Author: "Center for Plant Systems Biology (PSB Center)" - Searchworks@Jio Institute Digital Library Search Results

Your search keyword '"Center for Plant Systems Biology (PSB Center)"' showing total 98 results

Start Over Author "Center for Plant Systems Biology (PSB Center)"

98 results on '"Center for Plant Systems Biology (PSB Center)"'

1. BRASSINOSTEROID INSENSITIVE1 internalization can occur independent of ligand binding

Author: Lucas Alves Neubus Claus, Derui Liu, Ulrich Hohmann, Nemanja Vukašinović, Roman Pleskot, Jing Liu, Alexei Schiffner, Yvon Jaillais, Guang Wu, Sebastian Wolf, Daniël Van Damme, Michael Hothorn, Eugenia Russinova, Universiteit Gent = Ghent University (UGENT), Shandong Agricultural University (SDAU), VIB [Belgium], Université de Genève = University of Geneva (UNIGE), Austrian Academy of Sciences (OeAW), Institute of Experimental Botany of the Czech Academy of Sciences (IEB / CAS), Czech Academy of Sciences [Prague] (CAS), Shaanxi Normal University (SNNU), Universitätsklinikum Tübingen - University Hospital of Tübingen, Eberhard Karls Universität Tübingen = Eberhard Karls University of Tuebingen, Reproduction et développement des plantes (RDP), École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Center for Plant Systems Biology (PSB Center), Vlaams Instituut voor Biotechnologie [Ghent, Belgique] (VIB), and École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL)
Subjects: PERCEPTION, ligand-binding, RECEPTOR, Physiology, PROTEINS, ENDOCYTOSIS, Biology and Life Sciences, Plant Science, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, DEGRADATION, EXTRACELLULAR DOMAIN, BRI1, brassinosteroids, non-canonical, [SDE]Environmental Sciences, Genetics, KINASE, endocytosis, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, TRAFFICKING
Abstract: The brassinosteroid (BR) hormone and its plasma membrane (PM) receptor BR INSENSITIVE1 (BRI1) are one of the best-studied receptor–ligand pairs for understanding the interplay between receptor endocytosis and signaling in plants. BR signaling is mainly determined by the PM pool of BRI1, whereas BRI1 endocytosis ensures signal attenuation. As BRs are ubiquitously distributed in the plant, the tools available to study the BRI1 function without interference from endogenous BRs are limited. Here, we designed a BR binding-deficient Arabidopsis (Arabidopsis thaliana) mutant based on protein sequence-structure analysis and homology modeling of members of the BRI1 family. This tool allowed us to re-examine the BRI1 endocytosis and signal attenuation model. We showed that despite impaired phosphorylation and ubiquitination, BR binding-deficient BRI1 internalizes similarly to the wild type form. Our data indicate that BRI1 internalization relies on different endocytic machineries. In addition, the BR binding-deficient mutant provides opportunities to study non-canonical ligand-independent BRI1 functions.
Published: 2023

2. TPLATE complex dependent endocytosis is required for shoot apical meristem maintenance by attenuating CLAVATA1 signaling

Author: Jie Wang, Qihang Jiang, Roman Pleskot, Peter Grones, Grégoire Denay, Carlos Galván-Ampudia, Elmehdi Bahafid, Xiangyu Xu, Michael Vandorpe, Evelien Mylle, Ive De Smet, Teva Vernoux, Rüdiger Simon, Moritz K. Nowack, Daniel Van Damme, Chinese Academy of Sciences [Beijing] (CAS), Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences (SLU), Physiologie cellulaire et végétale (LPCV), Centre National de la Recherche Scientifique (CNRS)-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)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Grenoble Alpes (UGA), Reproduction et développement des plantes (RDP), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Dept of Plant Systems Biology and Dept of Plant Biotechnology and Bioinformatics, Universiteit Gent = Ghent University (UGENT), Department of plant Biotechnology and Bioinformatics, Flanders Institute for Biotechnology, Center for Plant Systems Biology (PSB Center), and Vlaams Instituut voor Biotechnologie [Ghent, Belgique] (VIB)
Subjects: [SDV]Life Sciences [q-bio]
Abstract: Endocytosis regulates the turnover of cell surface localized receptors, which are crucial for plants to sense and rapidly respond to both endogenous and environmental stimuli. The evolutionarily ancient TPLATE complex (TPC) plays an essential role in clathrin-mediated endocytosis (CME) in Arabidopsis plants. Knockout or strong knockdown of single TPC subunits causes male sterility and seedling lethality phenotypes, complicating analysis of the roles of TPC during plant development. Partially functional alleles of TPC subunits however only cause very mild developmental deviations. Here, we took advantage of the recently reported partially functional TPLATE allele, WDXM2, to investigate a role for TPC-dependent endocytosis in receptor-mediated signalling. We discovered that reduced TPC-dependent endocytosis confers a hypersensitivity to very low doses of CLAVATA3 (CLV3) peptide signalling. This hypersensitivity correlated with the abundance of the CLV3 receptor protein kinase CLAVATA1 (CLV1) at the plasma membrane. Genetic analysis and live-cell imaging revealed that TPC-dependent regulation of CLV3-dependent internalization of CLV1 from the plasma membrane is required for CLV3 function in the shoot. Our findings provide evidence that clathrin-mediated endocytosis of CLV1 is a mechanism to dampen CLV3-mediated signaling during plant development.
Published: 2022

3. bHLH heterodimer complex variations regulate cell proliferation activity in the meristems of Arabidopsis thaliana

Author: Eliana Mor, Markéta Pernisová, Max Minne, Guillaume Cerutti, Dagmar Ripper, Jonah Nolf, Jennifer Andres, Laura Ragni, Matias D. Zurbriggen, Bert De Rybel, Teva Vernoux, Center for Plant Systems Biology (PSB Center), Vlaams Instituut voor Biotechnologie [Ghent, Belgique] (VIB), Reproduction et développement des plantes (RDP), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Simulation et Analyse de la morphogenèse in siliCo (MOSAIC), Inria Lyon, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria), University of Tübingen, and Heinrich Heine Universität Düsseldorf = Heinrich Heine University [Düsseldorf]
Subjects: Molecular plant pathology, Plant biology, Biological sciences, Multidisciplinary, cell proliferation, Natural sciences, heterodimer complex, Biology and Life Sciences, [SDV.BDD.MOR]Life Sciences [q-bio]/Development Biology/Morphogenesis, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics
Abstract: International audience; Root, shoot, and lateral meristems are the main regions of cell proliferation in plants. It has been proposed that meristems might have evolved dedicated transcriptional networks to balance cell proliferation. Here, we show that basic helixloop-helix (bHLH) transcription factor heterodimers formed by members of the TARGET OF MONOPTEROS5 (TMO5) and LONESOME HIGHWAY (LHW) subclades are general regulators of cell proliferation in all meristems. Yet, genetics and expression analyses suggest specific functions of these transcription factors in distinct meristems, possibly due to their expression domains determining heterodimer complex variations within meristems, and to a certain extent to the absence of some of them in a given meristem. Target gene specificity analysis for heterodimer complexes focusing on the LONELY GUY gene targets further suggests differences in transcriptional responses through heterodimer diversification that could allow a common bHLH heterodimer complex module to contribute to cell proliferation control in multiple meristems.
Published: 2022

4. D8.1 EOSC-Life Methodology framework to enhance reproducibility within EOSC-Life – revised version

Author: Bietrix, Florence, Carazo, José-Maria, Capella-Gutierrez, Salvador, Coppens, Frederik, Chiusano, Maria-Luisa, David, Romain, Fernandez Jose, Maria, Fratelli, Maddalena, Heriche, Jean-Karim, Goble, Carole, Gribbon, Philip, Holub, Petr, P.Joosten, Robbie, Leo, Simone, Owen, Stuart, Parkinson, Helen, Pieruschka, Roland, Pireddu, Luca, Porcu, Luca, Raess, Michael, Rodriguez-Navas, Laura, Scherer, Andreas, Soiland-Reyes, Stian, Tang, Jing, Saunders, Gary, European Advanced Translational Research Infrastructure (EATRIS), National Center for Biotechnology Information (NCBI), Barcelona Supercomputing Center - Centro Nacional de Supercomputacion (BSC - CNS), Center for Plant Systems Biology (PSB Center), Vlaams Instituut voor Biotechnologie [Ghent, Belgique] (VIB), University of Naples Federico II = Università degli studi di Napoli Federico II, European Research Infrastructure on Highly Pathogenic Agents (ERINHA-AISBL), IRCCS - Istituto di Ricerche Farmacologiche 'Mario Negri' [Milan, Italy], European Molecular Biology Laboratory [Heidelberg] (EMBL), University of Manchester [Manchester], ITMP Drug Discovery (ITMP), Czech Academy of Sciences [Prague] (CAS), Department of Computer Science, University of Manchester, European Bioinformatics Institute [Hinxton] (EMBL-EBI), EMBL Heidelberg, Forschungszentrum Jülich GmbH | Centre de recherche de Juliers, Helmholtz-Gemeinschaft = Helmholtz Association, CRS4 Bioinformat, INFRAFRONTIER GmbH [Neuherberg], Department of Computer Science, The University of Manchester, TKK Helsinki University of Technology (TKK), Bietrix, Florence, Carazo, José Maria, Capella-Gutierrez, Salvador, Coppens, Frederik, Chiusano, Maria Luisa, David, Romain, Fernandez, Jose Maria, Fratelli, Maddalena, Heriche, Jean-Karim, Goble, Carole, Gribbon, Philip, Holub, Petr, P. Joosten, Robbie, Leo, Simone, Owen, Stuart, Parkinson, Helen, Pieruschka, Roland, Pireddu, Luca, Porcu, Luca, … Saunders, Gary. (2022). EOSC-Life Methodology framework to enhance reproducibility within EOSC-Life – revised version. Zenodo. https://doi.org/10.5281/zenodo.7137744, EOSC-Life, INFRAFRONTIER, VIB, EMBRC, ERINHA, IRFMN, EMBL-HD, UNIMAN, Fraunhofer, BBMRI-ERIC, NKI, EMBL-EBI, CSR4, HU, CSIC, BSC, and European Project: 824087,EOSC-Life
Subjects: Life science, Open Science, Framework Implementation, Data sharing, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], Data sharing tools, research infrastructures, Reproducibility
Abstract: The original scope of task 8.3 is to develop a framework to assess the impact on reproducibility of the availability of life-science open data and workflows in the cloud.Such a framework should include the understanding of the tools and services produced and made available, the gaps they are filling up and their expected impact.A great part of the activities within EOSC-Life is actually related to reproducibility and provides in several ways tools that will have an impact. We describe here such activities and explain why and how they will have an impact on reproducibility in life sciences. In addition, for each action, we provide an indication of how we could measure its impact in practical ways, using adequate proxies. For these reasons, we changed the title of the deliverable, from “framework to assess ...” to “framework to enhance reproducibility”.First of all, we reasoned on what can be the contribution of open science to improve the reproducibility of research. Publicly sharing data, protocols, tools and computational workflows makes it possible to compare or combine the data and outcomes from different studies within a discipline as well as integrate data across scientific domains. It allows conclusions to be validated and possibly corrected as well as being reinforced by meta-analyses. Replication data and test/training data can also be used in many applications to contribute to reproducible research. Moreover, new hypotheses, different from the original aims of the study, can be explored. Datasets can be re-used to develop and test new methods, to conduct scientific and technical benchmarking activities and to support training activities. Therefore, in addition to generating more value from research investments, data sharing has the potential to increase confidence in research outcomes and increase knowledge dissemination. These benefits of open sharing have long been recognized in some fields such as bioinformatics, which has a long history of publicly sharing data with, for example, public repositories for nucleotide sequences going back 30 years and the Protein Data Bank (PDB), a repository of information about the 3D structures of proteins, nucleic acids, and complex assemblies, that celebrates its 50th birthday this year.In this notion, any improvement in sharing of data, tools and workflows among scientists and across disciplines, which is the aim of EOSC-Life and the wider EOSC, will contribute to reproducible science. In addition to this general scope, several specific actions to frame transparency in the reporting of experimental protocols, data and analytical workflows warrant the reproducibility of every single object (experimental results, data, or workflows) that is made available on the cloud.We describe here the initiatives in EOSC-Life to implement existing tools for reproducibility as well as to develop new tools for its enhancement. As the final goal of EOSC-Life is to make data resources available to the wider community of life scientists, although necessarily technical in several points, this document aims at a general readership, including experimental in addition to data scientists.
Published: 2022

5. Alterations in the phenylpropanoid pathway affect poplar ability for ectomycorrhizal colonisation and susceptibility to root-knot nematodes

Author: Geert Goeminne, Mondher El Jaziri, Marie Baucher, Rebecca Van Acker, Marc Behr, Janice de Almeida Engler, Gilles Pilate, Wout Boerjan, Claire Veneault-Fourrey, Annegret Kohler, Fabien Baldacci-Cresp, Kris Morreel, Adeline Mol, Laboratoire de Biotechnologie Végétale, Université libre de Bruxelles (ULB), Interactions Arbres-Microorganismes (IAM), Université de Lorraine (UL)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Center for Plant Systems Biology (PSB Center), Vlaams Instituut voor Biotechnologie [Ghent, Belgique] (VIB), Department of Plant Biotechnology and Bioinformatics, Universiteit Gent = Ghent University [Belgium] (UGENT), Biologie intégrée pour la valorisation de la diversité des Arbres et de la Forêt (BioForA), Office National des Forêts (ONF)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut Sophia Agrobiotech (ISA), Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Côte d'Azur (UCA), Fonds de la Recherche Scientifique - FNRS T. 0004.14, Multidisciplinary Research Partnership Biotechnology for a sustainable economy, European Commission's Directorate-General for Research within the 7th Framework Program (FP7/2007-2013) 270,089, ANR-11_LABX-0002-01 CFP15, and United States Department of Energy (DOE)
Subjects: 0106 biological sciences, Nematoda, Cinnamyl-alcohol dehydrogenase, Plant Science, Fungus, Lignin, Transgenic poplar, 01 natural sciences, Secondarymetabolites, 03 medical and health sciences, chemistry.chemical_compound, Symbiosis, Gene Expression Regulation, Plant, Mycorrhizae, Botany, Genetics, medicine, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Animals, Root-knot nematode, Monolignol, Transcriptomics, Molecular Biology, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, 2. Zero hunger, 0303 health sciences, biology, Phenylpropanoid, fungi, food and beverages, General Medicine, Ectomycorrhiza . Monolignol . Root-knot nematode . Secondary metabolites . Transcriptomics . Transgenic poplar, 15. Life on land, biology.organism_classification, medicine.disease, Physiologie des plantes vasculaires, Mycologie, Ectomycorrhiza, Colonisation, Populus, Nematode infection, chemistry, 010606 plant biology & botany
Abstract: This study investigates the impact of the alteration of the monolignol biosynthesis pathway on the establishment of thein vitro interaction of poplar roots either with a mutualistic ectomycorrhizal fungus or with a pathogenic root-knotnematode. Overall, the five studied transgenic lines downregulated for caffeoyl-CoA O-methyltransferase(CCoAOMT), caffeic acid O-methyltransferase (COMT), cinnamoyl-CoA reductase (CCR), cinnamyl alcoholdehydrogenase (CAD) or both COMT and CAD displayed a lower mycorrhizal colonisation percentage, indicating alower ability for establishing mutualistic interaction than the wild-type. The susceptibility to root-knot nematode infectionwas variable in the five lines, and the CAD-deficient line was found to be less susceptible than the wild-type. Wediscuss these phenotypic differences in the light of the large shifts in the metabolic profile and gene expression patternoccurring between roots of the CAD-deficient line and wild-type. A role of genes related to trehalose metabolism,phytohormones, and cell wall construction in the different mycorrhizal symbiosis efficiency and nematode sensitivitybetween these two lines is suggested. Overall, these results show that the alteration of plant metabolism caused by therepression of a single gene within phenylpropanoid pathway results in significant alterations, at the root level, in theresponse towards mutualistic and pathogenic associates. These changes may constrain plant fitness and biomass production,which are of economic importance for perennial industrial crops such as poplar., info:eu-repo/semantics/published
Published: 2020

6. Rapid protein evolution, organellar reductions, and invasive intronic elements in the marine aerobic parasite dinoflagellate Amoebophrya spp

Author: Thierry Tonon, Patrick Wincker, Corinne Da Silva, Tristan Barbeyron, Tsinda Rukwavu, Jeremy Szymczak, Benjamin Noel, Ruibo Cai, Stephane Rombauts, Adriana Alberti, Erwan Corre, Catharina Alves-de-Souza, Ehsan Kayal, Laure Guillou, Florian Maumus, Karine Labadie, Estelle Bigeard, Pierre Rouzé, Benjamin Istace, Sarah Farhat, Jean-Marc Aury, Phuong Le, Yves Van de Peer, Isabelle Florent, Dominique Marie, Betina M. Porcel, Jonathan Mercier, Génomique métabolique (UMR 8030), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-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 Paris-Saclay-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)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), School of Marine and Atmospheric Sciences [Stony Brook] (SoMAS), Stony Brook University [SUNY] (SBU), State University of New York (SUNY)-State University of New York (SUNY), Center for Plant Systems Biology (PSB Center), Vlaams Instituut voor Biotechnologie [Ghent, Belgique] (VIB), 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), ECOlogy of MArine Plankton (ECOMAP), Adaptation et diversité en milieu marin (AD2M), 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)-Centre National de la Recherche Scientifique (CNRS), Unité de Recherche Génomique Info (URGI), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Molécules de Communication et Adaptation des Micro-organismes (MCAM), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Biologie Intégrative des Modèles Marins (LBI2M), 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)-Centre National de la Recherche Scientifique (CNRS), University of York [York, UK], University of North Carolina [Wilmington] (UNC), University of North Carolina System (UNC), Department of Biochemistry, Genetics and Microbiology [Pretoria], University of Pretoria [South Africa], ANR (Agence Nationale de la Recherche) Grant ANR-14-CE02-0007 HAPAR, the CEA and the Région Bretagne (RC doctoral grant ARED PARASITE 9450 and EK postdoctoral grant SAD HAPAR 9229), and the CNRS (X-life SEAgOInG)., ANR-14-CE02-0007,HAPAR,Le paradoxe de la spécialisation chez un parasite de microalgues responsables de marées rouges(2014), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), 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), Adaptation et diversité en milieu marin (ADMM), Institut national des sciences de l'Univers (INSU - CNRS)-Station biologique de Roscoff (SBR), and 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)
Subjects: APICOMPLEXAN, Physiology, Protozoan Proteins, DIVERSITY, Plant Science, Genome, MITOCHONDRIAL GENOMES, 0302 clinical medicine, Structural Biology, lcsh:QH301-705.5, GENE-EXPRESSION, Introner elements, 0303 health sciences, Non-canonical introns, biology, Ecology, Dinoflagellate, Biological Evolution, DNA TRANSPOSONS, Parasite, ALIGNMENT, Dinoflagellida, General Agricultural and Biological Sciences, Dinophyceae, Research Article, Biotechnology, Transposable element, Evolution, Genetics and Molecular Biology, SEQUENCE, General Biochemistry, Genetics and Molecular Biology, Evolution, Molecular, 03 medical and health sciences, REPEAT TRANSPOSABLE ELEMENTS, Behavior and Systematics, Gene family, OPEN SOFTWARE, 14. Life underwater, Gene, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, Synteny, Organelles, [SDV.GEN]Life Sciences [q-bio]/Genetics, Base Sequence, IDENTIFICATION, Intron, Biology and Life Sciences, Cell Biology, DNA, Protozoan, biology.organism_classification, Introns, lcsh:Biology (General), Evolutionary biology, General Biochemistry, 030217 neurology & neurosurgery, Developmental Biology
Abstract: Background Dinoflagellates are aquatic protists particularly widespread in the oceans worldwide. Some are responsible for toxic blooms while others live in symbiotic relationships, either as mutualistic symbionts in corals or as parasites infecting other protists and animals. Dinoflagellates harbor atypically large genomes (~ 3 to 250 Gb), with gene organization and gene expression patterns very different from closely related apicomplexan parasites. Here we sequenced and analyzed the genomes of two early-diverging and co-occurring parasitic dinoflagellate Amoebophrya strains, to shed light on the emergence of such atypical genomic features, dinoflagellate evolution, and host specialization. Results We sequenced, assembled, and annotated high-quality genomes for two Amoebophrya strains (A25 and A120), using a combination of Illumina paired-end short-read and Oxford Nanopore Technology (ONT) MinION long-read sequencing approaches. We found a small number of transposable elements, along with short introns and intergenic regions, and a limited number of gene families, together contribute to the compactness of the Amoebophrya genomes, a feature potentially linked with parasitism. While the majority of Amoebophrya proteins (63.7% of A25 and 59.3% of A120) had no functional assignment, we found many orthologs shared with Dinophyceae. Our analyses revealed a strong tendency for genes encoded by unidirectional clusters and high levels of synteny conservation between the two genomes despite low interspecific protein sequence similarity, suggesting rapid protein evolution. Most strikingly, we identified a large portion of non-canonical introns, including repeated introns, displaying a broad variability of associated splicing motifs never observed among eukaryotes. Those introner elements appear to have the capacity to spread over their respective genomes in a manner similar to transposable elements. Finally, we confirmed the reduction of organelles observed in Amoebophrya spp., i.e., loss of the plastid, potential loss of a mitochondrial genome and functions. Conclusion These results expand the range of atypical genome features found in basal dinoflagellates and raise questions regarding speciation and the evolutionary mechanisms at play while parastitism was selected for in this particular unicellular lineage.
Published: 2021

