organization of the United Nations (FAO), United Nations Organization, and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)
Subjects: 0106 biological sciences, 0301 basic medicine, Data Sharing, Best practice, Data management, Interoperability, Agriculture & Biotechnology, Knowledge organization system, Ontology (information science), 01 natural sciences, General Biochemistry, Genetics and Molecular Biology, [INFO.INFO-AI]Computer Science [cs]/Artificial Intelligence [cs.AI], Data interoperability, Data standards, Wheat, Bio-ontologies, Ontology repository, 03 medical and health sciences, General Pharmacology, Toxicology and Pharmaceutics, 2. Zero hunger, Metadata, General Immunology and Microbiology, business.industry, [INFO.INFO-WB]Computer Science [cs]/Web, Articles, General Medicine, Opinion Article, Data formats, 15. Life on land, Data science, Data sharing, Open data, 030104 developmental biology, Standard vocabularies, business, 010606 plant biology & botany
Abstract: In this article, we present a joint effort of the wheat research community, along with data and ontology experts, to develop wheat data interoperability guidelines. Interoperability is the ability of two or more systems and devices to cooperate and exchange data, and interpret that shared information. Interoperability is a growing concern to the wheat scientific community, and agriculture in general, as the need to interpret the deluge of data obtained through high-throughput technologies grows. Agreeing on common data formats, metadata, and vocabulary standards is an important step to obtain the required data interoperability level in order to add value by encouraging data sharing, and subsequently facilitate the extraction of new information from existing and new datasets. During a period of more than 18 months, the RDA Wheat Data Interoperability Working Group (WDI-WG) surveyed the wheat research community about the use of data standards, then discussed and selected a set of recommendations based on consensual criteria. The recommendations promote standards for data types identified by the wheat research community as the most important for the coming years: nucleotide sequence variants, genome annotations, phenotypes, germplasm data, gene expression experiments, and physical maps. For each of these data types, the guidelines recommend best practices in terms of use of data formats, metadata standards and ontologies. In addition to the best practices, the guidelines provide examples of tools and implementations that are likely to facilitate the adoption of the recommendations. To maximize the adoption of the recommendations, the WDI-WG used a community-driven approach that involved the wheat research community from the start, took into account their needs and practices, and provided them with a framework to keep the recommendations up to date. We also report this approach’s potential to be generalizable to other (agricultural) domains.
Published: 2017