7. Histone modification ChIP-seq on Arabidopsis thaliana plantlets

Author: Moussa Benhamed, David Latrasse, Juan Sebastian Ramirez-Prado, Center for Plant Systems Biology (PSB Center), Vlaams Instituut voor Biotechnologie [Ghent, Belgique] (VIB), 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), Institut Universitaire de France (IUF), and 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)
Subjects: biology, Arabidopsis thaliana, Immunoprecipitation, Strategy and Management, Mechanical Engineering, Metals and Alloys, biology.organism_classification, Industrial and Manufacturing Engineering, Chromatin, Cell biology, ChIP-seq, Histone, Gene expression, Methods Article, biology.protein, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Protein–DNA interaction, Chromatin immunoprecipitation, Epigenomics
Abstract: International audience; Characterizing the molecular mechanisms regulating gene expression is crucial for understanding the regulatory processes underlying physiological responses to environmental and developmental signals in eukaryotes. The covalent modification of histones contributes to the compaction levels of chromatin, as well as the recruitment of the transcriptional machinery to specific loci, facilitating metastable changes in gene activity. ChIP-seq (Chromatin Immunoprecipitation followed by sequencing) has become the gold standard method for determining histone modification profiles among different organisms, tissues, and genotypes. In the current protocol, we describe a highly robust method for performing ChIP-seq of histone modifications in Arabidopsis thaliana plantlets. Besides its robustness, this method uses in-house-prepared buffers for chromatin extraction, immunoprecipitation, washing, and elusion, making it cost-effective in contrast to commercial kits.
Published: 2021

8. SYNERGISTIC ON AUXIN AND CYTOKININ 1 positively regulates growth and attenuates soil pathogen resistance

Author: Hana Semerádová, Grégory Mouille, Freia Benade, Rishikesh Bhalearo, Ladislav Dokládal, Andrej Hurný, Jutta Ludwig-Müller, Krisztina Ötvös, András Gorzsás, Ingo Heilmann, Geert De Jaeger, Irene Stenzel, Thomas Rauter, Juan Carlos Montesinos, Jérôme Duclercq, Candela Cuesta, Marçal Gallemí, Eva Sýkorová, Eva Benková, Geert Persiau, Julien Sechet, Nicola Cavallari, Institute of Science and Technology, Departamento de Biología de Organismos y Sistemas, Universidad de Oviedo [Oviedo], Bioresources Unit, Center for Health & Bioresources, Austrian Institute of Technology [Vienna] (AIT)-Austrian Institute of Technology [Vienna] (AIT), Ecologie et Dynamique des Systèmes Anthropisés - UMR CNRS 7058 (EDYSAN), Centre National de la Recherche Scientifique (CNRS)-Université de Picardie Jules Verne (UPJV), Institute of Biophysics, Institute of Biophysics of the Czech Academy of Sciences (IBP / CAS), Czech Academy of Sciences [Prague] (CAS)-Czech Academy of Sciences [Prague] (CAS), Mendel Centre for Plant Genomics and Proteomics, CEITEC, Masaryk Memorial Cancer Institute (RECAMO)-Masaryk Memorial Cancer Institute (RECAMO), Molecular Biology and Biochemistry, Gottfried Schatz Research Center, University of Graz-University of Graz, Department of Cellular Biochemistry, Institute for Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg-Martin-Luther-University Halle-Wittenberg, Department of Plant Biotechnology and Bioinformatics, Universiteit Gent = Ghent University [Belgium] (UGENT), Center for Plant Systems Biology (PSB Center), Vlaams Instituut voor Biotechnologie [Ghent, Belgique] (VIB), Institut für Botanik [Dresden], Technische Universität Dresden = Dresden University of Technology (TU Dresden), Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Department of Chemistry, Umeå University, Institut Jean-Pierre Bourgin (IJPB), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Austrian Science Fund (FWF)FWF01_I1774SGerman Research Foundation (DFG)He3424/6-1People Programme (Marie Curie Actions) of the European Union's Seventh Framework Programme (FP7/2007-2013) under REA grant 291734European Commission609398Scientific Service Units of IST-Austria Saclay Plant Sciences-SPS ANR-17-EUR-0007, Université de Picardie Jules Verne (UPJV)-Centre National de la Recherche Scientifique (CNRS), and Karl-Franzens-Universität [Graz, Autriche]-Karl-Franzens-Universität [Graz, Autriche]
Subjects: 0106 biological sciences, 0301 basic medicine, Cytokinins, Arabidopsis, Vesicular Transport Proteins, Regulator, Golgi Apparatus, General Physics and Astronomy, PUTATIVE METHYLTRANSFERASE, Plasmodiophorida, Plant Roots, 01 natural sciences, Soil, chemistry.chemical_compound, APICAL HOOK, Arabidopsis-thaliana, Plant Growth Regulators, Gene Expression Regulation, Plant, Protein trafficking in plants, Auxin, heterocyclic compounds, lcsh:Science, Disease Resistance, 2. Zero hunger, chemistry.chemical_classification, Regulation of gene expression, Abiotic component, Secretory Pathway, Multidisciplinary, Cell wall, PLANT DEVELOPMENT, food and beverages, Plants, Genetically Modified, Cell biology, B Response Regulators, Cytokinin, PLASMODIOPHORA-BRASSICAE, CYTOKININ RECEPTOR, Chinese-cabbage, Science, Cytokinin Receptor, Plant Development, Genetics and Molecular Biology, Box Protein Tir1, Endosomes, Biology, BOX PROTEIN TIR1, Article, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, Putative Methyltransferase, Apical Hook, Biotic, Secretory pathway, Indoleacetic Acids, Arabidopsis Proteins, Gene Expression Profiling, fungi, Botany, Membrane Proteins, Biology and Life Sciences, B RESPONSE REGULATORS, Botanik, General Chemistry, Gene expression profiling, POLLEN-TUBE GROWTH, 030104 developmental biology, chemistry, General Biochemistry, ARABIDOPSIS-THALIANA, Pollen-tube Growth, lcsh:Q, [INFO.INFO-ET]Computer Science [cs]/Emerging Technologies [cs.ET], CHINESE-CABBAGE, Plasmodiophora-brassicae, Transcriptome, 010606 plant biology & botany, Hormone
Abstract: Plants as non-mobile organisms constantly integrate varying environmental signals to flexibly adapt their growth and development. Local fluctuations in water and nutrient availability, sudden changes in temperature or other abiotic and biotic stresses can trigger changes in the growth of plant organs. Multiple mutually interconnected hormonal signaling cascades act as essential endogenous translators of these exogenous signals in the adaptive responses of plants. Although the molecular backbones of hormone transduction pathways have been identified, the mechanisms underlying their interactions are largely unknown. Here, using genome wide transcriptome profiling we identify an auxin and cytokinin cross-talk component; SYNERGISTIC ON AUXIN AND CYTOKININ 1 (SYAC1), whose expression in roots is strictly dependent on both of these hormonal pathways. We show that SYAC1 is a regulator of secretory pathway, whose enhanced activity interferes with deposition of cell wall components and can fine-tune organ growth and sensitivity to soil pathogens., Cytokinin and auxin are two major hormonal regulators of plant growth. Here the authors identify SYAC1, a gene that is synergistically activated by the two hormones being applied together, and show that it is required for normal growth while negatively impacting pathogen resistance.
Published: 2020

9. Maize specialized metabolome networks reveal organ-preferential mixed glycosides

Author: Ruben Vanholme, Claudiu Niculaes, John Ralph, Hoon Kim, Atsushi Fukushima, Rebecca Dauwe, Wout Boerjan, Sandrien Desmet, Kris Morreel, Geert Goeminne, Yvan Saeys, Kevin Verstaen, Department of plant Biotechnology and Bioinformatics, Universiteit Gent = Ghent University (UGENT), Flanders Institute for Biotechnology, VIB-UGent Center for Inflammation Research [Gand, Belgique] (IRC), VIB [Belgium], Biologie des Plantes et Innovation - UR UPJV 3900 (BIOPI), Université de Picardie Jules Verne (UPJV)-Transfrontalière BioEcoAgro - UMR 1158 (BioEcoAgro), Université d'Artois (UA)-Université de Liège-Université de Picardie Jules Verne (UPJV)-Université du Littoral Côte d'Opale (ULCO)-Université de Lille-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-JUNIA (JUNIA), Université catholique de Lille (UCL)-Université catholique de Lille (UCL)-Université d'Artois (UA)-Université de Liège-Université du Littoral Côte d'Opale (ULCO)-Université de Lille-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-JUNIA (JUNIA), Université catholique de Lille (UCL)-Université catholique de Lille (UCL), Department of Pharmacy, and Research Institute of Life Pharmaceutical Sciences, Sunchon National University, Suncheon 57922, Republic of Korea, John Innes Centre [Norwich], Biotechnology and Biological Sciences Research Council (BBSRC), RIKEN Center for Sustainable Resource Science [Yokohama] (RIKEN CSRS), RIKEN - Institute of Physical and Chemical Research [Japon] (RIKEN), Center for Plant Systems Biology (PSB Center), Vlaams Instituut voor Biotechnologie [Ghent, Belgique] (VIB), University of Wisconsin-Madison, and Department of Plant Systems Biology, VIB, and Department of Plant Biotechnology and Bioinformatics
Subjects: Agriculture and Food Sciences, PREDICTION, Systems biology, [SDV]Life Sciences [q-bio], Biophysics, DIVERSITY, Spectral metadata analysis, Computational biology, Biochemistry, Zea mays, ANNOTATION, Specialized metabolism, 03 medical and health sciences, chemistry.chemical_compound, 0302 clinical medicine, Structural Biology, Arabidopsis, Genetics, Metabolome, Glycosyl, AUXIN BIOSYNTHESIS, ComputingMethodologies_COMPUTERGRAPHICS, 030304 developmental biology, chemistry.chemical_classification, 0303 health sciences, Phenylpropanoid, biology, Mass spectrometry, IDENTIFICATION, ELUCIDATION, Glycoside, Biology and Life Sciences, MASS-SPECTROMETRY, biology.organism_classification, ARABIDOPSIS, Computer Science Applications, ddc, Metabolic pathway, chemistry, 030220 oncology & carcinogenesis, Acyltransferase, FRAGMENTATION, PHENYLACETIC ACID, TP248.13-248.65, Research Article, Biotechnology
Abstract: Graphical abstract, Despite the scientific and economic importance of maize, little is known about its specialized metabolism. Here, five maize organs were profiled using different reversed-phase liquid chromatography-mass spectrometry methods. The resulting spectral metadata, combined with candidate substrate-product pair (CSPP) networks, allowed the structural characterization of 427 of the 5,420 profiled compounds, including phenylpropanoids, flavonoids, benzoxazinoids, and auxin-related compounds, among others. Only 75 of the 427 compounds were already described in maize. Analysis of the CSPP networks showed that phenylpropanoids are present in all organs, whereas other metabolic classes are rather organ-enriched. Frequently occurring CSPP mass differences often corresponded with glycosyl- and acyltransferase reactions. The interplay of glycosylations and acylations yields a wide variety of mixed glycosides, bearing substructures corresponding to the different biochemical classes. For example, in the tassel, many phenylpropanoid and flavonoid-bearing glycosides also contain auxin-derived moieties. The characterized compounds and mass differences are an important step forward in metabolic pathway discovery and systems biology research. The spectral metadata of the 5,420 compounds is publicly available (DynLib spectral database, https://bioit3.irc.ugent.be/dynlib/).
Published: 2020

10. Endocytosis of BRASSINOSTEROID INSENSITIVE1 Is Partly Driven by a Canonical Tyr-Based Motif

Author: Isabelle Vanhoutte, Eugenia Russinova, Lucas Alves Neubus Claus, Rajesh Kumar, Peng Wang, Wei Siao, Daniël Van Damme, Jiří Friml, Derui Liu, Xiuyang Zhao, Grégory Vert, Alexander W. Johnson, Klaas Yperman, Sara Martins, Kyle W. Bender, Universiteit Gent = Ghent University (UGENT), Center for Plant Systems Biology (PSB Center), Vlaams Instituut voor Biotechnologie [Ghent, Belgique] (VIB), Institute of Science and Technology [Klosterneuburg, Austria] (IST Austria), University of Illinois at Urbana-Champaign [Urbana], University of Illinois System, Laboratoire de Recherche en Sciences Végétales (LRSV), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Signalisation Cellulaire et Ubiquitination, Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), European Project: 1009584(2010), Universiteit Gent = Ghent University [Belgium] (UGENT), Institute of Science and Technology [Austria] (IST Austria), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), and Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3)
Subjects: POLAR LOCALIZATION, 0106 biological sciences, 0301 basic medicine, ADAPTER COMPLEX, Endocytic cycle, Amino Acid Motifs, MESH: Cell Membrane / metabolism, Arabidopsis, Plant Science, 01 natural sciences, chemistry.chemical_compound, MESH: Amino Acid Motifs, MESH: Endocytosis / physiology, Internalization, media_common, MESH: Arabidopsis / metabolism, TYROSINE PHOSPHORYLATION, biology, Signal transducing adaptor protein, CLATHRIN-MEDIATED ENDOCYTOSIS, ARABIDOPSIS, Plants, Genetically Modified, Endocytosis, Cell biology, MESH: Arabidopsis Proteins / genetics, FACTOR RECEPTOR, MESH: Protein Domains, MESH: Arabidopsis / genetics, EPIDERMAL-GROWTH-FACTOR, CELLULOSE SYNTHASE, MESH: Mutation, SORTING SIGNALS, media_common.quotation_subject, Green Fluorescent Proteins, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, Clathrin, In Brief, 03 medical and health sciences, MESH: Arabidopsis Proteins / metabolism, Protein Domains, MESH: Arabidopsis Proteins / chemistry, Kinase activity, MESH: Protein Kinases / chemistry, Arabidopsis Proteins, Cell Membrane, fungi, Biology and Life Sciences, Tyrosine phosphorylation, Cell Biology, Receptor-mediated endocytosis, MESH: Protein Kinases / genetics, MESH: Protein Kinases / metabolism, 030104 developmental biology, chemistry, MESH: Plants, Genetically Modified, MESH: Tyrosine / chemistry, Mutation, biology.protein, Tyrosine, MESH: Green Fluorescent Proteins / genetics, Protein Kinases, STRUCTURAL EXPLANATION, 010606 plant biology & botany
Abstract: Clathrin-mediated endocytosis (CME) and its core endocytic machinery are evolutionarily conserved across all eukaryotes. In mammals, the heterotetrameric adaptor protein complex-2 (AP-2) sorts plasma membrane (PM) cargoes into vesicles via the recognition of motifs based on Tyr or di-Leu in their cytoplasmic tails. However, in plants, very little is known about how PM proteins are sorted for CME and whether similar motifs are required. In Arabidopsis (Arabidopsis thaliana), the brassinosteroid (BR) receptor BR INSENSITIVE1 (BRI1) undergoes endocytosis, which depends on clathrin and AP-2. Here, we demonstrate that BRI1 binds directly to the medium AP-2 subunit (AP2M). The cytoplasmic domain of BRI1 contains five putative canonical surface-exposed Tyr-based endocytic motifs. The Tyr-to-Phe substitution in Y898KAI reduced BRI1 internalization without affecting its kinase activity. Consistently, plants carrying the BRI1Y898F mutation were hypersensitive to BRs. Our study demonstrates that AP-2–dependent internalization of PM proteins via the recognition of functional Tyr motifs also operates in plants.
Published: 2020

11. The Arabidopsis condensin CAP-D subunits arrange interphase chromatin

Author: Andrea Bräutigam, Celia Municio, Michiel Van Bel, Veit Schubert, Wojciech Antosz, Frederik Coppens, Ignacio Eguinoa, Klaus D. Grasser, Andreas Houben, Etienne Kornobis, Inna Lermontova, Katarzyna Zelkowska, Astrid Bruckmann, Leibniz Institute of Plant Genetics and Crop Plant Research [Gatersleben] (IPK-Gatersleben), University of Regensburg, Biomics (plateforme technologique), Institut Pasteur [Paris] (IP)-Université Paris Cité (UPCité), Hub Bioinformatique et Biostatistique - Bioinformatics and Biostatistics HUB, Center for Plant Systems Biology (PSB Center), Vlaams Instituut voor Biotechnologie [Ghent, Belgique] (VIB), Mendel Centre for Plant Genomics and Proteomics [Brno, Czech Republic], Masaryk University [Brno] (MUNI)-CEITEC - Central European Institute of Technology [Brno, Czech Republic], and The work was supported by a Marie Curie Initial Training Network fellowship (FP7-PEOPLE-2013-ITN, CHIP-ET). The A. Bruckmann and KDG laboratories were supported by the German Research Foundation through grant SFB960. IL was supported by European Regional Development ‘Fund-Project MSCAfellow@MUNI’ (no. CZ.02.2.69/0.0/0.0/17_050/0008496).
Subjects: 0106 biological sciences, 0301 basic medicine, chromosomes, Euchromatin, Arabidopsis thaliana, Physiology, Heterochromatin, Condensin, Arabidopsis, Plant Science, macromolecular substances, 01 natural sciences, [SDV.GEN.GPL]Life Sciences [q-bio]/Genetics/Plants genetics, 03 medical and health sciences, Condensin complex, Animals, Interphase, Adenosine Triphosphatases, biology, Chemistry, condensin, Biology and Life Sciences, biology.organism_classification, Chromatin, Cell biology, DNA-Binding Proteins, SMC proteins, 030104 developmental biology, Histone, Multiprotein Complexes, biology.protein, 010606 plant biology & botany, chromatin organization, interphase nuclei
Abstract: International audience; Condensins are best known for their role in shaping chromosomes. Other functions such as organizing interphase chromatin and transcriptional control have been reported in yeasts and animals, but little is known about their function in plants. To elucidate the specific composition of condensin complexes and the expression of CAP-D2 (condensin I) and CAP-D3 (condensin II), we performed biochemical analyses in Arabidopsis. The role of CAP-D3 in interphase chromatin organization and function was evaluated using cytogenetic and transcriptome analysis in cap-d3 T-DNA insertion mutants. CAP-D2 and CAP-D3 are highly expressed in mitotically active tissues. In silico and pulldown experiments indicate that both CAP-D proteins interact with the other condensin I and II subunits. In cap-d3 mutants, an association of heterochromatic sequences occurs, but the nuclear size and the general histone and DNA methylation patterns remain unchanged. Also, CAP-D3 influences the expression of genes affecting the response to water, chemicals, and stress. The expression and composition of the condensin complexes in Arabidopsis are similar to those in other higher eukaryotes. We propose a model for the CAP-D3 function during interphase in which CAP-D3 localizes in euchromatin loops to stiffen them and consequently separates centromeric regions and 45S rDNA repeats.
Published: 2020

12. Canonical correlations reveal adaptive loci and phenotypic responses to climate in perennial ryegrass

Author: Philippe Barre, Abraham J. Escobar-Gutiérrez, Elisabeth Veeckman, Klaas Vandepoele, Evelyn Willner, Matthew J. Hegarty, Thomas Keep, Tom Ruttink, Isabel Roldán-Ruiz, Klaus J. Dehmer, Hilde Muylle, Jean-Paul Sampoux, Thomas Ledauphin, José Luis Blanco-Pastor, Stéphanie Manel, Anna M. Roschanski, Unité de Recherche Pluridisciplinaire Prairies et Plantes Fourragères (P3F), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Leibniz Institute of Plant Genetics and Crop Plant Research [Gatersleben] (IPK-Gatersleben), Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, Research Institute for Agricultural, Fisheries and Food (ILVO), Universiteit Gent = Ghent University [Belgium] (UGENT), Center for Plant Systems Biology (PSB Center), Vlaams Instituut voor Biotechnologie [Ghent, Belgique] (VIB), Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Université Paul-Valéry - Montpellier 3 (UPVM)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), 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)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
Subjects: 0106 biological sciences, 0301 basic medicine, Germplasm, SELECTION, [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, quantitative genetics, Ecological selection, LEAF-AREA, Climate, adaptation, 01 natural sciences, R PACKAGE, agriculture, 2. Zero hunger, QUANTITATIVE TRAIT LOCI, Ecology, Ecological genetics, Adaptation, Physiological, L, Phenotype, climate change, Biotechnology, FLOWERING TIME, Genotype, Evolution, ecological genetics, Gene prediction, Quantitative trait locus, Biology, 010603 evolutionary biology, 03 medical and health sciences, Behavior and Systematics, Genetics, Lolium, GENOME-WIDE ASSOCIATION, Ecology, Evolution, Behavior and Systematics, LOLIUM-PERENNE, Biology and Life Sciences, landscape genetics, Phenotypic trait, Quantitative genetics, 15. Life on land, Plant Breeding, 030104 developmental biology, 13. Climate action, Evolutionary biology, Genetic Loci, Multivariate Analysis, Adaptation, COLLECTION
Abstract: International audience; Germplasm from perennial ryegrass (Lolium perenne L.) natural populations is useful for breeding because of its adaptation to a wide range of climates. Climate-adaptive genes can be detected from associations between genotype, phenotype and climate but an integrated framework for the analysis of these three sources of information is lacking. We used two approaches to identify adaptive loci in perennial ryegrass and their effect on phenotypic traits. First, we combined Genome-Environment Association (GEA) and GWAS analyses. Then, we implemented a new test based on a Canonical Correlation Analysis (CANCOR) to detect adaptive loci. Furthermore, we improved the previous perennial ryegrass gene set by de novo gene prediction and functional annotation of 39,967 genes. GEA-GWAS revealed eight outlier loci associated with both environmental variables and phenotypic traits. CANCOR retrieved 633 outlier loci associated with two climatic gradients, characterized by cold-dry winter versus mild-wet winter and long rainy season versus long summer, and pointed out traits putatively conferring adaptation at the extremes of these gradients. Our CANCOR test also revealed the presence of both polygenic and oligogenic climatic adaptations. Our gene annotation revealed that 374 of the CANCOR outlier loci were positioned within or close to a gene. Co-association networks of outlier loci revealed a potential utility of CANCOR for investigating the interaction of genes involved in polygenic adaptations. The CANCOR test provides an integrated framework to analyse adaptive genomic diversity and phenotypic responses to environmental selection pressures that could be used to facilitate the adaptation of plant species to climate change.
Published: 2020

13. Molecular networks regulating cell division during Arabidopsis leaf growth

Author: Jasmien Vercruysse, Alexandra Baekelandt, Nathalie Gonzalez, Dirk Inzé, Center for Plant Systems Biology (PSB Center), Vlaams Instituut voor Biotechnologie [Ghent, Belgique] (VIB), Department of Plant Systems Biology, VIB, and Department of Plant Biotechnology and Bioinformatics, Universiteit Gent = Ghent University [Belgium] (UGENT), Biologie du fruit et pathologie (BFP), and Université de Bordeaux (UB)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
Subjects: DEPENDENT KINASE INHIBITORS, 0106 biological sciences, 0301 basic medicine, Cell division, Arabidopsis thaliana, Physiology, [SDV]Life Sciences [q-bio], Arabidopsis, GENE FAMILY, Plant Science, Biology, 01 natural sciences, organ growth, LIGASE BIG BROTHER, 03 medical and health sciences, Gene Expression Regulation, Plant, PLAY DISTINCT ROLES, Gene family, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Transcription factor, Review Papers, ORGAN SIZE, Cell growth, Arabidopsis Proteins, AcademicSubjects/SCI01210, ANAPHASE-PROMOTING COMPLEX/CYCLOSOME, fungi, Biology and Life Sciences, food and beverages, Cell cycle, biology.organism_classification, Cell biology, DNA-Binding Proteins, Plant Leaves, TRANSCRIPTION FACTORS, 030104 developmental biology, cell proliferation, CHROMATIN-REMODELING COMPLEXES, leaf size, UBIQUITIN RECEPTOR DA1, Gibberellin, cell cycle, SMALL AUXIN, Cell Division, leaf development, 010606 plant biology & botany
Abstract: Numerous genes have been identified that regulate leaf growth, which can be grouped into regulatory modules. Here, we review six important gene modules that affect cell proliferation during leaf development., Leaves are the primary organs for photosynthesis, and as such have a pivotal role for plant growth and development. Leaf development is a multifactorial and dynamic process involving many genes that regulate size, shape, and differentiation. The processes that mainly drive leaf development are cell proliferation and cell expansion, and numerous genes have been identified that, when ectopically expressed or down-regulated, increase cell number and/or cell size during leaf growth. Many of the genes regulating cell proliferation are functionally interconnected and can be grouped into regulatory modules. Here, we review our current understanding of six important gene regulatory modules affecting cell proliferation during Arabidopsis leaf growth: ubiquitin receptor DA1–ENHANCER OF DA1 (EOD1), GROWTH REGULATING FACTOR (GRF)–GRF-INTERACTING FACTOR (GIF), SWITCH/SUCROSE NON-FERMENTING (SWI/SNF), gibberellin (GA)–DELLA, KLU, and PEAPOD (PPD). Furthermore, we discuss how post-mitotic cell expansion and these six modules regulating cell proliferation make up the final leaf size.
Published: 2020

14. Mitotic recombination between homologous chromosomes drives genomic diversity in diatoms

Author: Klaas Vandepoele, Thomas Mock, Koen Sabbe, Mirna Sekulic, Chris Bowler, Wim Vyverman, Petra Bulankova, Cristina Maria Osuna-Cruz, Emmelien Vancaester, Cock van Oosterhout, Denis Jallet, Tom O. Delmont, Charlotte Nef, Ilse Vercauteren, Fayza Daboussi, Lieven De Veylder, Center for Plant Systems Biology (PSB Center), Vlaams Instituut voor Biotechnologie [Ghent, Belgique] (VIB), Universiteit Gent = Ghent University (UGENT), Toulouse Biotechnology Institute (TBI), Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut de biologie de l'ENS Paris (IBENS), Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), University of East Anglia [Norwich] (UEA), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-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), The Wellcome Trust Sanger Institute [Cambridge], Gordon and Betty Moore Foundation GBMF 4966, Region Occitanie 15058490, French National Research Agency (ANR) ANR-16-CE05-000601, 3BCAR Carnot Institute, ANR-16-CE05-0006,SynDia,Conception d'une plateforme d'ingénierie génomique pour les microalgues(2016), European Project: 835067,DIATOMIC, Universiteit Gent = Ghent University [Belgium] (UGENT), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut de biologie de l'ENS Paris (UMR 8197/1024) (IBENS), École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Biologie - ENS Paris, and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)
Subjects: SELECTION, 0301 basic medicine, Mitotic crossover, DNA Copy Number Variations, Cell division, HETEROZYGOSITY, [SDV]Life Sciences [q-bio], Population, Genetics and Molecular Biology, Biology, CLONAL INTERFERENCE, SEQUENCE, Chromosomes, General Biochemistry, Genetics and Molecular Biology, MECHANISMS, Loss of heterozygosity, 03 medical and health sciences, 0302 clinical medicine, REVEALS, Homologous chromosome, YEAST, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Copy-number variation, Genetic variability, ADAPTATION, education, Alleles, Diatoms, Genetics, education.field_of_study, Clonal interference, Biology and Life Sciences, LIFE-CYCLE, EVOLUTION, 030104 developmental biology, General Biochemistry, General Agricultural and Biological Sciences, Cell Division, 030217 neurology & neurosurgery
Abstract: International audience; Diatoms, an evolutionarily successful group of microalgae, display high levels of intraspecific genetic variability in natural populations. However, the contribution of various mechanisms generating such diversity is unknown. Here we estimated the genetic micro-diversity within a natural diatom population and mapped the genomic changes arising within clonally propagated diatom cell cultures. Through quantification of haplotype diversity by next-generation sequencing and amplicon re-sequencing of selected loci, we documented a rapid accumulation of multiple haplotypes accompanied by the appearance of novel protein variants in cell cultures initiated from a single founder cell. Comparison of the genomic changes between mother and daughter cells revealed copy number variation and copy-neutral loss of heterozygosity leading to the fixation of alleles within individual daughter cells. The loss of heterozygosity can be accomplished by recombination between homologous chromosomes. To test this hypothesis, we established an endogenous readout system and estimated that the frequency of interhomolog mitotic recombination was under standard growth conditions 4.2 events per 100 cell divisions. This frequency is increased under environmental stress conditions, including treatment with hydrogen peroxide and cadmium. These data demonstrate that copy number variation and mitotic recombination between homologous chromosomes underlie clonal variability in diatom populations. We discuss the potential adaptive evolutionary benefits of the plastic response in the interhomolog mitotic recombination rate, and we propose that this may have contributed to the ecological success of diatoms.
Published: 2021

15. Unraveling new molecular players involved in the autoregulation of nodulation in Medicago truncatula

Author: Pierre Gautrat, Annick De Keyser, Sofie Goormachtig, Carole Laffont, Florian Frugier, Virginie Mortier, Justine Fromentin, Institut des Sciences des Plantes de Paris-Saclay (IPS2 (UMR_9213 / UMR_1403)), Institut National de la Recherche Agronomique (INRA)-Université Paris-Sud - Paris 11 (UP11)-Université Paris Diderot - Paris 7 (UPD7)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Universiteit Gent = Ghent University [Belgium] (UGENT), Center for Plant Systems Biology (PSB Center), Vlaams Instituut voor Biotechnologie [Ghent, Belgique] (VIB), Laboratoire des interactions plantes micro-organismes (LIPM), Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Labex 'Saclay Plant Science', Lidex 'Plant Phenotyping Pipeline' (3P), Research Foundation-Flanders : G.0350.04N, G.0066.07N : Paris-Saclay University, Institut National de la Recherche Agronomique (INRA)-Université Paris-Sud - Paris 11 (UP11)-Université Paris Diderot - Paris 7 (UPD7)-Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Department of Plant Systems Biology, State University of Ghent, Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA), and Universiteit Gent = Ghent University (UGENT)
Subjects: 0106 biological sciences, 0301 basic medicine, Physiology, PROTEIN, Plant Science, 01 natural sciences, F-box protein, Plant Root Nodulation, Transcriptome, Gene Expression Regulation, Plant, SIGNALS, Homeostasis, ComputingMilieux_MISCELLANEOUS, Plant Proteins, SEQUENCE ALIGNMENT, biology, Autoregulation of nodulation (AON), food and beverages, Research Papers, Medicago truncatula, Cell biology, CLE PEPTIDES, RECEPTOR KINASE, REGULATES NODULE NUMBER, Root Nodules, Plant, Lotus japonicus, Down-Regulation, rhizobia, Rhizobia, 03 medical and health sciences, Gene silencing, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Gene, PERCEPTION, Nod factor perception (NFP), fungi, Biology and Life Sciences, Too Much Love (TML), biology.organism_classification, symbiotic nodulation, GENE, TRANSPORT, CLAVATA signaling peptide, ROOT DEVELOPMENT, 030104 developmental biology, Plant—Environment Interactions, biology.protein, Ectopic expression, 010606 plant biology & botany
Abstract: We provide new insights into the autoregulation of nodulation that allow us to better understand how the legume Medicago truncatula restricts further nodulation once enough nodules have been formed., The number of legume root nodules resulting from a symbiosis with rhizobia is tightly controlled by the plant. Certain members of the CLAVATA3/Embryo Surrounding Region (CLE) peptide family, specifically MtCLE12 and MtCLE13 in Medicago truncatula, act in the systemic autoregulation of nodulation (AON) pathway that negatively regulates the number of nodules. Little is known about the molecular pathways that operate downstream of the AON-related CLE peptides. Here, by means of a transcriptome analysis, we show that roots ectopically expressing MtCLE13 deregulate only a limited number of genes, including three down-regulated genes encoding lysin motif receptor-like kinases (LysM-RLKs), among which are the nodulation factor (NF) receptor NF Perception gene (NFP) and two up-regulated genes, MtTML1 and MtTML2, encoding Too Much Love (TML)-related Kelch-repeat containing F-box proteins. The observed deregulation was specific for the ectopic expression of nodulation-related MtCLE genes and depended on the Super Numeric Nodules (SUNN) AON RLK. Moreover, overexpression and silencing of these two MtTML genes demonstrated that they play a role in the negative regulation of nodule numbers. Hence, the identified MtTML genes are the functional counterpart of the Lotus japonicus TML gene shown to be central in the AON pathway. Additionally, we propose that the down-regulation of a subset of LysM-RLK-encoding genes, among which is NFP, might contribute to the restriction of further nodulation once the first nodules have been formed.
Published: 2019

16. RNAi-suppression of barley caffeic acid O-methyltransferase modifies lignin despite redundancy in the gene family

Author: David Marshall, Ruben Vanholme, Marta Maluk, Abdellah Barakate, Yukiko Tsuji, Claire Halpin, Wout Boerjan, Paul Daly, John Ralph, Jennifer Stephens, Catherine Lapierre, Christopher McClellan, Robbie Waugh, Geert Goeminne, Helena Oakey, University of Dundee, University of Adelaide, Institut Jean-Pierre Bourgin (IJPB), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Université Paris Saclay (COmUE), The James Hutton Institute, Cell and Molecular Sciences, University of Wisconsin-Madison, Universiteit Gent = Ghent University [Belgium] (UGENT), Center for Plant Systems Biology (PSB Center), Vlaams Instituut voor Biotechnologie [Ghent, Belgique] (VIB), Univ Ghent, Dept Plant Biotechnol & Bioinformat, Ghent, Belgium, and Partenaires INRAE
Subjects: 0106 biological sciences, 0301 basic medicine, brown-midrib, DOWN-REGULATION, [SDV]Life Sciences [q-bio], Cinnamyl-alcohol dehydrogenase, Mutant, straw, Plant Science, 01 natural sciences, 7. Clean energy, chemistry.chemical_compound, Gene Expression Regulation, Plant, RNA interference, MOLECULAR-BASIS, SACCHARIFICATION, [SDV.IDA]Life Sciences [q-bio]/Food engineering, Caffeic acid, Lignin, caffeic acid O-methyltransferase (comt), MUTATION, Phylogeny, Research Articles, Plant Proteins, 2. Zero hunger, food and beverages, caffeic acid O-methyltransferase (COMT), brown‐midrib, barley (Hordeum vulgare), Biochemistry, RNA Interference, Brachypodium, Research Article, Biotechnology, EXPRESSION, lignin, Biology, Genes, Plant, behavioral disciplines and activities, 03 medical and health sciences, biofuels, CINNAMYL ALCOHOL-DEHYDROGENASE, mental disorders, LIGNIFICATION, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Gene family, [SPI.GPROC]Engineering Sciences [physics]/Chemical and Process Engineering, BIOSYNTHESIS, caffeic acid O‐methyltransferase (COMT), REDUCES RECALCITRANCE, fungi, Biology and Life Sciences, Hordeum, Methyltransferases, biology.organism_classification, 030104 developmental biology, chemistry, Biofuels, ARABIDOPSIS-THALIANA, Hordeum vulgare, Agronomy and Crop Science, 010606 plant biology & botany
Abstract: International audience; Caffeic acid O-methyltransferase (COMT), the lignin biosynthesis gene modified in many brown-midrib high-digestibility mutants of maize and sorghum, was targeted for downregulation in the small grain temperate cereal, barley (Hordeum vulgare), to improve straw properties. Phylogenetic and expression analyses identified the barley COMT orthologue(s) expressed in stems, defining a larger gene family than in brachypodium or rice with three COMT genes expressed in lignifying tissues. RNAi significantly reduced stem COMT protein and enzyme activity, and modestly reduced stem lignin content while dramatically changing lignin structure. Lignin syringyl-to-guaiacyl ratio was reduced by similar to 50%, the 5-hydroxyguaiacyl (5-OH-G) unit incorporated into lignin at 10--15-fold higher levels than normal, and the amount of p-coumaric acid ester-linked to cell walls was reduced by similar to 50%. No brown-midrib phenotype was observed in any RNAi line despite significant COMT suppression and altered lignin. The novel COMT gene family structure in barley highlights the dynamic nature of grass genomes. Redundancy in barley COMTs may explain the absence of brown-midrib mutants in barley and wheat. The barley COMT RNAi lines nevertheless have the potential to be exploited for bioenergy applications and as animal feed.
Published: 2019