38. Community-Driven Data Analysis Training for Biology

Author: Dannon Baker, Aisanjiang Wubuli, Anthony Bretaudeau, Saskia Hiltemann, John Chilton, Bérénice Batut, Vivek Bhardwaj, Thomas Manke, Loraine Brillet-Guéguen, Mallory A. Freeberg, Olivia Doppelt-Azeroual, Fabien Mareuil, Gildas Le Corguillé, Nicola Soranzo, Fidel Ramírez, Joachim Wolff, Clemens Blank, Rolf Backofen, Anton Nekrutenko, Pavankumar Videm, Youri Hoogstrate, Dave Clements, Dilmurat Yusuf, Delphine Larivière, Markus Wolfien, Anika Erxleben, Simon Gladman, Devon Ryan, James Taylor, Florian Christoph Sigloch, Björn Grüning, Hans-Rudolf Hotz, Torsten Houwaart, Pratik D. Jagtap, Martin Čech, Andrea Bagnacani, Bioinformatics Group [Freiburg], Department of Computer Science [Freiburg], Albert-Ludwigs-Universität Freiburg-Albert-Ludwigs-Universität Freiburg, Erasmus University Medical Center [Rotterdam] (Erasmus MC), Department of Systems Biology and Bioinformatics, University of Rostock, Johns Hopkins University (JHU), Department of Biology [Fribourg], University of Freiburg [Freiburg], Plateforme bioinformatique GenOuest [Rennes], Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Plateforme Génomique Santé Biogenouest®-Inria Rennes – Bretagne Atlantique, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-GESTION DES DONNÉES ET DE LA CONNAISSANCE (IRISA-D7), Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Université de Bretagne Sud (UBS)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National de Recherche en Informatique et en Automatique (Inria)-École normale supérieure - Rennes (ENS Rennes)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-CentraleSupélec-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Bretagne Sud (UBS)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-École normale supérieure - Rennes (ENS Rennes)-Centre National de la Recherche Scientifique (CNRS)-CentraleSupélec-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT), Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Institut National de la Recherche Agronomique (INRA)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), ABiMS - Informatique et bioinformatique = Analysis and Bioinformatics for Marine Science (FR2424), Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Pennsylvania State University (Penn State), Penn State System, Hub Bioinformatique et Biostatistique - Bioinformatics and Biostatistics HUB, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), European Bioinformatics Institute [Hinxton] (EMBL-EBI), EMBL Heidelberg, Melbourne Bioinformatics [Australia], University of Melbourne, Friedrich Miescher Institute for Biomedical Research (FMI), Novartis Research Foundation, University of Minnesota Medical School, University of Minnesota System, Max Planck Institute of Immunobiology and Epigenetics (MPI-IE), Max-Planck-Gesellschaft, Earlham Institute [Norwich], Leibniz Institute for Farm Animal Biology (FBN), This project was supported by Collaborative Research Centre 992 Medical Epigenetics (DFG grant SFB 992/1 2012), German Federal Ministry of Education and Research (BMBF grant 031 A538A RBC [de.NBI]), NIH grants U41 HG006620 and R01 AI134384-01, as well as NSF grant 1661497., The authors are grateful to the Freiburg Galaxy and Core Galaxy teams as, without these resources, this work would not be possible. Adoption of Galaxy Tours has been accelerated with the introduction of Galaxy Tour Builder (https://zenodo.org/record/830481) by William Durand (https://tailordev.fr)., Galaxy Training Network, Pathology, Urology, Université de Rennes (UR)-Plateforme Génomique Santé Biogenouest®-Inria Rennes – Bretagne Atlantique, Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Université de Rennes (UR)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-INSTITUT AGRO Agrocampus Ouest, ABiMS - Informatique et bioinformatique = Analysis and Bioinformatics for Marine Science (ABIMS), Fédération de recherche de Roscoff (FR2424), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), and Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0301 basic medicine, Histology, data analysis, Space (commercial competition), Training (civil), Article, Pathology and Forensic Medicine, Education, Distance, 03 medical and health sciences, proteomics, 0302 clinical medicine, Software, ComputingMilieux_COMPUTERSANDEDUCATION, genomics, Feature (machine learning), Humans, Curriculum, Web browser, training, business.industry, 4. Education, Computational Biology, Cell Biology, Data science, Research Personnel, 030104 developmental biology, Key (cryptography), Data analysis, next-generation sequencing, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], business, 030217 neurology & neurosurgery
Abstract: La version finale de l'article a été déposée sur PMC. The final version of this article has been deposed on PMC; The primary problem with the explosion of biomedical datasets is not the data, not computational resources, and not the required storage space, but the general lack of trained and skilled researchers to manipulate and analyze these data. Eliminating this problem requires development of comprehensive educational resources. Here we present a community-driven framework that enables modern, interactive teaching of data analytics in life sciences and facilitates the development of training materials. The key feature of our system is that it is not a static but a continuously improved collection of tutorials. By coupling tutorials with a web-based analysis framework, biomedical researchers can learn by performing computation themselves through a web browser without the need to install software or search for example datasets. Our ultimate goal is to expand the breadth of training materials to include fundamental statistical and data science topics and to precipitate a complete re-engineering of undergraduate and graduate curricula in life sciences. This project is accessible at https://training.galaxyproject.org.
Published: 2018

39. Charge-density analysis using multipolar atom and spherical charge models: 2-methyl-1,3-cyclopentanedione, a compound displaying a resonance-assisted hydrogen bond