17. Design and visualization of second-generation cyanoisoindole-based fluorescent strigolactone analogs

Author: Sofie Goormachtig, Anna M. Kaczmarek, Lukas Braem, Sylwia Magdalena Struk, Rik Van Deun, François-Didier Boyer, Melissa Van Overtveldt, Thomas S. A. Heugebaert, Christian V. Stevens, Kris Gevaert, Université d’Opole, Universiteit Gent = Ghent University [Belgium] (UGENT), Dept Med Prot Res, Flanders Institute for Biotechnology, Center for Plant Systems Biology (PSB Center), Vlaams Instituut voor Biotechnologie [Ghent, Belgique] (VIB), and Research Foundation - Flanders (FWO Vlaanderen)
Subjects: 0106 biological sciences, 0301 basic medicine, Arabidopsis, Strigolactone, Repressor, parasitic seed germination, Germination, Plant Science, Protein degradation, fluorescence labeling, 01 natural sciences, smxl6 degradation, 03 medical and health sciences, Lactones, Plant Growth Regulators, In vivo, Genetics, Arabidopsis thaliana, Moiety, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, strigolactone, Fluorescent Dyes, biology, Arabidopsis Proteins, hypocotyl elongation, arabidopsis thaliana, Cell Biology, phelipanche ramosa, biology.organism_classification, isoindole, Fluorescence, Terpenoid, Hypocotyl, 030104 developmental biology, Biochemistry, pyrroloindole, Proteolysis, Seeds, 010606 plant biology & botany, Signal Transduction
Abstract: International audience; Strigolactones (SLs) are a family of terpenoid allelochemicals that were recognized as plant hormones only a decade ago. They influence a myriad of both above- and below-ground developmental processes, and are an important survival strategy for plants in nutrient-deprived soils. A rapidly emerging approach to gain knowledge on hormone signaling is the use of traceable analogs. A unique class of labeled SL analogs was constructed, in which the original tricyclic lactone moiety of natural SLs is replaced by a fluorescent cyanoisoindole ring system. Biological evaluation as parasitic seed germination stimulant and hypocotyl elongation repressor proved the potency of the cyanoisoindole strigolactone analogs (CISAs) to be comparable to the commonly accepted standard GR24. Additionally, via a SMXL6 protein degradation assay, we provided molecular evidence that the compounds elicit SL-like responses through the natural signaling cascade. All CISAs were shown to exhibit fluorescent properties, and the high quantum yield and Stokes shift of the pyrroloindole derivative CISA-7 also enabled in vivo visualization in plants. In contrast to the previously reported fluorescent analogs, CISA-7 displays a large similarity in shape and structure with natural SLs, which renders the analog a promising tracer to investigate the spatiotemporal distribution of SLs in plants and fungi.
Published: 2018

18. Quantitative Tandem Affinity Purification, an Effective Tool to Investigate Protein Complex Composition in Plant Hormone Signaling: Strigolactones in the Spotlight

Author: Sylwia Struk, Lukas Braem, Alan Walton, Annick De Keyser, François-Didier Boyer, Geert Persiau, Geert De Jaeger, Kris Gevaert, Sofie Goormachtig, Center for Plant Systems Biology (PSB Center), Vlaams Instituut voor Biotechnologie [Ghent, Belgique] (VIB), Institut de Chimie des Substances Naturelles (ICSN), Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC), Department of Plant Systems Biology, Department of Plant Biotechnology and Genetics, Universiteit Gent = Ghent University [Belgium] (UGENT), Flanders Institute for Biotechnology, Dept Med Prot Res, Strategic-Basic-Research fellowship of the Research Foundation-Flanders, and Goormachtig, Sofie
Subjects: strigolactones, SMXL7, qTAP, plant hormone signaling, protein dynamics, 0106 biological sciences, 0301 basic medicine, TRANSCRIPTION FACTOR COMPLEXES, Repressor, Plant Science, lcsh:Plant culture, Proteomics, 01 natural sciences, 03 medical and health sciences, Methods, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Arabidopsis thaliana, lcsh:SB1-1110, Mode of action, SHOOT DEVELOPMENT, Tandem affinity purification, IDENTIFICATION, biology, Chemistry, Protein dynamics, Biology and Life Sciences, REPRESSOR, MASS-SPECTROMETRY, DEGRADATION, QUANTIFICATION, biology.organism_classification, Cell biology, 030104 developmental biology, ARABIDOPSIS-THALIANA, PROTEOMICS, GROWTH, Plant hormone, Signal transduction, 010606 plant biology & botany
Abstract: International audience; Phytohormones tightly regulate plant growth by integrating changing environmental and developmental cues. Although the key players have been identified in many plant hormonal pathways, the molecular mechanisms and mode of action of perception and signaling remain incompletely resolved. Characterization of protein partners of known signaling components provides insight into the formed protein complexes, but, unless quantification is involved, does not deliver much, if any, information about the dynamics of the induced or disrupted protein complexes. Therefore, in proteomics research, the discovery of what actually triggers, regulates or interrupts the composition of protein complexes is gaining importance. Here, tandem affinity purification coupled to mass spectrometry (TAP-MS) is combined with label-free quantification (LFQ) to a highly valuable tool to detect physiologically relevant, dynamic protein-protein interactions in Arabidopsis thaliana cell cultures. To demonstrate its potential, we focus on the signaling pathway of one of the most recently discovered phytohormones, strigolactones.
Published: 2018

19. The Physcomitrella patens chromosome-scale assembly reveals moss genome structure and evolution

Author: Cristina Vives, Sebastian N. W. Hoernstein, Dennis W. Stevenson, Anders Larsson, Klaus F. X. Mayer, Fabian B. Haas, Jane Grimwood, Priya Ranjan, Lucas Schneider, Yong Zhang, Ralf Reski, Florian Maumus, Stuart F. McDaniel, Michael Tillich, Thomas Widiez, Carl J. Rothfels, Andreas Zimmer, Daniel S. Rokshar, Yasuko Kamisugi, Heidrun Gundlach, Sean W. Graham, Klaas Vandepoele, Richard D. Hayes, Aikaterini Symeonidi, Omar Abu Saleh, Andrew C. Cuming, Jeremy Schmutz, Jordi Morata, Shengqiang Shu, Jérôme Salse, Joerg Fuchs, Ralph S. Quatrano, Daniel Lang, Juan Carlos Villarreal Aguilar, Kristian K. Ullrich, Gerald A. Tuskan, Fay-Wei Li, Mathieu Piednoël, Pierre-François Perroud, Florent Murat, Ann M. Wymore, Gane Ka-Shu Wong, Manuel Hiss, Jerry Jenkins, Lee E. Gunter, Josep M. Casacuberta, Nico van Gessel, Wellington Muchero, Jeremy Phillips, Michiel Van Bel, Eva L. Decker, Rabea Meyberg, Stefan A. Rensing, Guillaume Blanc, Fritz Thümmler, David Goodstein, Fakultät für Biologie = Faculty of Biology [Freiburg], Albert-Ludwigs-Universität Freiburg, Génétique Diversité et Ecophysiologie des Céréales (GDEC), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), United States Department of Energy, Institut méditerranéen d'océanologie (MIO), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Toulon (UTLN), Inst Bioinformat & Syst Biol, Munich Informat Ctr Prot Sequences, Helmholtz-Zentrum München (HZM), Center for Research in Agricultural Genomics, Freiburg Initiative in Systems Biology, University of Freiburg [Freiburg], Laboratoire de Physique Statistique de l'ENS (LPS), Fédération de recherche du Département de physique de l'Ecole Normale Supérieure - ENS Paris (FRDPENS), Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université Paris Diderot - Paris 7 (UPD7)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Department of Energy / Joint Genome Institute (DOE), Los Alamos National Laboratory (LANL), London School of Hygiene and Tropical Medicine (LSHTM), Luleå University of Technology (LUT), BioSciences Division [Oak Ridge], Oak Ridge National Laboratory [Oak Ridge] (ORNL), UT-Battelle, LLC-UT-Battelle, LLC, Reproduction et développement des plantes (RDP), Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA)-École normale supérieure - Lyon (ENS Lyon), Department of Biological Sciences [Edmonton], University of Alberta, Wolfgang Pauli Institute (WPI), University of Vienna [Vienna], Department of Molecular Psychiatry, Rheinische Friedrich-Wilhelms-Universität Bonn, Center for Plant Systems Biology (PSB Center), Vlaams Instituut voor Biotechnologie [Ghent, Belgique] (VIB), Plant Biotechnology, Faculty of Biology, University of Freiburg, Unité de Recherche Génomique Info (URGI), Institut National de la Recherche Agronomique (INRA), Office of Science of the US Department of Energy [DEAC02-05CH11231], German Research Foundation [DFG RE 837/10-2], Excellence Initiative of the German Federal and State Governments [EXC 294], German Federal Ministry of Education and Research [BMBF FRISYS], US National Science Foundation [IOS339156, IOS-1444490], U.S. National Science Foundation [DBI-0735191, DBI-1265383], UK Biological Sciences and Biotechnology Research Council [BB/F001797/1], Ghent University’s Multidisciplinary Research Partnership ‘Bioinformatics: from nucleotides to networks’ Project [01MR0410W], Spanish Ministerio de Economıa y Competitividad [AGL2013-43244-R], Alberta Ministry of Innovation and Advanced Education, Alberta Innovates Technology Futures (AITF), Innovates Centres of Research Excellence (iCORE), Musea Ventures, BGI-Shenzhen and China National Genebank (CNGB), EMBO Long-Term Fellowships [ALTF 1166-2011], German Research Foundation [SFB924], German Ministry of Education and Research [BMBF, 031A536/de.NBI], European Project: 267146,EC:FP7:PEOPLE,FP7-PEOPLE-2010-COFUND,EMBOCOFUND2010(2011), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), Helmholtz Zentrum München = German Research Center for Environmental Health, École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Diderot - Paris 7 (UPD7)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), École normale supérieure de Lyon (ENS de Lyon)-Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Biotechnology and Biological Sciences Research Council (UK), Ministerio de Economía y Competitividad (España), European Commission, Génétique Diversité et Ecophysiologie des Céréales - Clermont Auvergne (GDEC), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne (UCA), Centre National de la Recherche Scientifique (CNRS)-Université de Toulon (UTLN)-Aix Marseille Université (AMU)-Institut de Recherche pour le Développement (IRD), Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris)-Université Paris Diderot - Paris 7 (UPD7)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), École normale supérieure - Lyon (ENS Lyon)-Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), VIB Department of Plant Systems Biology, Ghent University [Belgium] (UGENT), Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Institut National de la Recherche Agronomique (INRA), and École normale supérieure - Paris (ENS Paris)
Subjects: 0301 basic medicine, Sequence assembly, Plant Biology, plant, Plant Science, Genome, Gene duplication, chromosome, ComputingMilieux_MISCELLANEOUS, Recombination, Genetic, biology, synteny, food and beverages, Single Nucleotide, Biological Evolution, Chromatin, ddc:580, duplication, Evolution, Chromosome, Plant, Moss, Methylation, Duplication, Synteny, Physcomitrella Patens, Physcomitrellapatens, Genome, Plant, Biotechnology, Transposable element, Centromere, Plant Biology & Botany, Physcomitrella patens, Polymorphism, Single Nucleotide, Chromosomes, Plant, Chromosomes, moss, 03 medical and health sciences, Genetic, evolution, Genetics, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Polymorphism, Gene, genome, Human Genome, Genetic Variation, Cell Biology, DNA Methylation, biology.organism_classification, Bryopsida, Recombination, 030104 developmental biology, Evolutionary biology, DNA Transposable Elements, Biochemistry and Cell Biology, methylation
Abstract: et al., The draft genome of the moss model, Physcomitrella patens, comprised approximately 2000 unordered scaffolds. In order to enable analyses of genome structure and evolution we generated a chromosome-scale genome assembly using genetic linkage as well as (end) sequencing of long DNA fragments. We find that 57% of the genome comprises transposable elements (TEs), some of which may be actively transposing during the life cycle. Unlike in flowering plant genomes, gene- and TE-rich regions show an overall even distribution along the chromosomes. However, the chromosomes are mono-centric with peaks of a class of Copia elements potentially coinciding with centromeres. Gene body methylation is evident in 5.7% of the protein-coding genes, typically coinciding with low GC and low expression. Some giant virus insertions are transcriptionally active and might protect gametes from viral infection via siRNA mediated silencing. Structure-based detection methods show that the genome evolved via two rounds of whole genome duplications (WGDs), apparently common in mosses but not in liverworts and hornworts. Several hundred genes are present in colinear regions conserved since the last common ancestor of plants. These syntenic regions are enriched for functions related to plant-specific cell growth and tissue organization. The P. patens genome lacks the TE-rich pericentromeric and gene-rich distal regions typical for most flowering plant genomes. More non-seed plant genomes are needed to unravel how plant genomes evolve, and to understand whether the P. patens genome structure is typical for mosses or bryophytes., The work conducted by the US Department of Energy Joint Genome Institute is supported by the Office of Science of the US Department of Energy under Contract No. DE-AC02-05CH11231. Support to RR and SAR by the German Research Foundation (DFG RE 837/10-2), the Excellence Initiative of the German Federal and State Governments (EXC 294), and by the German Federal Ministry of Education and Research (BMBF FRISYS), is highly appreciated. CoGe is supported by the US National Science Foundation under Award Numbers IOS-339156 and IOS-1444490, CyVerse is supported by the U.S. National Science Foundation under Award Numbers DBI-0735191 and DBI-1265383. YK and ACC are grateful for support from the UK Biological Sciences and Biotechnology Research Council (Grant BB/F001797/1). KV acknowledges the Multidisciplinary Research Partnership ‘Bioinformatics: from nucleotides to networks’ Project (no 01MR0410W) of Ghent University. JC is grateful for support from the Spanish Ministerio de Economía y Competitividad (Grant AGL2013-43244-R). RSQ is grateful to Monsanto (St. Louis, MO, USA) for sequencing genomic DNA of P. patens accession Kaskaskia. The 1000 Plants (1 KP) initiative, led by GKSW, is funded by the Alberta Ministry of Innovation and Advanced Education, Alberta Innovates Technology Futures (AITF), Innovates Centres of Research Excellence (iCORE), Musea Ventures, BGI-Shenzhen and China National Genebank (CNGB). TW was supported by EMBO Long-Term Fellowships (ALTF 1166-2011) and by Marie Curie Actions (European Commission EMBOCOFUND2010, GA-2010-267146). The work conducted at PGSB was supported by the German Research Foundation (SFB924) and German Ministry of Education and Research (BMBF, 031A536/de.NBI).
Published: 2018

20. Gearing up to handle the mosaic nature of life in the quest for orthologs

Author: Forslund, Kristoffer, Pereira, Cécile, Capella-Gutiérrez, Salvador, da Silva, Alan Sousa, Altenhoff, Adrian, Huerta-Cepas, Jaime, Muffato, Matthieu, Patricio, Mateus, Vandepoele, Klaas, Ebersberger, Ingo, Blake, Judith, Fernández Breis, Jesualdo Tomás, Boeckmann, Brigitte, Gabaldon, Toni, Sonnhammer, Erik, Dessimoz, Christophe, Lewis, Suzanna, Bello, Carla, Briois, Sébastien, Chalstrey, Edward, Chiba, Hirokazu, Conchillo-Solé, Oscar, Daubin, Vincent, DeLuca, Todd, Dufayard, Jean-François, Durand, Dannie, Fernández-Breis, Jesualdo Tomás, Glover, Natasha, Hauser, Alexander, Heller, Davide, Kaduk, Mateus, Koch, Jan, Koonin, Eugene, Kriventseva, Evgenia, Kuraku, Shigehiro, Lecompte, Odile, Lespinet, Olivier, Levy, Jeremy, Liebeskind, Benjamin, Linard, Benjamin, Marcet-Houben, Marc, Kauffmann, Martin, McWhite, Claire, Mekhedov, Sergei, Moretti, Sebastien, Müller, Steven, Nadia, El-Mabrouk, Notredame, Cedric, Penel, Simon, Pilizota, Ivana, Redestig, Henning, Robinson-Rechavi, Marc, Schreiber, Fabian, Sjölander, Kimmen, Škunca, Nives, Steinegger, Martin, Szklarczyk, Damian, Thomas, Paul, Thuer, Ernst, Train, Clément, Uchiyama, Ikuo, Wittwer, Lucas, Xenarios, Ioannis, Yates, Bethan, Zdobnov, Evgeny, Waterhouse, Robert, European Molecular Biology Laboratory [Heidelberg] (EMBL), University of Florida [Gainesville], Institut de Biologie Intégrative de la Cellule (I2BC), Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Bioinformatique (LRI) (BioInfo - LRI), Laboratoire de Recherche en Informatique (LRI), Université Paris-Sud - Paris 11 (UP11)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Sud - Paris 11 (UP11)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS), Universitat Pompeu Fabra [Barcelona], Swiss Institute of Bioinformatics (SIB), Centre for Genomic Regulation (CRG), European Bioinformatics Institute [Hinxton] (EMBL-EBI), EMBL Heidelberg, VIB Department of Plant Systems Biology, Ghent University [Belgium] (UGENT), Senckenberg Climate and Research, Applied Bioinformatics, University of Southern California (USC), Department of Computer Science, Laboratoire de Biologie Cellulaire et Moléculaire du Contrôle de la Prolifération (LBCMCP), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Bioinformatique, phylogénie et génomique évolutive (BPGE), Département PEGASE [LBBE] (PEGASE), Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Harvard Medical School [Boston] (HMS), Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), 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), Universidad de Murcia, National Center for Biotechnology Information (NCBI), University of Geneva Medical School, Genome Resource and Analysis Unit (GRAS), RIKEN Center for Developmental Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Université de Strasbourg (UNISTRA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS), Méthodes et Algorithmes pour la Bioinformatique (MAB), 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), Swiss Institute of Bioinformatics, Comparative Bioinformatics, Department of Ecology and Evolution, Université de Lausanne (UNIL), Lawrence Berkeley National Laboratory [Berkeley] (LBNL), Universität Zürich [Zürich] (UZH), Defence Science and Technology Laboratory (Dstl), Ministry of Defence (UK) (MOD), Swiss Institute of Bioinformatics [Genève] (SIB), Medical School, Université de Genève (UNIGE), University of Florida [Gainesville] (UF), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Universitat Pompeu Fabra [Barcelona] (UPF), Swiss Institute of Bioinformatics [Lausanne] (SIB), Center for Plant Systems Biology (PSB Center), Vlaams Instituut voor Biotechnologie [Ghent, Belgique] (VIB), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Centre de Biologie Intégrative (CBI), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), 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), Department of Ecology and Evolution [Lausanne], Universität Zürich [Zürich] = University of Zurich (UZH), 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 National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Université de Lausanne = University of Lausanne (UNIL), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Centre de Biologie Intégrative (CBI), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Université de Genève = University of Geneva (UNIGE), European Molecular Biology Laboratory [Heidelberg] ( EMBL ), University of Florida [Gainesville] ( UF ), Institut de Biologie Intégrative de la Cellule ( I2BC ), Université Paris-Sud - Paris 11 ( UP11 ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ), Bioinformatique (LRI) ( BioInfo - LRI ), Laboratoire de Recherche en Informatique ( LRI ), Université Paris-Sud - Paris 11 ( UP11 ) -Institut National de Recherche en Informatique et en Automatique ( Inria ) -CentraleSupélec-Centre National de la Recherche Scientifique ( CNRS ) -Université Paris-Sud - Paris 11 ( UP11 ) -Institut National de Recherche en Informatique et en Automatique ( Inria ) -CentraleSupélec-Centre National de la Recherche Scientifique ( CNRS ), Centre for Genomic Regulation ( CRG ), European Bioinformatics Institute [Hinxton] ( EMBL-EBI ), European Molecular Biology Laboratory [Hinxton], Ghent University [Belgium] ( UGENT ), Center for Integrative Bioinformatics Vienna, Max F. Perutz Laboratories, University of Southern California ( USC ), Swiss Federal Institute of Technology in Zürich ( ETH Zürich ), LBCMCP, Centre National de la Recherche Scientifique ( CNRS ), Laboratoire de Biométrie et Biologie Evolutive ( LBBE ), Université Claude Bernard Lyon 1 ( UCBL ), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique ( Inria ) -Centre National de la Recherche Scientifique ( CNRS ), Harvard Medical School [Boston] ( HMS ), Amélioration génétique et adaptation des plantes méditerranéennes et tropicales ( UMR AGAP ), Institut national de la recherche agronomique [Montpellier] ( INRA Montpellier ) -Centre international d'études supérieures en sciences agronomiques ( Montpellier SupAgro ) -Centre de Coopération Internationale en Recherche Agronomique pour le Développement ( CIRAD ) -Institut national d’études supérieures agronomiques de Montpellier ( Montpellier SupAgro ), National Center for Biotechnology Information ( NCBI ), Genome Resource and Analysis Unit ( GRAS ), Institut de Génétique et de Biologie Moléculaire et Cellulaire ( IGBMC ), Université de Strasbourg ( UNISTRA ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Centre National de la Recherche Scientifique ( CNRS ), Méthodes et Algorithmes pour la Bioinformatique ( MAB ), 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 ), Université de Lausanne ( UNIL ), University of California [Berkeley], Universität Zürich [Zürich] ( UZH ), Defence Science and Technology Laboratory ( Dstl ), Ministry of Defence (UK) ( MOD ), Swiss Institute of Bioinformatics [Genève] ( SIB ), Université de Genève ( UNIGE ), Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Saclay, Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Toulouse III - Paul Sabatier (UT3), and Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées
Subjects: [ INFO.INFO-BI ] Computer Science [cs]/Bioinformatics [q-bio.QM], [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], ComputingMilieux_MISCELLANEOUS
Abstract: International audience; The Quest for Orthologs (QfO) is an open collaboration framework for experts in comparative phylogenomics and related research areas who have an interest in highly accurate orthology predictions and their applications. We here report highlights and discussion points from the QfO meeting 2015 held in Barcelona. Achievements in recent years have established a basis to support developments for improved orthology prediction and to explore new approaches. Central to the QfO effort is proper benchmarking of methods and services, as well as design of standardized datasets and standardized formats to allow sharing and comparison of results. Simultaneously, analysis pipelines have been improved, evaluated and adapted to handle large datasets. All this would not have occurred without the long-term collaboration of Consortium members. Meeting regularly to review and coordinate complementary activities from a broad spectrum of innovative researchers clearly benefits the community. Highlights of the meeting include addressing sources of and legitimacy of disagreements between orthology calls, the context dependency of orthology definitions, special challenges encountered when analyzing very anciently rooted orthologies, orthology in the light of whole-genome duplications, and the concept of orthologous versus paralogous relationships at different levels, including domain-level orthology. Furthermore, particular needs for different applications (e.g. plant genomics, ancient gene families and others) and the infrastructure for making orthol-ogy inferences available (e.g. interfaces with model organism databases) were discussed, with several ongoing efforts that are expected to be reported on during the upcoming 2017 QfO meeting.
Published: 2018

21. Ten steps to get started in Genome Assembly and Annotation

Author: Lieven Sterck, Brane Leskošek, Lucile Soler, Cederic Notredame, Erik Hjerde, Stéphanie Bocs, Mahesh Binzer-Panchal, Laurent Bouri, Henrik Lantz, Joelle Amselem, Christophe Klopp, Jean-François Gibrat, Olga Vinnere Pettersson, Salvadors Capella-Gutierrez, Anna Vlasova, Victoria Dominguez Del Angel, Institut Français de Bioinformatique, Université Paris-Saclay, Department of Chemistry, RIDER UNIVERSITY, Department of Plant Biotechnology and Bioinformatics, Ghent University [Belgium] (UGENT), Department of Plant Systems Biology, VIB, Spanish National Bioinformatics Institute (INB), Centro Nacional de Supercomputación, BSC Electronics, Centre for Genomic Regulation (CRG), Universitat Pompeu Fabra [Barcelona], Uppsala Genome Center, NGI/SciLifeLab - Department of Immunology, Genetics and Pathology, Uppsala University, Unité de Recherche Génomique Info (URGI), Institut National de la Recherche Agronomique (INRA), Université de Tunis [Tunis], Laboratory of Technologies of Information and Communication and Electrical Engineering, National Superior School of Engineers of Tunis, Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), 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), South Green Bioinformatics Platform, Unité de Mathématiques et Informatique Appliquées de Toulouse (MIAT INRA), Mathématiques et Informatique Appliquées du Génome à l'Environnement [Jouy-En-Josas] (MaIAGE), Faculty of Medicine, Institute for Biostatistics and Medical Informatics, University of Ljubljana, IMBIM/NBIS/SciLifeLab, Institut Français de Bioinformatique - UMS CNRS 3601 (IFB-CORE), Institut National de la Recherche Agronomique (INRA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM), Universiteit Gent = Ghent University [Belgium] (UGENT), Center for Plant Systems Biology (PSB Center), Vlaams Instituut voor Biotechnologie [Ghent, Belgique] (VIB), Barcelona Supercomputing Center - Centro Nacional de Supercomputacion (BSC - CNS), Universitat Pompeu Fabra [Barcelona] (UPF), Université de Tunis, 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 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), Barcelona Supercomputing Center, Institut National de la Recherche Agronomique (INRA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Universiteit Gent = Ghent University (UGENT), South Green Bioinformatics Platform [Montpellier], and Hjerde, Erik
Subjects: 0301 basic medicine, Computer science, General assembly, Data management, [SDV]Life Sciences [q-bio], Annotation, Interoperability, Assembly, Sequence assembly, Bioinformatik och systembiologi, Genome, General Biochemistry, Genetics and Molecular Biology, F30 - Génétique et amélioration des plantes, Workflows, World Wide Web, 03 medical and health sciences, DNA--Analysis, Genomes, General Pharmacology, Toxicology and Pharmaceutics, ADN--Anàlisi, FAIR, Genome assembly, Bioinformatics and Systems Biology, General Immunology and Microbiology, business.industry, Biology and Life Sciences, General Medicine, Genome project, Articles, DNA, Opinion Article, L10 - Génétique et amélioration des animaux, ELIXIR-EXCELERATE, 030104 developmental biology, Workflow, NGS, business, Ciències de la salut [Àrees temàtiques de la UPC], Genome annotation
Abstract: As a part of the ELIXIR-EXCELERATE efforts in capacity building, we present here 10 steps to facilitate researchers getting started in genome assembly and genome annotation. The guidelines given are broadly applicable, intended to be stable over time, and cover all aspects from start to finish of a general assembly and annotation project. Intrinsic properties of genomes are discussed, as is the importance of using high quality DNA. Different sequencing technologies and generally applicable workflows for genome assembly are also detailed. We cover structural and functional annotation and encourage readers to also annotate transposable elements, something that is often omitted from annotation workflows. The importance of data management is stressed, and we give advice on where to submit data and how to make your results Findable, Accessible, Interoperable, and Reusable (FAIR). ELIXIR-EXCELERATE is funded by the European Commission within the Research Infrastructures Programme of Horizon 2020 [676559].
Published: 2018

22. Methodologies for in vitro and in vivo evaluation of efficacy of antifungal and antibiofilm agents and surface coatings against fungal biofilms

Author: Elizabeth M. Johnson, Mahmoud A. Ghannoum, Michael R. Yeaman, Carol A. Munro, Patrick Van Dijck, Jeniel E. Nett, Dominique Sanglard, Richard Calderone, Leah E. Cowen, Johan Maertens, Maiken Cavling Arendrup, Axel A. Brakhage, Judith Berman, Katrien Lagrou, Christophe d'Enfert, Karin Thevissen, Paul Cos, Gordon Ramage, Jelmer Sjollema, Tom Coenye, Isabel Spriet, Paul E. Verweij, Jose L. Lopez-Ribot, Ana Espinel-Ingroff, Sebastian A. J. Zaat, Emilia Cantón, Mary Ann Jabra-Rizk, David R. Andes, Neil A. R. Gow, Scott G. Filler, Mira Edgerton, Maurizio Sanguinetti, Michael A. Pfaller, Joost Wauters, Bruno P. A. Cammue, Clarissa J. Nobile, Hubertus Haas, Adilia Warris, Shawn R. Lockhart, Van Dijck, Patrick, Sjollema, Jelmer, Thevissen, Karin, Catholic University of Leuven - Katholieke Universiteit Leuven (KU Leuven), University Medical Center Groningen [Groningen] (UMCG), Vlaams Instituut voor Biotechnologie [Ghent, Belgique] (VIB), Center for Plant Systems Biology (PSB Center), Tel Aviv University [Tel Aviv], Biologie et Pathogénicité fongiques, Institut Pasteur [Paris]-Institut National de la Recherche Agronomique (INRA), University of Wisconsin-Madison, Statens Serum Institut [Copenhagen], Rigshospitalet [Copenhagen], Copenhagen University Hospital, University of Copenhagen = Københavns Universitet (KU), Leibniz Institute for Natural Product Research and Infection Biology (Hans Knoell Institute), Friedrich-Schiller-Universität = Friedrich Schiller University Jena [Jena, Germany], Georgetown University Medical Center, Medical Research Institute La Fe, Partenaires INRAE, Universiteit Gent = Ghent University [Belgium] (UGENT), ESCMID [Basel], University of Antwerp (UA), University of Toronto, University at Buffalo [SUNY] (SUNY Buffalo), State University of New York (SUNY), Virginia Commonwealth University (VCU), Harbor UCLA Medical Center [Torrance, Ca.], University Hospitals of Cleveland, Case Western Reserve University [Cleveland], University of Aberdeen, Innsbruck Medical University [Austria] (IMU), University of Maryland [Baltimore], Public Health England, Centers for Disease Control and Prevention [Atlanta] (CDC), Centers for Disease Control and Prevention, The University of Texas at San Antonio (UTSA), UZ Leuven, University of California [Merced], University of California, University of Iowa [Iowa City], JMI Laboratories, University of Glasgow, Université de Lausanne (UNIL), Centre Hospitalier Universitaire Vaudois [Lausanne] (CHUV), Università cattolica del Sacro Cuore [Roma] (Unicatt), Radboud university [Nijmegen], Univ Aberdeen, Aberdeen Fungal Grp, MRC Ctr Med Mycol, Foresterhill, Aberdeen, Scotland, University Hospitals Leuven [Leuven], Academic Medical Center - Academisch Medisch Centrum [Amsterdam] (AMC), University of Amsterdam [Amsterdam] (UvA), Industrial Research Fund [IOFm/05/022], Israel Science Foundation [314/13], Wellcome Trust, MRC, Agence Nationale de Recherche [ANR-10-LABX-62-IBEID], National Institutes of Health [R35GM124594, R21AI125801], Wellcome Trust Strategic Award [097377], MRC Centre for Medical Mycology at the University of Aberdeen [MR/N006364/1], Astellas, Basilea, Gilead, MSD, NovaBiotics, Pfizer, T2Biosystems, F2G, Cidara, Amplyx, MRC [MR/N006364/1], FWO [FWO WO.009.16N]., ANR-10-LABX-0062,IBEID,Integrative Biology of Emerging Infectious Diseases(2010), European Project: 340087,EC:FP7:ERC,ERC-2013-ADG,RAPLODAPT(2014), Tel Aviv University (TAU), Biologie et Pathogénicité fongiques (BPF), Institut National de la Recherche Agronomique (INRA)-Institut Pasteur [Paris] (IP), University of Copenhagen = Københavns Universitet (UCPH), Universiteit Gent = Ghent University (UGENT), Innsbruck Medical University = Medizinische Universität Innsbruck (IMU), Universitair Ziekenhuis Leuven (UZ Leuven), University of California [Merced] (UC Merced), University of California (UC), Université de Lausanne = University of Lausanne (UNIL), Università cattolica del Sacro Cuore = Catholic University of the Sacred Heart [Roma] (Unicatt), and Radboud University [Nijmegen]
Subjects: 0301 basic medicine, diagnosis, [SDV]Life Sciences [q-bio], LIPOSOMAL, lnfectious Diseases and Global Health Radboud Institute for Molecular Life Sciences [Radboudumc 4], Applied Microbiology and Biotechnology, immune response, biofilm, High morbidity, transcriptomics, MINIMUM FUNGICIDAL, CONCENTRATIONS, Amphotericin B, eradication, Medicine, GUINEA-PIG MODEL, LIPOSOMAL AMPHOTERICIN-B, lcsh:QH301-705.5, AMPHOTERICIN-B, antibiofilm material coating, antifungal susceptibility testing, biofilm eradication, biofilm inhibition, in vivo models, antifungal susceptibility testing, biofilm inhibition, biofilm eradication, antibiofilm material coating, in vivo models, 3. Good health, CANDIDA-ALBICANS BIOFILMS, GALLERIA-MELLONELLA, Infectious Diseases, tuberculosis, 5.1 Pharmaceuticals, HUMAN-PATHOGENIC FUNGI, Development of treatments and therapeutic interventions, Infection, Fungal biofilm, Life Sciences & Biomedicine, VULVO-VAGINAL CANDIDIASIS, medicine.drug, Antifungal, latent infection, Medical mycology, medicine.drug_class, OXYSPORUM SPECIES COMPLEX, 030106 microbiology, INVASIVE PULMONARY ASPERGILLOSIS, Biochemistry, Genetics and Molecular Biology (miscellaneous), Microbiology, GALLERIA-MELLONELLA LARVAE, 03 medical and health sciences, proteomics, In vivo, Virology, Genetics, Molecular Biology, Biology, Science & Technology, business.industry, LARVAE, Biofilm, Biology and Life Sciences, Cell Biology, In vitro, Emerging Infectious Diseases, Good Health and Well Being, lcsh:Biology (General), point-of-care, Parasitology, MINIMUM FUNGICIDAL CONCENTRATIONS, Human medicine, Antimicrobial Resistance, RAT SUBCUTANEOUS MODEL, business
Abstract: Contains fulltext : 196638.pdf (Publisher’s version ) (Open Access) Unlike superficial fungal infections of the skin and nails, which are the most common fungal diseases in humans, invasive fungal infections carry high morbidity and mortality, particularly those associated with biofilm formation on indwelling medical devices. Therapeutic management of these complex diseases is often complicated by the rise in resistance to the commonly used antifungal agents. Therefore, the availability of accurate susceptibility testing methods for determining antifungal resistance, as well as discovery of novel antifungal and antibiofilm agents, are key priorities in medical mycology research. To direct advancements in this field, here we present an overview of the methods currently available for determining (i) the susceptibility or resistance of fungal isolates or biofilms to antifungal or antibiofilm compounds and compound combinations; (ii) the in vivo efficacy of antifungal and antibiofilm compounds and compound combinations; and (iii) the in vitro and in vivo performance of anti-infective coatings and materials to prevent fungal biofilm-based infections.
Published: 2018

23. Application of Py-GC/MS coupled with PARAFAC2 and PLS-DA to study fast pyrolysis of genetically engineered poplars

Author: Ruben Vanholme, Frederik Ronsse, Gilles Pilate, Guy B. Marin, Victor Abrahamsson, Rebecca Van Acker, Kevin Van Geem, Wout Boerjan, Hilal Ezgi Toraman, Laboratory for Chemical Technology, Universiteit Gent = Ghent University [Belgium] (UGENT), Lund University [Lund], Center for Plant Systems Biology (PSB Center), Vlaams Instituut voor Biotechnologie [Ghent, Belgique] (VIB), Department of Biosystems Engineering [Ghent], Biologie intégrée pour la valorisation de la diversité des arbres et de la forêt (BioForA), Institut National de la Recherche Agronomique (INRA)-Office National des Forêts (ONF), Funding from the European Research Council under the European Union's Seventh Framework Programme FP7/2007-2013/ERC grant agreement n° 290793. SBO proposal 'Bioleum' supported by the Institute for promotion of Innovation through Science and Technology in Flanders (IWT) and the EU-funded project ENERGYPOPLAR (FB7-211917). V.A. acknowledges the support from Swedish Research Council VR (2010-5439, 2010-333, 2013-4356, 2014-4052) and the Royal Physiographic Society in Lund., European Project: 290793,EC:FP7:ERC,ERC-2011-ADG_20110209,MADPII(2012), Universiteit Gent = Ghent University (UGENT), and Institut National de la Recherche Agronomique (INRA)-Office national des forêts (ONF)
Subjects: 0106 biological sciences, [SDV.BIO]Life Sciences [q-bio]/Biotechnology, 020209 energy, Lignocellulosic biomass, Bio-oil, Gas-chromatography, 02 engineering and technology, PLS-DA, 01 natural sciences, Analytical Chemistry, chemistry.chemical_compound, Thermochemical conversion, PARAFAC2, Partial least squares regression, 0202 electrical engineering, electronic engineering, information engineering, Lignin, Organic chemistry, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Phenylpropanoid, Lignin biosynthesis, Phenolic compounds, Fuel Technology, chemistry, Biosynthetic-pathway, Environmental chemistry, Field-grown transgenic plants, Principal component analysis, Cinnamoyl-CoA reductase, Gas chromatography–mass spectrometry, Pyrolysis, 010606 plant biology & botany
Abstract: International audience; Field-grown genetically engineered and wild-type poplars were pyrolyzed in a micro-pyrolysis (Py-GC/MS) setup under fast pyrolysis conditions. Poplars (Populus tremula x P. alba) down-regulated for cirmamoyl-CoA reductase (CCR), which catalyzes the first step of the monolignol-specific branch of the phenylpropanoid biosynthetic pathway, were grown in field trials in France and harvested after a full rotation of 2 years. The effect of small compositional differences, specifically small shifts in lignin composition and their impact on the bio-oil composition, could not be identified using principal component analysis (PCA), necessitating the use of more advanced analysis techniques. The combination of parallel factor analysis 2 (PARAFAC2) and partial least squares discriminant analysis (PLS-DA) for detailed characterization and classification of the pyrolysis data enabled the classification of the poplars with a success rate above 99% using the PARAFAC2 scores. This methodology proved to be extremely valuable to identify subtle information in complex datasets, such as the one used in this study. The obtained PLS-DA models were validated by cross-validation, jackknifing and permutation tests in order to ensure that the model was not overfitting the data. PLS-DA showed that down-regulation of CCR dis-favored the relative amount of both guaiacyl and syringyl lignin-derived compounds. This study shows that lignin engineering can be a promising strategy to alter the lignin composition of the biomass for the production of high value-added phenolic compounds.
Published: 2018