Author: Grzegorz Dutkiewicz, Christian Jelsch, Jonathan P. Wright, Ayoub Nassour, Teresa Borowiak, Maciej Kubicki, Claude Lecomte, Cristallographie, Résonance Magnétique et Modélisations (CRM2), Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS), Faculty of Chemistry, Adam Mickiewicz University in Poznań (UAM), Earlham Institute [Norwich], European Synchrotron Radiation Facility (ESRF), and Centre National de la Recherche Scientifique (CNRS)-Université de Lorraine (UL)
Subjects: Electron density, Chemistry, Hydrogen bond, Intermolecular force, Metals and Alloys, Charge density, 02 engineering and technology, Resonance-assisted hydrogen bond, 010402 general chemistry, 021001 nanoscience & nanotechnology, Resonance (chemistry), 01 natural sciences, Atomic and Molecular Physics, and Optics, 0104 chemical sciences, Electronic, Optical and Magnetic Materials, Atom, Materials Chemistry, [CHIM.CRIS]Chemical Sciences/Cristallography, [CHIM]Chemical Sciences, Atomic physics, 0210 nano-technology, Lone pair
Abstract: International audience; The experimental charge-density distribution in 2-methyl-1,3-cyclopentanedione in the crystal state was analyzed by synchrotron X-ray diffraction data collection at 0.33 angstrom resolution. The molecule in the crystal is in the enol form. The experimental electron density was refined using the Hansen-Coppens multipolar model and an alternative modeling, based on spherical atoms and additional charges on the covalent bonds and electron lone-pair sites. The crystallographic refinements, charge-density distributions, molecular electrostatic potentials, dipole moments and intermolecular interaction energies obtained from the different charge-density models were compared. The experimental results are also compared with the theoretical charge densities using theoretical structure factors obtained from periodic quantum calculations at the B3LYP/6-31G** level. A strong intermolecular O-H center dot center dot center dot O hydrogen bond connects molecules along the [001] direction. The deformation density maps show the resonance within the O=C-C=C-OH fragment and merged lone pair lobes on the hydroxyl O atom. This resonance is further confirmed by the analysis of charges and topology of the electron density.
Published: 2014

40. Dispersal strategies shape persistence and evolution of human gut bacteria

Author: Clémence Frioux, Toni I. Gossmann, Pernille Neve Myers, Ezgi Özkurt, Peer Bork, Michael Kuhn, Pamela Ferretti, Henrik Nielsen, Falk Hildebrand, Mohammad Bahram, Quadram Institute, Biotechnology and Biological Sciences Research Council (BBSRC), Earlham Institute [Norwich], Universität Bielefeld = Bielefeld University, from patterns to models in computational biodiversity and biotechnology (PLEIADE), Laboratoire Bordelais de Recherche en Informatique (LaBRI), Université de Bordeaux (UB)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Centre National de la Recherche Scientifique (CNRS)-Université de Bordeaux (UB)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Centre National de la Recherche Scientifique (CNRS)-Inria Bordeaux - Sud-Ouest, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Biodiversité, Gènes & Communautés (BioGeCo), Université de Bordeaux (UB)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Clinical-Microbiomics, European Molecular Biology Laboratory (EMBL), Swedish University of Agricultural Sciences (SLU), and Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Inria Bordeaux - Sud-Ouest
Subjects: Adult, Male, Firmicutes, gut microbiome, Zoology, Population genetics, Gut flora, Microbiology, antibiotics, Feces, Young Adult, strain resolution, 03 medical and health sciences, Short Article, 0302 clinical medicine, Virology, Humans, Phylogeny, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, metagenomics, 0303 health sciences, Bacteria, biology, Phylum, Host (biology), Microbiota, bacterial dispersal, Infant, population genetics, Middle Aged, biology.organism_classification, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Anti-Bacterial Agents, Gastrointestinal Microbiome, Microbiology (Microbiology in the medical area to be 30109), Metagenomics, Cardiovascular and Metabolic Diseases, Child, Preschool, Metagenome, Biological dispersal, Female, Parasitology, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], 030217 neurology & neurosurgery
Abstract: Summary Human gut bacterial strains can co-exist with their hosts for decades, but little is known about how these microbes persist and disperse, and evolve thereby. Here, we examined these processes in 5,278 adult and infant fecal metagenomes, longitudinally sampled in individuals and families. Our analyses revealed that a subset of gut species is extremely persistent in individuals, families, and geographic regions, represented often by locally successful strains of the phylum Bacteroidota. These “tenacious” bacteria show high levels of genetic adaptation to the human host but a high probability of loss upon antibiotic interventions. By contrast, heredipersistent bacteria, notably Firmicutes, often rely on dispersal strategies with weak phylogeographic patterns but strong family transmissions, likely related to sporulation. These analyses describe how different dispersal strategies can lead to the long-term persistence of human gut microbes with implications for gut flora modulations., Graphical abstract, Highlights • Bacterial strains may persist within family members through transfer • Bacteria adapt dispersal strategies: heredipersistent, spatiopersistent, and tenacious • Dispersal strategies correlate with genetic bottlenecks and effective population size, Hildebrand et al., investigated strategies of bacterial persistence using publicly available time series metagenomes from stool samples. They found that three major dispersal strategies underlie human gut bacterial persistence. These have distinct evolutionary patterns such as the accumulation of rare variation and differences in their strength of selection.
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41. From synthetic communities to synthetic ecosystems: exploring causalities in plant-microbe-environment interactions.