24. Overexpression of theArabidopsis thalianasignalling peptide TAXIMIN1 affects lateral organ development

Author: Nokwanda P. Makunga, Géraldine Brunoud, Takayuki Tohge, Teva Vernoux, Alisdair R. Fernie, Alain Goossens, Rebecca De Clercq, Laurens Pauwels, J. Colling, Center for Plant Systems Biology (PSB Center), Vlaams Instituut voor Biotechnologie [Ghent, Belgique] (VIB), Department of plant Biotechnology and Bioinformatics, University of Gent, Stellenbosch University, Max Planck Institute of Molecular Plant Physiology (MPI-MP), Max-Planck-Gesellschaft, Reproduction et développement des plantes (RDP), Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA)-École normale supérieure - Lyon (ENS Lyon), Department of plant systems biology, Flanders Institute for Biotechnology, Universiteit Gent = Ghent University (UGENT), École normale supérieure de Lyon (ENS de Lyon)-Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), and Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, Physiology, Arabidopsis, COMMUNICATION, Plant Science, 01 natural sciences, Gene Expression Regulation, Plant, Gene expression, Arabidopsis thaliana, Peptide sequence, GENE-EXPRESSION, SECRETORY PEPTIDE, chemistry.chemical_classification, 0303 health sciences, Plant Stems, biology, PLANT DEVELOPMENT, Intracellular Signaling Peptides and Proteins, food and beverages, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, paraclade junction, Biochemistry, lateral organ fusion, GROWTH, Signal transduction, Research Paper, Boundary genes, Meristem, BOUNDARY FORMATION, INFLORESCENCE ARCHITECTURE, Protein Sorting Signals, cysteine-rich peptide, 03 medical and health sciences, Auxin, STOMATAL DEVELOPMENT, Amino Acid Sequence, Transcription factor, 030304 developmental biology, SHOOT MERISTEM, Arabidopsis Proteins, Biology and Life Sciences, biology.organism_classification, Plant Leaves, chemistry, fruit development, boundary genes, Peptides, Sequence Alignment, AUXIN TRANSPORT, 010606 plant biology & botany
Abstract: Highlight Overexpression of a new secreted cysteine-rich signalling peptide in Arabidopsis results in developmental defects, including lateral organ fusion. This finding suggests that organ boundary formation involves small peptide signalling., Lateral organ boundary formation is highly regulated by transcription factors and hormones such as auxins and brassinosteroids. However, in contrast to many other developmental processes in plants, no role for signalling peptides in the regulation of this process has been reported yet. The first characterization of the secreted cysteine-rich TAXIMIN (TAX) signalling peptides in Arabidopsis is presented here. TAX1 overexpression resulted in minor alterations in the primary shoot and root metabolome, abnormal fruit morphology, and fusion of the base of cauline leaves to stems forming a decurrent leaf attachment. The phenotypes at the paraclade junction match TAX1 promoter activity in this region and are similar to loss of LATERAL ORGAN FUSION (LOF) transcription factor function. Nevertheless, TAX1 expression was unchanged in lof1lof2 paraclade junctions and, conversely, LOF gene expression was unchanged in TAX1 overexpressing plants, suggesting TAX1 may act independently. This study identifies TAX1 as the first plant signalling peptide influencing lateral organ separation and implicates the existence of a peptide signal cascade regulating this process in Arabidopsis.
Published: 2015

25. JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework

Author: Oriol Fornes, Anthony Mathelier, Benoit Ballester, Jeanne Chèneby, Marius Gheorghe, Arnaud Stigliani, Ge Tan, François Parcy, Aziz Khan, David J. Arenillas, Robin van der Lee, Wyeth W. Wasserman, Klaas Vandepoele, Jaime A. Castro-Mondragon, Damir Baranasic, Albin Sandelin, Shubhada Rajabhau Kulkarni, Boris Lenhard, Adrien Bessy, Centre for Molecular Medicine Norway (NCMM), Faculty of Medicine [Oslo], University of Oslo (UiO)-University of Oslo (UiO)-Rigshospitalet [Copenhagen], Department of Medical Genetics, Faculty of Medicine-Child and Family Research Institute-Centre for Molecular Medicine and Therapeutics-University of British Columbia (UBC), Physiologie cellulaire et végétale (LPCV), Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-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), Theories and Approaches of Genomic Complexity (TAGC), Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Department of Plant Systems Biology, VIB, and Department of Plant Biotechnology and Bioinformatics, Ghent University [Belgium] (UGENT), Computational Regulatory Genomics, Imperial College London, Institute of Clinical Sciences, MRC Clinical Sciences Centre, Faculty of Medicine, Imperial College London, Bioinformatics Centre, Department of Biology [Copenhagen], Faculty of Science [Copenhagen], University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU)-Faculty of Science [Copenhagen], University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU), Sars International Centre for Marine Molecular Biology, University of Bergen (UIB), Oslo University Hospital Radiumhospitalet, Genome Canada and Canadian Institutes of Health Research (On-Target Grants) [255ONT and BOP-149430], Natural Sciences and Engineering Research Council of Canada (Discovery Grant) [RGPIN-2017–06824], Independent Research Fund Denmark, Innovation Fund Denmark, Elixir Denmark, Wellcome Trust [106954], Biotechnology and Biological Sciences Research Council [BB/N023358/1], Medical Research Council UK [MC UP 1102/1], Weston Brain Institute: [20R74681], Research Foundation Flanders Grant [G001015N], Lundbeck Foundation, ANR-10- LABX-49-01,Labex GRAL,Labex GRAL, Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute and Department of Medical Genetics, University of British Columbia (UBC), Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Copenhagen University Hospital-Copenhagen University Hospital, Radboud University Medical Center [Nijmegen], Universiteit Gent = Ghent University [Belgium] (UGENT), Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute-University of British Columbia (UBC), Biotech Research and Innovation Centre (BRIC), University of Copenhagen = Københavns Universitet (KU), Center for Plant Systems Biology (PSB Center), Vlaams Instituut voor Biotechnologie [Ghent, Belgique] (VIB), Centre for Molecular Medicine and Therapeutics-University of British Columbia (UBC), Laboratoire de physiologie cellulaire végétale (LPCV), Université Joseph Fourier - Grenoble 1 (UJF)-Institut National de la Recherche Agronomique (INRA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS), VIB Department of Plant Systems Biology, University of Bergen (UiB), ANR-10-LABX-0049,GRAL,Grenoble Alliance for Integrated Structural Cell Biology(2010), Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Universiteit Gent = Ghent University (UGENT), University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH)-Faculty of Science [Copenhagen], University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH), University of Copenhagen = Københavns Universitet (UCPH), Biotechnology and Biological Sciences Research Council (BBSRC), and Wellcome Trust
Subjects: 0301 basic medicine, REPRESENTATION, Nematodes, [SDV]Life Sciences [q-bio], 05 Environmental Sciences, SPECIFICITIES, DIVERSITY, Genome browser, computer.software_genre, Genome, Bioconductor, User-Computer Interface, 0302 clinical medicine, Databases, Genetic, Database Issue, Taxonomic rank, base de données, 0303 health sciences, Database, Web application framework, BIOINFORMATICS, Genomics, Plants, ARABIDOPSIS, Multiple species, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], GENOME, Insects, 030220 oncology & carcinogenesis, Vertebrates, Erratum, Life Sciences & Biomedicine, Protein Binding, EXPRESSION, Biochemistry & Molecular Biology, libre accès, Biology, 03 medical and health sciences, Open Access, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], JASPAR, Journal Article, Genetics, Animals, Humans, Position-Specific Scoring Matrices, 030304 developmental biology, Internet, Science & Technology, Binding Sites, LANDSCAPE, Fungi, Biology and Life Sciences, 06 Biological Sciences, Binding, SITE PREDICTIONS, 030104 developmental biology, DISCOVERY, profil, 08 Information and Computing Sciences, actualisation, Transcription factor, computer, facteur de transcription, Developmental Biology, Transcription Factors
Abstract: International audience; JASPAR (http://jaspar.genereg.net) is an open-access database of curated, non-redundant transcription factor (TF)-binding profiles stored as position frequency matrices (PFMs) and TF flexible models (TFFMs) for TFs across multiple species in six tax-onomic groups. In the 2018 release of JASPAR, the CORE collection has been expanded with 322 new PFMs (60 for vertebrates and 262 for plants) and 33 PFMs were updated (24 for vertebrates, 8 for plants and 1 for insects). These new profiles represent a 30% expansion compared to the 2016 release. In addition , we have introduced 316 TFFMs (95 for vertebrates , 218 for plants and 3 for insects). This release incorporates clusters of similar PFMs in each taxon and each TF class per taxon. The JASPAR 2018 CORE vertebrate collection of PFMs was used to predict TF-binding sites in the human genome. The predictions are made available to the scientific community through a UCSC Genome Browser track data hub. Finally , this update comes with a new web framework with an interactive and responsive user-interface, along with new features. All the underlying data can be retrieved programmatically using a RESTful API and through the JASPAR 2018 R/Bioconductor package .
Published: 2017

26. Self-protection of cytosolic malate dehydrogenase against oxidative stress in Arabidopsis

Author: Mohamed Ragab Abdel-Gawwad, Didier Vertommen, Florence Vignols, Joris Messens, Jean-Philippe Reichheld, Nandita Bodra, Laetitia Bariat, Frank Van Breusegem, Bo Wei, Talaat Bashandy, Jingjing Huang, Leonardo Astolfi Rosado, David Young, Adnan Khan Niazi, Khadija Wahni, Department of Plant Biotechnology and Bioinformatics, Center for Plant Systems Biology (PSB Center), Vlaams Instituut voor Biotechnologie [Ghent, Belgique] (VIB), VIB-VUB Center for Structural Biology, Brussels Center for Redox Biology, Structural Biology Brussels, Structural Biology Brussels (SBB), Vrije Universiteit Brussel (VUB), Laboratoire Génome et développement des plantes (LGDP), Université de Perpignan Via Domitia (UPVD)-Centre National de la Recherche Scientifique (CNRS), Université de Perpignan Via Domitia (UPVD), Centre National de la Recherche Scientifique (CNRS), de Duve Institute, Université Catholique de Louvain = Catholic University of Louvain (UCL), Department of Bio-engineering Sciences, Faculty of Sciences and Bioengineering Sciences, UCL - SSS/DDUV - Institut de Duve, and UCL - SSS/DDUV/PHOS - Protein phosphorylation
Subjects: 0301 basic medicine, Physiology, Mutant, Arabidopsis, Plant Science, overoxidation, H2O2-triggered oxdation, Malate dehydrogenase, 03 medical and health sciences, Cytosol, Oxidoreductase, Malate Dehydrogenase, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, chemistry.chemical_classification, CytMDH1, dimerization, biology, Chemistry, thioredoxin, Hydrogen Peroxide, biology.organism_classification, sulfenic acid, H O -triggered oxdation, Metabolic pathway, Oxidative Stress, 030104 developmental biology, Biochemistry, physiology, Thioredoxin, Branched-chain alpha-keto acid dehydrogenase complex, Oxidation-Reduction
Abstract: Plant malate dehydrogenase (MDH) isoforms are found in different cell compartments and function in key metabolic pathways. It is well known that the chloroplastic NADP-dependent MDH activities are strictly redox regulated and controlled by light. However, redox dependence of other NAD-dependent MDH isoforms have been less studied. Here, we show by in vitro biochemical characterization that the major cytosolic MDH isoform (cytMDH1) is sensitive to H2O2 through sulfur oxidation of cysteines and methionines. CytMDH1 oxidation affects the kinetics, secondary structure, and thermodynamic stability of cytMDH1. Moreover, MS analyses and comparison of crystal structures between the reduced and H2O2-treated cytMDH1 further show that thioredoxin-reversible homodimerization of cytMDH1 through Cys330 disulfide formation protects the protein from overoxidation. Consistently, we found that cytosolic thioredoxins interact specifically with cytMDH in a yeast two-hybrid system. Importantly, we also show that cytosolic and chloroplastic, but not mitochondrial NAD-MDH activities are sensitive to H2O2 stress in Arabidopsis. NAD-MDH activities decreased both in a catalase2 mutant and in an NADP-thioredoxin reductase mutant, emphasizing the importance of the thioredoxin-reducing system to protect MDH from oxidation in vivo. We propose that the redox switch of the MDH activity contributes to adapt the cell metabolism to environmental constraints.
Published: 2017

27. A Key Role for Apoplastic H 2 O 2 in Norway Spruce Phenolic Metabolism

Author: Teemu H. Teeri, Kean-Jin Lim, Kaloian Iliev Nickolov, Günter Brader, Adrien Gauthier, Kris Morreel, Bastian Schiffthaler, Nathaniel R. Street, Nicolas Delhomme, Anna Kärkönen, Wout Boerjan, Teresa Laitinen, Dept Plant Syst Biol, Universiteit Gent = Ghent University [Belgium] (UGENT), Plante - microbe - environnement : biochimie, biologie cellulaire et écologie (PMEBBCE), Centre National de la Recherche Scientifique (CNRS)-Université de Bourgogne (UB)-Institut National de la Recherche Agronomique (INRA)-Etablissement National d'Enseignement Supérieur Agronomique de Dijon (ENESAD), Austrian Institute of Technology [Vienna] (AIT), Plant Physiology, Umeå University, Center for Plant Systems Biology (PSB Center), Vlaams Instituut voor Biotechnologie [Ghent, Belgique] (VIB), Ghent University [Belgium] (UGENT), Etablissement National d'Enseignement Supérieur Agronomique de Dijon (ENESAD)-Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-Centre National de la Recherche Scientifique (CNRS), Department of Plant Systems Biology, and State University of Ghent
Subjects: 0106 biological sciences, 0301 basic medicine, BENZYLIC ETHER REDUCTASE, Physiology, CULTURES, macromolecular substances, Plant Science, TRAP MASS-SPECTROMETRY, PEROXIDASES, 01 natural sciences, Cell wall, 03 medical and health sciences, chemistry.chemical_compound, CONIFERYL ALCOHOL, LIGNIN BIOSYNTHETIC-PATHWAY, Genetics, CELL-SUSPENSION, Lignin, Shikimate pathway, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, OXIDATIVE STRESS, ComputingMilieux_MISCELLANEOUS, biology, Chemistry, TRANSCRIPTIONAL REGULATION, fungi, Biology and Life Sciences, food and beverages, Metabolism, PICEA-ABIES, Apoplast, GENE REGULATORY NETWORK, 030104 developmental biology, Biochemistry, biology.protein, Monolignol, CLASS-III, 010606 plant biology & botany, Coniferyl alcohol, Peroxidase
Abstract: Apoplastic events such as monolignol oxidation and lignin polymerization are difficult to study in intact trees. To investigate the role of apoplastic hydrogen peroxide (H2O2) in gymnosperm phenolic metabolism, an extracellular lignin-forming cell culture of Norway spruce (Picea abies) was used as a research model. Scavenging of apoplastic H2O2 by potassium iodide repressed lignin formation, in line with peroxidases activating monolignols for lignin polymerization. Time-course analyses coupled to candidate substrate-product pair network propagation revealed differential accumulation of low-molecular-weight phenolics, including (glycosylated) oligolignols, (glycosylated) flavonoids, and proanthocyanidins, in lignin-forming and H2O2-scavenging cultures and supported that monolignols are oxidatively coupled not only in the cell wall but also in the cytoplasm, where they are coupled to other monolignols and proanthocyanidins. Dilignol glycoconjugates with reduced structures were found in the culture medium, suggesting that cells are able to transport glycosylated dilignols to the apoplast. Transcriptomic analyses revealed that scavenging of apoplastic H2O2 resulted in remodulation of the transcriptome, with reduced carbon flux into the shikimate pathway propagating down to monolignol biosynthesis. Aggregated coexpression network analysis identified candidate enzymes and transcription factors for monolignol oxidation and apoplastic H2O2 production in addition to potential H2O2 receptors. The results presented indicate that the redox state of the apoplast has a profound influence on cellular metabolism.
Published: 2017

28. Evolutionary relationships and expression analysis of EUL domain proteins in rice (Oryza sativa)

Author: Klaas Vandepoele, Mariya Tsankova Tsaneva, Els J.M. Van Damme, Pierre Rougé, Kristof De Schutter, Shubhada Rajabhau Kulkarni, Universiteit Gent = Ghent University [Belgium] (UGENT), Center for Plant Systems Biology (PSB Center), Vlaams Instituut voor Biotechnologie [Ghent, Belgique] (VIB), Pharmacochimie et Biologie pour le Développement (PHARMA-DEV), Institut de Recherche pour le Développement (IRD)-Institut de Chimie de Toulouse (ICT-FR 2599), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut de Chimie du CNRS (INC)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Institut de Chimie du CNRS (INC), Universiteit Gent = Ghent University (UGENT), Institut de Recherche pour le Développement (IRD)-Institut de Chimie de Toulouse (ICT), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut de Chimie de Toulouse (ICT-FR 2599), and Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut de Chimie du CNRS (INC)-Institut de Recherche pour le Développement (IRD)
Subjects: 0301 basic medicine, Carbohydrate, RESPONSIVE GENES, Architecture domain, [SDV]Life Sciences [q-bio], Protein domain, Soil Science, CIS-REGULATORY ELEMENTS, Plant Science, lcsh:Plant culture, Genome, DROUGHT TOLERANCE, 03 medical and health sciences, Phylogenetics, Domain architecture, Botany, EUL, Arabidopsis thaliana, CRYSTAL-STRUCTURE, lcsh:SB1-1110, STREPTOMYCES-OLIVACEOVIRIDIS E-86, GENOME-WIDE ANALYSIS, Gene, Phylogeny, 2. Zero hunger, Genetics, Oryza sativa, biology, Biology and Life Sciences, Lectin, food and beverages, ABSCISIC-ACID, biology.organism_classification, BINDING SITES, 030104 developmental biology, ARABIDOPSIS-THALIANA, biology.protein, Original Article, Rice, TRANSCRIPTION FACTOR FAMILY, Agronomy and Crop Science
Abstract: Background Lectins, defined as ‘Proteins that can recognize and bind specific carbohydrate structures’, are widespread among all kingdoms of life and play an important role in various biological processes in the cell. Most plant lectins are involved in stress signaling and/or defense. The family of Euonymus-related lectins (EULs) represents a group of stress-related lectins composed of one or two EUL domains. The latter protein domain is unique in that it is ubiquitous in land plants, suggesting an important role for these proteins. Results Despite the availability of multiple completely sequenced rice genomes, little is known on the occurrence of lectins in rice. We identified 329 putative lectin genes in the genome of Oryza sativa subsp. japonica belonging to nine out of 12 plant lectin families. In this paper, an in-depth molecular characterization of the EUL family of rice was performed. In addition, analyses of the promoter sequences and investigation of the transcript levels for these EUL genes enabled retrieval of important information related to the function and stress responsiveness of these lectins. Finally, a comparative analysis between rice cultivars and several monocot and dicot species revealed a high degree of sequence conservation within the EUL domain as well as in the domain organization of these lectins. Conclusions The presence of EULs throughout the plant kingdom and the high degree of sequence conservation in the EUL domain suggest that these proteins serve an important function in the plant cell. Analysis of the promoter region of the rice EUL genes revealed a diversity of stress responsive elements. Furthermore analysis of the expression profiles of the EUL genes confirmed that they are differentially regulated in response to several types of stress. These data suggest a potential role for the EULs in plant stress signaling and defense. Electronic supplementary material The online version of this article (doi:10.1186/s12284-017-0164-3) contains supplementary material, which is available to authorized users.
Published: 2017

29. Strobilurins as growth-promoting compounds: How Stroby regulates Arabidopsis leaf growth

Author: Van Dingenen, Judith, Antoniou, Chrystalla, Filippou, Panagiota, Pollier, Jacob, Gonzalez, Nathalie, Dhondt, Stijn, Goossens, Alain, Fotopoulos, Vasileios, Inze, Dirk, Universiteit Gent = Ghent University [Belgium] (UGENT), Center for Plant Systems Biology (PSB Center), and Vlaams Instituut voor Biotechnologie [Ghent, Belgique] (VIB)
Subjects: Leaf growth, Subgroup Ib bHLH transcription factor, Other Agricultural Sciences, Agricultural Sciences, [SDV]Life Sciences [q-bio], fungi, food and beverages, Nitric oxide, Strobilurins
Abstract: Strobilurins are an important class of agrochemical fungicides used throughout the world on a wide variety of crops as protection against fungal pathogens. In addition to this protective role, they are reported to also positively influence plant physiology. In this study, we analysed the effect of Stroby (R) WG, a commercially available fungicide consisting of 50% (w/w) kresoxim-methyl (KM) as active strobilurin compound, on Arabidopsis leaf growth. Treatment of seedlings with Stroby resulted in larger leaves due to an increase in cell number. Transcriptome analysis of Stroby-treated rosettes demonstrated an increased expression of genes involved in redox homeostasis, iron metabolism and sugar transport. Stroby treatment strongly induced the expression of the subgroup Ib basic helix-loop-helix (bHLH) transcription factors, which have a role in iron homeostasis under iron-limiting conditions. Single loss-of-function mutants of three bHLHs and their triple bhlh039, bhlh100 and bhlh101 mutant did not respond to Stroby treatment. Although iron and sucrose content was not affected, nitric oxide (NO) levels and nitrate reductase (NR) activity were significantly increased in Stroby-treated rosettes as compared with control plants. In conclusion, we suggest that the Stroby-mediated effects on growth depend on the increased expression of the subgroup Ib bHLHs and higher NO levels.
Published: 2017

30. Ubiquitylation activates a peptidase that promotes cleavage and destabilization of its activating E3 ligases and diverse growth regulatory proteins to limit cell proliferation in Arabidopsis

Author: Dong, Hui, Dumenil, Jack, Lu, Fu-Hao, Na, Li, Vanhaeren, Hannes, Naumann, Christin, Klecker, Maria, Prior, Rachel, Smith, Caroline, McKenzie, Neil, Saalbach, Gerhard, Chen, Liangliang, Xia, Tian, Gonzalez, Nathalie, Seguela, Mathilde, Inze, Dirk, Dissmeyer, Nico, Li, Yunhai, Bevan, Michael W., Center for Plant Systems Biology (PSB Center), and Vlaams Instituut voor Biotechnologie [Ghent, Belgique] (VIB)
Subjects: [SDV]Life Sciences [q-bio], human activities
Abstract: Ubiquitylation activates a peptidase that promotes cleavage and destabilization of its activating E3 ligases and diverse growth regulatory proteins to limit cell proliferation in Arabidopsis. Ubiquitylation activates a peptidase that promotes cleavage and destabilization of its activating E3 ligases and diverse growth regulatory proteins to limit cell proliferation in Arabidopsis
Published: 2017

31. A new version of the grapevine reference genome assembly (12X.v2) and of its annotation (VCost.v3)

Author: I. Le Clainche, Rémi Bounon, Simone Scalabrin, Stephane Rombauts, Michele Morgante, Jérôme Grimplet, Aurélie Canaguier, Dominique Brunel, M-C Le Paslier, A-F Adam-Blondon, Nathalie Choisne, Eric Duchêne, Aurélie Bérard, A. Chauveau, Nacer Mohellibi, G. Di Gaspero, C Rustenholz, Cécile Guichard, Etude du Polymorphisme des Génomes Végétaux (EPGV), Institut National de la Recherche Agronomique (INRA), Unité de recherche en génomique végétale (URGV), Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE)-Institut National de la Recherche Agronomique (INRA), Université Paris-Saclay, Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Instituto de Ciencias de la Vid y del Vino, Universidad de La Rioja (UR), Universidad de la Rioja, Istituto di Genomica Applicata, Applied Genomics Institute (IGA), Santé de la vigne et qualité du vin (SVQV), Institut National de la Recherche Agronomique (INRA)-Université Louis Pasteur - Strasbourg I, Unité de Recherche Génomique Info (URGI), Institut des Sciences des Plantes de Paris-Saclay (IPS2 (UMR_9213 / UMR_1403)), Institut National de la Recherche Agronomique (INRA)-Université Paris-Sud - Paris 11 (UP11)-Université Paris Diderot - Paris 7 (UPD7)-Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), VIB Center for Plant Systems Biology, ANR-Plant-KBBE-2008-GrapeReSeq and ANR-2008-Muscares, ANR-08-GENM-0007,MUSCARES,Génomique comparée de Vitis vinifera et Muscadinia rotundifolia pour l'analyse de la résistance aux maladies chez les Vitaceae(2008), ANR-08-KBBE-0008,GRAPERESEQ,Large scale re-sequencing in the Vitis genus for identification of resistance genes, SNP discovery and high throughput genotyping(2008), Institut National de la Recherche Agronomique (INRA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA)-Université de Strasbourg (UNISTRA), Center for Plant Systems Biology (PSB Center), Vlaams Instituut voor Biotechnologie [Ghent, Belgique] (VIB), Institut National de la Recherche Agronomique (France), Università degli Studi di Udine, Institute of Applied Genomics (Italy), Flanders Institute for Biotechnology, Ghent University, European Cooperation in Science and Technology, Agence Nationale de la Recherche (France), Ministero delle Politiche Agricole Alimentari e Forestali, Adam-Blondon, Anne-Françoise [0000-0002-3412-9086], Université de Strasbourg (UNISTRA)-Institut National de la Recherche Agronomique (INRA), Morgante, Michele, and Adam-Blondon, Anne-Françoise
Subjects: 0301 basic medicine, lcsh:QH426-470, Gene prediction, Genomic data, [SDV]Life Sciences [q-bio], Gene annotation, annotation génomique, Biology, Chromosomes assembly, Genome, Vitis vinifera, Biotechnology, Biochemistry, Molecular Medicine, Genetics, 03 medical and health sciences, Annotation, appariement chromosomique, Data in Brief, 2. Zero hunger, synapsis, génome, Biology and Life Sciences, Gene Annotation, genome, chromosomes assembly, gene annotation, GENE-PREDICTION, 3. Good health, FAMILY, lcsh:Genetics, ALIGNMENT, 030104 developmental biology, GenBank, INTEGRATION, Reference genome
Abstract: The grapevine reference genome was published by Jaillon et al. [1]. The sequence for the first version of the genome, called the 8X version, was obtained using a whole genome shotgun strategy and the Sanger sequencing technology and was assembled from reads representing 8X coverage. Soon after, the assembly was improved through the addition of 4X of additional coverage, including more Bacterial Artificial Chromosome end sequences that greatly improved the scaffolding of the sequence contigs [2], [3]. The corresponding scaffolds and raw sequences were deposited in European Molecular Biology Laboratory (EMBL) archives (FN594950-FN597014, 2065 entries, release 102). A new chromosome assembly was also developed, based on an improved version of the maps used for the 8X genome version [2], [3], [4], [5] and was also archived at EMBL (FN597015-FN597047, 33 entries, release 102): it is referenced in the grapevine community as the 12X.v0 version of the grapevine reference genome. The chromosome sequence scaffolding of this version still necessitated improvements as around 9% of the sequence was not anchored to chromosomes (with the corresponding scaffolds stacked in the “Unknown” chromosome) and 3.5% of the sequence could be assigned to a chromosome but without certain placement and orientation within the chromosome (stacked in additional “random” chromosomes)., This work was supported by the French National Institute for Agriculture (INRA, France), the University of Udine and the Institute of Applied Genomics (Italy), the Vlaams Institut voor Biotechnologie and the University of Ghent (Belgium), the Istituto de Ciencas de la Vid et del Vino (Logroño, Spain) and several grants: ANR-Plant-KBBE-2008- GrapeReSeq and ANR-2008-Muscares funded by the French National Research Agency (ANR), Valorizzazione dei Principali Vitigni Autoctoni Italiani e dei loro Terroir (Vigneto, no. COSVIR27129) funded by the Italian Ministry of Agriculture and the COST action FA1106 funded under the European FP7 Research Program
Published: 2017

32. Natural Variation of Molecular and Morphological Gibberellin Responses

Author: Nam, Youn-Jeong, Herman, Dorota, Blomme, Jonas, Chae, Eunyoung, Kojima, Mikiko, Coppens, Frederik, Storme, Veronique, Van Daele, Twiggy, Dhondt, Stijn, Sakakibara, Hitoshi, Weigel, Detlef, Inze, Dirk, Gonzalez, Nathalie, Center for Plant Systems Biology (PSB Center), and Vlaams Instituut voor Biotechnologie [Ghent, Belgique] (VIB)
Subjects: [SDV]Life Sciences [q-bio], food and beverages
Abstract: Natural Variation of Molecular and Morphological Gibberellin Responses. Natural Variation of Molecular and Morphological Gibberellin Responses
Published: 2017

33. Two interacting PPR proteins are major Arabidopsis editing factors in plastid and mitochondria

Author: Benjamin Broche, Etienne Delannoy, Alexandra Avon, Mizuki Takenaka, Damien Guillaumot, Richard Berthomé, Geert De Jaeger, Kevin Baudry, Guillem Rigaill, Andéol Falcon de Longevialle, Mauricio Lopez-Obando, Claire Lurin, Institut des Sciences des Plantes de Paris-Saclay (IPS2 (UMR_9213 / UMR_1403)), Institut National de la Recherche Agronomique (INRA)-Université Paris-Sud - Paris 11 (UP11)-Université Paris Diderot - Paris 7 (UPD7)-Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA), Université Paris Sud (Paris 11), Université d'Evry Val d'Essonne, Université Paris-Saclay, Université Paris Diderot - Paris 7 (UPD7), Université Sorbonne Paris Cité (USPC), Laboratoire Plant Process Innovation, Génopole, Molekulare Botanik, Universität Ulm - Ulm University [Ulm, Allemagne], Laboratoire des interactions plantes micro-organismes (LIPM), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA), Department of Plant Biotechnology and Bioinformatics, Ghent University [Belgium] (UGENT), VIB Center for Plant Systems Biology, Ministere de la Recherche et de l'Enseignement Superieur, Labex Saclay Plant Sciences-SPS postdoctoral fellowship, DFG, Labex Saclay Plant Sciences-SPS : ANR-10-LABX-0040-SPS, Institut National de la Recherche Agronomique (INRA)-Université Paris-Sud - Paris 11 (UP11)-Université Paris Diderot - Paris 7 (UPD7)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Universiteit Gent = Ghent University [Belgium] (UGENT), Center for Plant Systems Biology (PSB Center), Vlaams Instituut voor Biotechnologie [Ghent, Belgique] (VIB), Institut National de la Recherche Agronomique (INRA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Diderot - Paris 7 (UPD7)-Université Paris-Saclay-Université Paris-Sud - Paris 11 (UP11), Lurin, Claire, and Universiteit Gent = Ghent University (UGENT)
Subjects: 0301 basic medicine, RNA editing, Chloroplasts, RNA-binding protein, Biology, plastide, arn mitochondrial, organelles, pentatricopeptide repeat, 03 medical and health sciences, Gene expression, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Plastid, plastids, Tandem affinity purification, Genetics, Multidisciplinary, Vegetal Biology, Arabidopsis Proteins, RNA, RNA-Binding Proteins, Biological Sciences, Mitochondria, arabidopsis, 030104 developmental biology, Pentatricopeptide repeat, Biogenesis, Biologie végétale
Abstract: RNA editing is converting hundreds of cytosines into uridines during organelle gene expression of land plants. The pentatricopeptide repeat (PPR) proteins are at the core of this posttranscriptional RNA modification. Even if a PPR protein defines the editing site, a DYW domain of the same or another PPR protein is believed to catalyze the deamination. To give insight into the organelle RNA editosome, we performed tandem affinity purification of the plastidial CHLOROPLAST BIOGENESIS 19 (CLB19) PPR editing factor. Two PPR proteins, dually targeted to mitochondria and chloroplasts, were identified as potential partners of CLB19. These two proteins, a P-type PPR and a member of a small PPR-DYW subfamily, were shown to interact in yeast. Insertional mutations resulted in embryo lethality that could be rescued by embryo-specific complementation. A transcriptome analysis of these complemented plants showed major editing defects in both organelles with a very high PPR type specificity, indicating that the two proteins are core members of E+-type PPR editosomes.
Published: 2017

34. Forever Young: The Role of Ubiquitin Receptor DA1 and E3 Ligase BIG BROTHER in Controlling Leaf Growth and Development

Author: Vanhaeren, Hannes, Nam, Youn-Jeong, De Milde, Liesbeth, Chae, Eunyoung, Storme, Veronique, Weigel, Detlef, Gonzalez, Nathalie, Inze, Dirk, Center for Plant Systems Biology (PSB Center), and Vlaams Instituut voor Biotechnologie [Ghent, Belgique] (VIB)
Subjects: congenital, hereditary, and neonatal diseases and abnormalities, [SDV]Life Sciences [q-bio], fungi, food and beverages
Abstract: Forever Young: The Role of Ubiquitin Receptor DA1 and E3 Ligase BIG BROTHER in Controlling Leaf Growth and Development. Forever Young: The Role of Ubiquitin Receptor DA1 and E3 Ligase BIG BROTHER in Controlling Leaf Growth and Development
Published: 2017

35. The Mitochondrial DNA (mtDNA)-Associated Protein SWIB5 Influences mtDNA Architecture and Homologous Recombination

Author: Catherine Colas des Francs-Small, Dirk Inzé, Jonas Blomme, Michiel De Bruyne, Olivier Van Aken, Jasmien Vercruysse, Geert De Jaeger, Twiggy Van Daele, Mattias Vermeersch, Teddy Jégu, Riet De Rycke, Moussa Benhamed, Liesbeth De Milde, Nathalie Gonzalez, A. Harvey Millar, Jonah Nolf, Jelle Van Leene, Universiteit Gent = Ghent University [Belgium] (UGENT), Center for Plant Systems Biology (PSB Center), and Vlaams Instituut voor Biotechnologie [Ghent, Belgique] (VIB)
Subjects: 0301 basic medicine, H-NS, Mitochondrial DNA, DNA repair, [SDV]Life Sciences [q-bio], Arabidopsis, Plant Science, Mitochondrion, Biology, DOUBLE-STRAND BREAKS, Genome, DNA, Mitochondrial, Mitochondrial Proteins, 03 medical and health sciences, chemistry.chemical_compound, Gene Expression Regulation, Plant, Organelle, Arabidopsis thaliana, DAMAGE RESPONSE, SNF COMPLEX, Research Articles, GENE-EXPRESSION, Genetics, PLASMODIUM-FALCIPARUM, Arabidopsis Proteins, fungi, Biology and Life Sciences, food and beverages, Cell Biology, biology.organism_classification, LEAF DEVELOPMENT, Mitochondria, BINDING-PROTEIN, 030104 developmental biology, chemistry, CHROMATIN REMODELING COMPLEXES, ARABIDOPSIS-THALIANA, Homologous recombination, DNA
Abstract: In addition to the nucleus, mitochondria and chloroplasts in plant cells also contain genomes. Efficient DNA repair pathways are crucial in these organelles to fix damage resulting from endogenous and exogenous factors. Plant organellar genomes are complex compared with their animal counterparts, and although several plant-specific mediators of organelle DNA repair have been reported, many regulators remain to be identified. Here, we show that a mitochondrial SWI/SNF (nucleosome remodeling) complex B protein, SWIB5, is capable of associating with mitochondrial DNA (mtDNA) in Arabidopsis thaliana. Gain-and loss-of-function mutants provided evidence for a role of SWIB5 in influencing mtDNA architecture and homologous recombination at specific intermediate-sized repeats both under normal and genotoxic conditions. SWIB5 interacts with other mitochondrial SWIB proteins. Gene expression and mutant phenotypic analysis of SWIB5 and SWIB family members suggests a link between organellar genome maintenance and cell proliferation. Taken together, our work presents a protein family that influences mtDNA architecture and homologous recombination in plants and suggests a link between organelle functioning and plant development.
Published: 2017

36. From lateral root density to nodule number, the strigolactone analogue GR24 shapes the root architecture of Medicago truncatula

Author: Justine Fromentin, Annick De Keyser, Bruno Guillotin, François-Didier Boyer, Rosita Endah Yocgo, Karl J. Kunert, Sofie Goormachtig, Carolien De Cuyper, Center for Plant Systems Biology (PSB Center), Vlaams Instituut voor Biotechnologie [Ghent, Belgique] (VIB), Institut de Chimie des Substances Naturelles (ICSN), and Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)
Subjects: 0106 biological sciences, Physiology, GR24, Strigolactone, Plant Science, Root system, root architecture, Plant Root Nodulation, Plant Roots, 01 natural sciences, Lactones, 03 medical and health sciences, Botany, ethylene, [CHIM]Chemical Sciences, nodulation, 030304 developmental biology, 0303 health sciences, Rhizosphere, ENOD11, biology, fungi, Lateral root, food and beverages, medicago truncatula, biology.organism_classification, Medicago truncatula, Arbuscular mycorrhiza, Crosstalk (biology), Sinorhizobium, Heterocyclic Compounds, 3-Ring, 010606 plant biology & botany
Abstract: International audience; In the rhizosphere, strigolactones not only act as crucial signalling molecules in the communication of plants with parasitic weeds and arbuscular mycorrhiza, but they also play a key role in regulating different aspects of the root system. Here we investigated how strigolactones influence the root architecture of Medicago truncatula. We provide evidence that addition of the synthetic strigolactone analogue GR24 has an inhibitory effect on the lateral root density. Moreover, treatment with GR24 of Sinorhizobium meliloti-inoculated M. truncatula plants affects the nodule number both positively and negatively, depending on the concentration. Plants treated with 0.1 microM GR24 had a slightly increased number of nodules, whereas concentrations of 2 and 5 microM strongly reduced it. This effect was independent of the autoregulation of nodulation mechanism that is controlled by SUPER NUMERIC NODULE. Furthermore, we demonstrate that GR24 controls the nodule number through crosstalk with SICKLE-dependent ethylene signalling. Additionally, because the expression of the nodulation marker EARLY NODULATION11 was strongly reduced in GR24-treated plants, we concluded that strigolactones influence nodulation at a very early stage of the symbiotic interaction.
Published: 2014

37. A mi<scp>R</scp>169 isoform regulates specific<scp>NF</scp>‐<scp>YA</scp>targets and root architecture in<scp>A</scp>rabidopsis

Author: Thomas Blein, Linnan Ma, Céline Sorin, Marie Declerck, Caroline Hartmann, Maria Fransiska Njo, Aurélie Christ, Christine Lelandais-Brière, Martin Crespi, Tom Beeckman, Institute of Plant Sciences, Agricultural Research Organization-The Volcani Center, Institut des sciences du végétal (ISV), Centre National de la Recherche Scientifique (CNRS), Institut des Sciences du Végétal, UPR 2355, Institut des Sciences des Plantes de Paris-Saclay (IPS2 (UMR_9213 / UMR_1403)), Institut National de la Recherche Agronomique (INRA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Diderot - Paris 7 (UPD7)-Université Paris-Saclay-Université Paris-Sud - Paris 11 (UP11), Department of Plant Systems Biology, State University of Ghent, Institut National de la Recherche Agronomique (INRA)-Université Paris-Sud - Paris 11 (UP11)-Université Paris Diderot - Paris 7 (UPD7)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Conseil General de l'Essonne, French Ministry of Education, ROOT KBBE project, LabEx SPS, Interuniversity Attraction Poles Programme from the Belgian Federal Science Policy Office [IAP VI/33, IUAP P7/29], Center for Plant Systems Biology (PSB Center), and Vlaams Instituut voor Biotechnologie [Ghent, Belgique] (VIB)
Subjects: Gene isoform, root branching, Physiology, Meristem, Arabidopsis, Gene Expression, Transcription factor complex, Plant Science, Biology, Plant Roots, Gene Expression Regulation, Plant, Genes, Reporter, Gene expression, RNA Isoforms, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Gene, Transcription factor, ComputingMilieux_MISCELLANEOUS, 2. Zero hunger, Nuclear Factor Y subunit A (NF-YA), Messenger RNA, Arabidopsis Proteins, Plants, Genetically Modified, biology.organism_classification, Molecular biology, Cell biology, MicroRNAs, Phenotype, CCAAT-Binding Factor, RNA, Plant, miR169 isoforms, mimicry
Abstract: International audience; In plants, roots are essential for water and nutrient acquisition. MicroRNAs (miRNAs) regulate their target mRNAs by transcript cleavage and/or inhibition of protein translation and are known as major post-transcriptional regulators of various developmental pathways and stress responses. In Arabidopsis thaliana, four isoforms of miR169 are encoded by 14 different genes and target diverse mRNAs, encoding subunits A of the NF-Y transcription factor complex. These miRNA isoforms and their targets have previously been linked to nutrient signalling in plants. By using mimicry constructs against different isoforms of miR169 and miR-resistant versions of NF-YA genes we analysed the role of specific miR169 isoforms in root growth and branching. We identified a regulatory node involving the particular miR169defg isoform and NF-YA2 and NF-YA10 genes that acts in the control of primary root growth. The specific expression of MIM169defg constructs altered specific cell type numbers and dimensions in the root meristem. Preventing miR169defg-regulation of NF-YA2 indirectly affected laterial root initiation. We also showed that the miR169defg isoform affects NF-YA2 transcripts both at mRNA stability and translation levels. We propose that a specific miR169 isoform and the NF-YA2 target control root architecture in Arabidopsis.
Published: 2014