Author: Chesneau G, Herpell J, Garrido-Oter R, and Hacquard S
Abstract: The plant microbiota research field has rapidly shifted from efforts aimed at gaining a descriptive understanding of microbiota composition to a focus on acquiring mechanistic insights into microbiota functions and assembly rules. This evolution was driven by our ability to establish comprehensive collections of plant-associated microbes and to reconstruct meaningful microbial synthetic communities (SynComs). We argue that this powerful deconstruction-reconstruction strategy can be used to reconstitute increasingly complex synthetic ecosystems (SynEcos) and mechanistically understand high-level biological organization. The transitioning from simple to more advanced, fully tractable and programmable gnotobiotic SynEcos is ongoing and aims at rationally simplifying natural ecosystems by engineering them. Such reconstitution ecology approaches represent an untapped strategy for bridging the gap between ecology and functional biology and for unraveling plant-microbiota-environment mechanisms that modulate ecosystem health, assembly, and functioning., (© 2024 The Author(s). New Phytologist © 2024 New Phytologist Foundation.)
Published: 2024
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42. CTLA-4 expressing innate lymphoid cells modulate mucosal homeostasis in a microbiota dependent manner.

Author: Lo JW, Schroeder JH, Roberts LB, Mohamed R, Cozzetto D, Beattie G, Omer OS, Ross EM, Heuts F, Jowett GM, Read E, Madgwick M, Neves JF, Korcsmaros T, Jenner RG, Walker LSK, Powell N, and Lord GM
Subjects: Animals, Humans, Mice, Mice, Inbred C57BL, Female, Inflammatory Bowel Diseases immunology, Inflammatory Bowel Diseases microbiology, Mice, Knockout, Male, Cytokines metabolism, Disease Models, Animal, Immunity, Mucosal, CTLA-4 Antigen metabolism, CTLA-4 Antigen immunology, Immunity, Innate, Homeostasis, Intestinal Mucosa immunology, Intestinal Mucosa microbiology, Intestinal Mucosa metabolism, Gastrointestinal Microbiome immunology, Lymphocytes immunology, Lymphocytes metabolism, Colitis immunology, Colitis microbiology
Abstract: The maintenance of intestinal homeostasis is a fundamental process critical for organismal integrity. Sitting at the interface of the gut microbiome and mucosal immunity, adaptive and innate lymphoid populations regulate the balance between commensal micro-organisms and pathogens. Checkpoint inhibitors, particularly those targeting the CTLA-4 pathway, disrupt this fine balance and can lead to inflammatory bowel disease and immune checkpoint colitis. Here, we show that CTLA-4 is expressed by innate lymphoid cells and that its expression is regulated by ILC subset-specific cytokine cues in a microbiota-dependent manner. Genetic deletion or antibody blockade of CTLA-4 in multiple in vivo models of colitis demonstrates that this pathway plays a key role in intestinal homeostasis. Lastly, we have found that this observation is conserved in human IBD. We propose that this population of CTLA-4-positive ILC may serve as an important target for the treatment of idiopathic and iatrogenic intestinal inflammation., (© 2024. The Author(s).)
Published: 2024
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43. Community standards and future opportunities for synthetic communities in plant-microbiota research.

Author: Northen TR, Kleiner M, Torres M, Kovács ÁT, Nicolaisen MH, Krzyżanowska DM, Sharma S, Lund G, Jelsbak L, Baars O, Kindtler NL, Wippel K, Dinesen C, Ferrarezi JA, Marian M, Pioppi A, Xu X, Andersen T, Geldner N, Schulze-Lefert P, Vorholt JA, and Garrido-Oter R
Subjects: Agriculture, Bacteria genetics, Bacteria classification, Synthetic Biology methods, Plants microbiology, Microbiota
Abstract: Harnessing beneficial microorganisms is seen as a promising approach to enhance sustainable agriculture production. Synthetic communities (SynComs) are increasingly being used to study relevant microbial activities and interactions with the plant host. Yet, the lack of community standards limits the efficiency and progress in this important area of research. To address this gap, we recommend three actions: (1) defining reference SynComs; (2) establishing community standards, protocols and benchmark data for constructing and using SynComs; and (3) creating an infrastructure for sharing strains and data. We also outline opportunities to develop SynCom research through technical advances, linking to field studies, and filling taxonomic blind spots to move towards fully representative SynComs., (© 2024. Springer Nature Limited.)
Published: 2024
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44. Building pangenome graphs.

Author: Garrison E, Guarracino A, Heumos S, Villani F, Bao Z, Tattini L, Hagmann J, Vorbrugg S, Marco-Sola S, Kubica C, Ashbrook DG, Thorell K, Rusholme-Pilcher RL, Liti G, Rudbeck E, Golicz AA, Nahnsen S, Yang Z, Mwaniki MN, Nobrega FL, Wu Y, Chen H, de Ligt J, Sudmant PH, Huang S, Weigel D, Soranzo N, Colonna V, Williams RW, and Prins P
Subjects: Genomics methods, Genome genetics, Humans, Algorithms, Computational Biology methods, Phylogeny, Software
Abstract: Pangenome graphs can represent all variation between multiple reference genomes, but current approaches to build them exclude complex sequences or are based upon a single reference. In response, we developed the PanGenome Graph Builder, a pipeline for constructing pangenome graphs without bias or exclusion. The PanGenome Graph Builder uses all-to-all alignments to build a variation graph in which we can identify variation, measure conservation, detect recombination events and infer phylogenetic relationships., (© 2024. The Author(s), under exclusive licence to Springer Nature America, Inc.)
Published: 2024
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45. A history-dependent integrase recorder of plant gene expression with single-cell resolution.

Author: Maranas CJ, George W, Scallon SK, VanGilder S, Nemhauser JL, and Guiziou S
Subjects: Plant Roots genetics, Plant Roots metabolism, Plant Roots growth & development, Single-Cell Analysis methods, Plants, Genetically Modified, Arabidopsis Proteins genetics, Arabidopsis Proteins metabolism, Promoter Regions, Genetic genetics, Cell Differentiation genetics, Genes, Reporter, Arabidopsis genetics, Gene Expression Regulation, Plant, Integrases metabolism, Integrases genetics, Plant Stomata genetics, Plant Stomata metabolism
Abstract: During development, most cells experience a progressive restriction of fate that ultimately results in a fully differentiated mature state. Understanding more about the gene expression patterns that underlie developmental programs can inform engineering efforts for new or optimized forms. Here, we present a four-state integrase-based recorder of gene expression history and demonstrate its use in tracking gene expression events in Arabidopsis thaliana in two developmental contexts: lateral root initiation and stomatal differentiation. The recorder uses two serine integrases to mediate sequential DNA recombination events, resulting in step-wise, history-dependent switching between expression of fluorescent reporters. By using promoters that express at different times along each of the two differentiation pathways to drive integrase expression, we tie fluorescent status to an ordered progression of gene expression along the developmental trajectory. In one snapshot of a mature tissue, our recorder is able to reveal past gene expression with single cell resolution. In this way, we are able to capture heterogeneity in stomatal development, confirming the existence of two alternate paths of differentiation., (© 2024. The Author(s).)
Published: 2024
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46. mulea: An R package for enrichment analysis using multiple ontologies and empirical false discovery rate.

Author: Turek C, Ölbei M, Stirling T, Fekete G, Tasnádi E, Gul L, Bohár B, Papp B, Jurkowski W, and Ari E
Subjects: Databases, Genetic, Computational Biology methods, Software, Gene Ontology
Abstract: Traditional gene set enrichment analyses are typically limited to a few ontologies and do not account for the interdependence of gene sets or terms, resulting in overcorrected p-values. To address these challenges, we introduce mulea, an R package offering comprehensive overrepresentation and functional enrichment analysis. mulea employs a progressive empirical false discovery rate (eFDR) method, specifically designed for interconnected biological data, to accurately identify significant terms within diverse ontologies. mulea expands beyond traditional tools by incorporating a wide range of ontologies, encompassing Gene Ontology, pathways, regulatory elements, genomic locations, and protein domains. This flexibility enables researchers to tailor enrichment analysis to their specific questions, such as identifying enriched transcriptional regulators in gene expression data or overrepresented protein domains in protein sets. To facilitate seamless analysis, mulea provides gene sets (in standardised GMT format) for 27 model organisms, covering 22 ontology types from 16 databases and various identifiers resulting in almost 900 files. Additionally, the muleaData ExperimentData Bioconductor package simplifies access to these pre-defined ontologies. Finally, mulea's architecture allows for easy integration of user-defined ontologies, or GMT files from external sources (e.g., MSigDB or Enrichr), expanding its applicability across diverse research areas. mulea is distributed as a CRAN R package downloadable from https://cran.r-project.org/web/packages/mulea/ and https://github.com/ELTEbioinformatics/mulea . It offers researchers a powerful and flexible toolkit for functional enrichment analysis, addressing limitations of traditional tools with its progressive eFDR and by supporting a variety of ontologies. Overall, mulea fosters the exploration of diverse biological questions across various model organisms., (© 2024. The Author(s).)
Published: 2024
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47. Author Correction: The European Reference Genome Atlas: piloting a decentralised approach to equitable biodiversity genomics.

Author: Mc Cartney AM, Formenti G, Mouton A, De Panis D, Marins LS, Leitão HG, Diedericks G, Kirangwa J, Morselli M, Salces-Ortiz J, Escudero N, Iannucci A, Natali C, Svardal H, Fernández R, De Pooter T, Joris G, Strazisar M, Wood JMD, Herron KE, Seehausen O, Watts PC, Shaw F, Davey RP, Minotto A, Fernández JM, Böhne A, Alegria C, Alioto T, Alves PC, Amorim IR, Aury JM, Backstrom N, Baldrian P, Baltrunaite L, Barta E, BedHom B, Belser C, Bergsten J, Bertrand L, Bilandija H, Binzer-Panchal M, Bista I, Blaxter M, Borges PAV, Dias GB, Bosse M, Brown T, Bruggmann R, Buena-Atienza E, Burgin J, Buzan E, Cariani A, Casadei N, Chiara M, Chozas S, Čiampor F Jr, Crottini A, Cruaud C, Cruz F, Dalen L, De Biase A, Del Campo J, Delic T, Dennis AB, Derks MFL, Diroma MA, Djan M, Duprat S, Eleftheriadi K, Feulner PGD, Flot JF, Forni G, Fosso B, Fournier P, Fournier-Chambrillon C, Gabaldon T, Garg S, Gissi C, Giupponi L, Gomez-Garrido J, González J, Grilo ML, Grüning B, Guerin T, Guiglielmoni N, Gut M, Haesler MP, Hahn C, Halpern B, Harrison PW, Heintz J, Hindrikson M, Höglund J, Howe K, Hughes GM, Istace B, Cock MJ, Janžekovič F, Jonsson ZO, Joye-Dind S, Koskimäki JJ, Krystufek B, Kubacka J, Kuhl H, Kusza S, Labadie K, Lähteenaro M, Lantz H, Lavrinienko A, Leclère L, Lopes RJ, Madsen O, Magdelenat G, Magoga G, Manousaki T, Mappes T, Marques JP, Redondo GIM, Maumus F, McCarthy SA, Megens HJ, Melo-Ferreira J, Mendes SL, Montagna M, Moreno J, Mosbech MB, Moura M, Musilova Z, Myers E, Nash WJ, Nater A, Nicholson P, Niell M, Nijland R, Noel B, Noren K, Oliveira PH, Olsen RA, Ometto L, Oomen RA, Ossowski S, Palinauskas V, Palsson S, Panibe JP, Pauperio J, Pavlek M, Payen E, Pawlowska J, Pellicer J, Pesole G, Pimenta J, Pippel M, Pirttilä AM, Poulakakis N, Rajan J, M C Rego R, Resendes R, Resl P, Riesgo A, Rodin-Morch P, Soares AER, Fernandes CR, Romeiras MM, Roxo G, Rüber L, Ruiz-Lopez MJ, Saarma U, da Silva LP, Sim-Sim M, Soler L, Sousa VC, Santos CS, Spada A, Stefanovic M, Steger V, Stiller J, Stöck M, Struck TH, Sudasinghe H, Tapanainen R, Tellgren-Roth C, Trindade H, Tukalenko Y, Urso I, Vacherie B, Van Belleghem SM, Van Oers K, Vargas-Chavez C, Velickovic N, Vella N, Vella A, Vernesi C, Vicente S, Villa S, Pettersson OV, Volckaert FAM, Voros J, Wincker P, Winkler S, Ciofi C, Waterhouse RM, and Mazzoni CJ
Published: 2024
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48. Socially plastic responses in females are robust to evolutionary manipulations of adult sex ratio and adult nutrition.

Author: McConnell N, Haerty W, Gage MJG, and Chapman T
Subjects: Animals, Female, Male, Fertility, Sexual Behavior, Animal physiology, Animal Nutritional Physiological Phenomena, Social Behavior, Sex Ratio, Biological Evolution, Drosophila melanogaster physiology
Abstract: Socially plastic behaviours are widespread among animals and can have a significant impact on fitness. Here, we investigated whether the socially plastic responses of female Drosophila melanogaster can evolve in predictable ways following long-term manipulation of adult sex ratio and adult nutrient availability. Previous reports show that female D. melanogaster respond plastically to their same-sex social environment and lay significantly fewer eggs after mating when previously exposed to other females. In this study, we tested 2 hypotheses, using females drawn from lines with an evolutionary history of exposure to variation in adult sex ratio (male-biased, female-biased or equal sex ratio) and adult nutritional environment (high or low quality). The first was that a history of elevated competition in female-biased regimes would select for increased plastic fecundity responses in comparison to females from other lines. The second was that these responses would also be magnified under poor nutritional resource regimes. Neither hypothesis was supported. Instead, we found that plastic fecundity responses were retained in females from all lines and did not differ significantly across any of them. The lack of differences does not appear to be due to insufficient selection, as we did observe significant evolutionary responses in virgin egg-laying patterns according to sex ratio and nutritional regime. The lack of variation in the magnitude of predicted plasticity is consistent with the idea that the costs of maintaining plasticity are low, benefits high, and that plasticity itself can be relatively hard wired., (© The Author(s) 2024. Published by Oxford University Press on behalf of the European Society of Evolutionary Biology.)
Published: 2024
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49. Single-cell RNA sequencing offers opportunities to explore the depth of physiology, adaptation, and biochemistry in non-model organisms exposed to pollution.

Author: Collí-Dulá RC and Papatheodorou I
Abstract: Single-cell Sequencing technology (scSeq) has revolutionized our understanding of individual cells, uncovering unprecedented heterogeneity within tissues and cell populations, principality through single-cell RNA Sequencing (scRNA-Seq). This short review highlights the pivotal role of scRNA-Seq in elucidating genotype-phenotype relationships, particularly in biological systems. Based on published articles, our analysis involved manual curation and automated Scopus tools to illustrate recent advances in the application of scRNA-Seq. The results reveal that scRNA-Seq has been extensively utilized in various biological areas, including biochemistry, genetics, molecular biology, immunology, and microbiology, followed by health sciences covering studies related to the nervous system, immune system, human health, development, and diseases, with a particular focus on cancer research. However, the potential of scRNA-Seq extends beyond disease research, offering insights into non-model organisms' responses to environmental contaminants. By enabling the study of cellular reactions at a molecular level, scRNA-Seq provides a comprehensive understanding of intracellular heterogeneity that enhances our comprehension of physiological, biochemical, and pathological environmental impacts on non-model organisms exposed to pollution. This understanding has many practical benefits, as it can aid in regulation and conservation efforts that benefit the environment and the use of economically essential and ecologically relevant organisms., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024. Published by Elsevier Inc.)
Published: 2024
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50. Genomics-informed captive breeding can reduce inbreeding depression and the genetic load in zoo populations.

Author: Speak SA, Birley T, Bortoluzzi C, Clark MD, Percival-Alwyn L, Morales HE, and van Oosterhout C
Subjects: Animals, Animals, Zoo, Genetic Load, Genomics, Conservation of Natural Resources, Computer Simulation, Inbreeding Depression, Columbidae genetics, Columbidae physiology, Breeding methods
Abstract: Zoo populations of threatened species are a valuable resource for the restoration of wild populations. However, their small effective population size poses a risk to long-term viability, especially in species with high genetic load. Recent bioinformatic developments can identify harmful genetic variants in genome data. Here, we advance this approach, analysing the genetic load in the threatened pink pigeon (Nesoenas mayeri). We lifted the mutation-impact scores that had been calculated for the chicken (Gallus gallus) to estimate the genetic load in six pink pigeons. Additionally, we perform in silico crossings to predict the genetic load and realized load of potential offspring. We thus identify the optimal mate pairs that are theoretically expected to produce offspring with the least inbreeding depression. We use computer simulations to show how genomics-informed conservation can reduce the genetic load whilst reducing the loss of genome-wide diversity. Genomics-informed management is likely to become instrumental in maintaining the long-term viability of zoo populations., (© 2024 The Authors. Molecular Ecology Resources published by John Wiley & Sons Ltd.)
Published: 2024
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