38. Multiple Functions of Kip-Related Protein5 Connect Endoreduplication and Cell Elongation

Author: Elodie Hudik, David Latrasse, Catherine Bergounioux, Mickael Bourge, Lieven De Veylder, Cécile Raynaud, Marianne Delarue, Sophie Blanchet, Teddy Jégu, Moussa Benhamed, Céline Charon, Christelle Mazubert, Marie-Noëlle Soler, Institut des sciences du végétal (ISV), Centre National de la Recherche Scientifique (CNRS), Centre National de Génotypage (CNG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Center for Plant Systems Biology (PSB Center), and Vlaams Instituut voor Biotechnologie [Ghent, Belgique] (VIB)
Subjects: Transcriptional Activation, 0106 biological sciences, Physiology, Heterochromatin, Cellular differentiation, Arabidopsis, Plant Science, Biology, Genes, Plant, Models, Biological, 01 natural sciences, 03 medical and health sciences, Cyclin-dependent kinase, Cyclins, Genetics, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Endoreduplication, Cyclin-Dependent Kinase Inhibitor Proteins, 030304 developmental biology, Cyclin, 0303 health sciences, Arabidopsis Proteins, Cell Biology, Cell cycle, biology.organism_classification, Chromatin, Cell biology, Protein Transport, Seedlings, Mutation, biology.protein, Protein Binding, 010606 plant biology & botany
Abstract: Despite considerable progress in our knowledge regarding the cell cycle inhibitor of the Kip-related protein (KRP) family in plants, less is known about the coordination of endoreduplication and cell differentiation. In animals, the role of cyclin-dependent kinase (CDK) inhibitors as multifunctional factors coordinating cell cycle regulation and cell differentiation is well documented and involves not only the inhibition of CDK/cyclin complexes but also other mechanisms, among them the regulation of transcription. Interestingly, several plant KRPs have a punctuated distribution in the nucleus, suggesting that they are associated with heterochromatin. Here, one of these chromatin-bound KRPs, KRP5, has been studied in Arabidopsis (Arabidopsis thaliana). KRP5 is expressed in endoreduplicating cells, and loss of KRP5 function decreases endoreduplication, indicating that KRP5 is a positive regulator of endoreduplication. This regulation relies on several mechanisms: in addition to its role in cyclin/CDK kinase inhibition previously described, chromatin immunoprecipitation sequencing data combined with transcript quantification provide evidence that KRP5 regulates the transcription of genes involved in cell wall organization. Furthermore, KRP5 overexpression increases chromocenter decondensation and endoreduplication in the Arabidopsis trithorax-related protein5 (atxr5) atxr6 double mutant, which is deficient for the deposition of heterochromatin marks. Hence, KRP5 could bind chromatin to coordinately control endoreduplication and chromatin structure and allow the expression of genes required for cell elongation.
Published: 2013

39. A Fluorescent Alternative to the Synthetic Strigolactone GR24

Author: Rik Van Deun, Danny Geelen, François-Didier Boyer, Christian V. Stevens, Amanda Rasmussen, Cedrick Matthys, Sofie Goormachtig, Thomas S. A. Heugebaert, Institut de Chimie des Substances Naturelles (ICSN), Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC), Center for Plant Systems Biology (PSB Center), Vlaams Instituut voor Biotechnologie [Ghent, Belgique] (VIB), Faculty of Bioscience Engineering, Ghent University, Universiteit Gent = Ghent University [Belgium] (UGENT), Department of Plant Production [Ghent], Faculty of Bioscience Engineering [Ghent], Universiteit Gent = Ghent University [Belgium] (UGENT)-Universiteit Gent = Ghent University [Belgium] (UGENT), FP7 Marie Curie International Incoming Fellowships, Hercules Foundation [AUGE/09/024], Research Foundation-Flanders [0081.10N], and Ghent University [01N01010]
Subjects: 0106 biological sciences, Arabidopsis, Strigolactone, Germination, strigolactones, Plant Science, Isoindoles, Plant Roots, 01 natural sciences, Lactones, 03 medical and health sciences, 4-Butyrolactone, Gene Expression Regulation, Plant, In vivo, branching, Botany, adventitious rooting, Molecular Biology, 030304 developmental biology, 0303 health sciences, biology, [CHIM.ORGA]Chemical Sciences/Organic chemistry, Arabidopsis Proteins, Orobanche, Biological activity, biology.organism_classification, In vitro, Spectrometry, Fluorescence, fluorescent markers, Biochemistry, parasitic weed seed germination, Shoot, Signal transduction, Carrier Proteins, Plant Shoots, 010606 plant biology & botany
Abstract: International audience; Strigolactones have recently been implicated in both above- and below-ground developmental pathways in higher plants. To facilitate the molecular and chemical properties of strigolactones in vitro and in vivo, we have developed a fluorescent strigolactone molecule, CISA-1, synthesized via a novel method which was robust, high-yielding, and used simple starting materials. We demonstrate that CISA-1 has a broad range of known strigolactone activities and further report on an adventitious rooting assay in Arabidopsis which is a highly sensitive and rapid method for testing biological activity of strigolactone analogs. In this rooting assay and the widely used Orobanche germination assay, CISA-1 showed stronger biological activity than the commonly tested GR24. CISA-1 and GR24 were equally effective at inhibiting branching in Arabidopsis inflorescence stems. In both the branching and adventitious rooting assay, we also demonstrated that CISA-1 activity is dependent on the max strigolactone signaling pathway. In water methanol solutions, CISA-1 was about threefold more stable than GR24, which may contribute to the increased activity observed in the various biological tests.
Published: 2013

40. The Medicago Genome Provides Insight into the Evolution of Rhizobial Symbioses

Author: Claude Scarpelli, Thomas Schiex, Ghislaine Magdelenat, Michael K. Udvardi, Baifang Qin, Xinbin Dai, Jeff J. Doyle, Patrick X. Zhao, Hélène Bergès, Vagner A. Benedito, Arvind K. Bharti, Chrystel Gibelin, Dong-Hoon Jeong, Stéphane De Mita, Stephane Rombauts, Mingyi Wang, Nathalie Choisne, Simone L. Macmil, Patrick Wincker, Senjuti Sinharoy, Sylvie Samain, Christopher D. Town, Susan R. Singer, Heidrun Gundlach, Anne Berger, Jane Rogers, Kathrin Klee, Sarah Sims, Nevin D. Young, Stéphanie Fouteau, Claire Riddle, Iryna Sanders, John Gish, Limei Yang, René Geurts, Gregory D. May, Shiguo Zhou, Shweta Deshpande, David C. Schwartz, Anika Jöcker, Christine Nicholson, Ton Bisseling, Klaus F. X. Mayer, Antoine Zuber, Roxanne Denny, Chunting Lang, Carolien Franken, Douglas R. Cook, Ruihua Shi, Frédéric Debellé, Valérie Barbe, Giles E. D. Oldroyd, Foo Cheung, Lucy Matthews, Blake C. Meyers, Jeremy D. Murray, Dong-Jin Kim, Joann Mudge, Agnès Viollet, Heiko Schoof, Graham B. Wiley, Benjamin D. Rosen, Jean Dénarié, Florent Prion, Keqin Wang, Arnaud Bellec, Béatrice Segurens, Jeong Hwan Mun, Ernest F. Retzel, Sean Humphray, Andrew Farmer, D. Janine Sherrier, Lieven Sterck, Richard A. Dixon, Steven B. Cannon, Steve Kenton, Philippe Bardou, Alvaro J. González, Haibao Tang, Julie Poulain, Arnaud Couloux, Majesta O'Bleness, Pamela J. Green, Manuel Spannagl, Shelby L. Bidwell, Jixian Zhai, Asis Hallab, Anne Marie Dudez, Michael Bechner, Marina Naoumkina, James D. White, Francis Quetier, Marijke Hartog, Erin L. Monaghan, Charles Paule, Chunmei Qu, Andrew J. Severin, Céline Noirot, Fu Ying, Shaoping Lin, Ziyun Yao, Vivek Krishnakumar, Steven A. Goldstein, Axin Hua, Erika Sallet, Bing Bing Wang, Peng Zhou, Hongshing Lai, Yanbo Xing, Nicolas Samson, Jamison McCorrison, Doug White, Yi Jing, Olivier Saurat, Liping Zhou, Kevin A. T. Silverstein, Jean Weissenbach, Bruce A. Roe, Sebastian Proost, Yves Van de Peer, Xiaohong Wang, Jens Warfsmann, Jérôme Gouzy, Fares Z. Najar, University of Minnesota [Twin Cities] (UMN), University of Minnesota System, Unité mixte de recherche interactions plantes-microorganismes, Institut National de la Recherche Agronomique (INRA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Laboratoire des interactions plantes micro-organismes (LIPM), Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Department of Disease and Stress Biology, John Innes Centre [Norwich], Laboratory of Molecular Biology, Department of Plant Science, Wageningen University and Research [Wageningen] (WUR), Corn Insects and Crop Genetics Research Unit, USDA-ARS : Agricultural Research Service, Department of Agronomy, Purdue University [West Lafayette], Plant Biology Division, The Samuel Roberts Noble Foundation, West Virginia University, German Research Center for Environmental Health - Helmholtz Center München (GmbH), Centre National de la Recherche Scientifique (CNRS), Rheinische Friedrich-Wilhelms-Universität Bonn, Center for Plant Systems Biology (PSB Center), Vlaams Instituut voor Biotechnologie [Ghent, Belgique] (VIB), Department plant pathology, Pennsylvania State University (Penn State), Penn State System-Penn State System, University of Delaware [Newark], J. Craig Venter Institute [La Jolla, USA] (JCVI), Interactions Arbres-Microorganismes (IAM), Institut National de la Recherche Agronomique (INRA)-Université de Lorraine (UL), Laboratory for Molecular and Computational Genomics, University of Wisconsin-Madison, National center for genome resources (NCGR), BBSRC John Innes Centre, Partenaires INRAE, Bayer Cropscience, Centre National de Ressources Génomiques Végétales (CNRGV), Institut National de la Recherche Agronomique (INRA), College of Science [Swansea], Swansea University, University of Oklahoma (OU), Department of Plant Biology, Royal Veterinary and Agricultural University = Kongelige Veterinær- og Landbohøjskole (KVL ), Max Planck Institute for Plant Breeding Research (MPIPZ), Wageningen University and Research Centre (WUR), Wellcome Trust, International Institute of Tropical Agriculture, Department of Plant Pathology, University of Kentucky, Rural Development Administration, Unité de Biométrie et Intelligence Artificielle (UBIA), Carleton College, Funding support to N.D.Y., C. D. T. and B. A. R. from The Noble Foundation and NSF-PGRP 0321460, 0604966, to N.D.Y., J.M. and G. D. M. from NSF-PGRP 0820005, to C. D. T. from NSF-PGRP 0821966, to F. D., G.E.D.O., R. G., K. F. X. M., T. B., J. Denarie, F. Q. and J. R. from FP6 EU project GLIP/Grain Legumes FOOD-CT-2004-506223, to G.E.D.O. and J.R. from BBSRC BBS/B/11524, to F. D. and F. Q. from ANR project SEQMEDIC 2006-01122, to R. G. from the Dutch Science Organization VIDI 864.06.007, ERA-PG FP-06.038A, to Y.V.d.P. from the Belgian Federal Science Policy Office IUAP P6/25, Fund for Scientific Research Flanders, Institute for the Promotion of Innovation by Science and Technology in Flanders and Ghent University (MRP N2N), to D. R. C. from NSF IOS-0531408, IOS-0605251, to D.J.S., B. C. M. and P.J.G. from USDA CSREES 2006-03567, and to J. Gouzy from 'Laboratoire d'Excellence' (LABEX) TULIP (ANR-10-LABX-41). We also acknowledge technical support from the University of Minnesota Supercomputer Institute and thank Y.W. Nam for a BamHI BAC library used by Genoscope, S. Park and M. Accerbi for RNA isolation, T. Paape for statistical consulting, and M. Harrison for supplying myc infected and control root tissues used to make small RNA libraries.
Subjects: 0106 biological sciences, multidisciplinary science, 01 natural sciences, Genome, genomic, flavonoid biosynthesis, Vitis, genes, 2. Zero hunger, 0303 health sciences, Multidisciplinary, Medicago, biology, truncatula, food and beverages, Biological Evolution, Medicago truncatula, plant science, duplications, Rhizobium, Laboratory of Molecular Biology, Genome, Plant, signal-transduction, science and technology, Lotus japonicus, Molecular Sequence Data, Genomics, Synteny, tetraploidy, Article, 03 medical and health sciences, Nitrogen Fixation, Botany, evolution, expression, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Laboratorium voor Moleculaire Biologie, Medicago sativa, Symbiosis, 030304 developmental biology, fungi, Fabaceae, sequence, biology.organism_classification, arabidopsis, leguminosae, Soybeans, genetic, EPS, 010606 plant biology & botany
Abstract: Chantier qualité GA; International audience; Legumes (Fabaceae or Leguminosae) are unique among cultivated plants for their ability to carry out endosymbiotic nitrogen fixation with rhizobial bacteria, a process that takes place in a specialized structure known as the nodule. Legumes belong to one of the two main groups of eurosids, the Fabidae, which includes most species capable of endosymbiotic nitrogen fixation1. Legumes comprise several evolutionary lineages derived from a common ancestor 60 million years ago (Myr ago). Papilionoids are the largest clade, dating nearly to the origin of legumes and containing most cultivated species2. Medicago truncatula is a long-established model for the study of legume biology. Here we describe the draft sequence of the M. truncatula euchromatin based on a recently completed BAC assembly supplemented with Illumina shotgun sequence, together capturing ~94% of all M. truncatula genes. A whole-genome duplication (WGD) approximately 58 Myr ago had a major role in shaping the M. truncatula genome and thereby contributed to the evolution of endosymbiotic nitrogen fixation. Subsequent to the WGD, the M. truncatula genome experienced higher levels of rearrangement than two other sequenced legumes, Glycine max and Lotus japonicus. M. truncatula is a close relative of alfalfa (Medicago sativa), a widely cultivated crop with limited genomics tools and complex autotetraploid genetics. As such, the M. truncatula genome sequence provides significant opportunities to expand alfalfa’s genomic toolbox.
Published: 2011

41. Green Evolution and Dynamic Adaptations Revealed by Genomes of the Marine Picoeukaryotes Micromonas

Author: Robert Otillar, Olivier Panaud, Aaron Poliakov, Ian T. Paulsen, Eve Toulza, Steven Robbens, Heidrun Gundlach, Pedro M. Coutinho, E. Virginia Armbrust, Jill E. Gready, Klaus F. X. Mayer, Jasmyn Pangilinan, Kemin Zhou, Igor V. Grigoriev, Wenche Eikrem, Marie L. Cuvelier, Elif Demir, Ursula Goodenough, Jonathan H. Badger, Hervé Moreau, Susan Lucas, Peter von Dassow, Yves Van de Peer, Evelyne Derelle, Pierre Rouzé, Andrew E. Allen, Erika Lindquist, Uwe John, Elodie Foulon, Jeremy Schmutz, Fabrice Not, William Lanier, Meredith V. Everett, Alex N. Zelensky, Sarah M. McDonald, Benoît Piégu, Jane Grimwood, Tania Wyss, Chelle L. Gentemann, Aasf Salamov, Micaela S. Parker, Stephane Rombauts, Alexandra Z. Worden, Carolyn A. Napoli, Thomas Mock, Bernard Henrissat, Jae-Hyeok Lee, Inna Dubchak, Melinda P. Simmons, Andrea Aerts, Debashish Bhattacharya, Monterey Bay Aquarium Research Institute (MBARI), Monterey Bay Aquarium Research Institute, School of Oceanography [Seattle], University of Washington [Seattle], Center for Plant Systems Biology (PSB Center), Vlaams Instituut voor Biotechnologie [Ghent, Belgique] (VIB), Department of Energy / Joint Genome Institute (DOE), Los Alamos National Laboratory (LANL), Observatoire océanologique de Banyuls (OOB), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Adaptation et diversité en milieu marin (AD2M), Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Stanford School of Medicine [Stanford], Stanford Medicine, Stanford University-Stanford University, Architecture et fonction des macromolécules biologiques (AFMB), Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU)-Institut National de la Recherche Agronomique (INRA), Biology Institute, University of Arizona, Laboratoire Génome et développement des plantes (LGDP), Université de Perpignan Via Domitia (UPVD)-Centre National de la Recherche Scientifique (CNRS), Department of Plant Systems Biology, State University of Ghent, Stanford University School of Medicine [Stanford], Stanford University [Stanford], and Institut National de la Recherche Agronomique (INRA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, MESH: Sequence Analysis, DNA, RNA, Untranslated, MESH: Oceans and Seas, MESH: Introns, MESH: Plants, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, 01 natural sciences, Genome, 18S ribosomal RNA, Bathycoccus, MESH: Chlorophyta, MESH: RNA, Untranslated, Chlorophyta, MESH: Ecosystem, MESH: Genetic Variation, Photosynthesis, MESH: Phylogeny, Clade, Phylogeny, MESH: Photosynthesis, Plant evolution, 0303 health sciences, Multidisciplinary, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], biology, Ecology, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], [SDV.BBM.MN]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular Networks [q-bio.MN], MESH: Transcription Factors, Plants, Adaptation, Physiological, Biological Evolution, MESH: Gene Expression Regulation, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], MESH: Genes, [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biomolecules [q-bio.BM], Meiosis, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biomolecules [q-bio.BM], MESH: DNA Transposable Elements, Oceans and Seas, Molecular Sequence Data, MESH: Biological Evolution, Genomics, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, [SDV.GEN.GPL]Life Sciences [q-bio]/Genetics/Plants genetics, 03 medical and health sciences, Phylogenetics, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, MESH: Genome, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, 14. Life underwater, [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biochemistry [q-bio.BM], Ecosystem, Repetitive Sequences, Nucleic Acid, 030304 developmental biology, Micromonas, [SDV.GEN]Life Sciences [q-bio]/Genetics, MESH: Repetitive Sequences, Nucleic Acid, MESH: Molecular Sequence Data, Genetic Variation, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, Sequence Analysis, DNA, biology.organism_classification, MESH: Adaptation, Physiological, Introns, MESH: Meiosis, [SDV.BV.AP]Life Sciences [q-bio]/Vegetal Biology/Plant breeding, Gene Expression Regulation, Genes, Phytoplankton, DNA Transposable Elements, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], Transcription Factors, MESH: Phytoplankton, 010606 plant biology & botany
Abstract: Picoeukaryotes are a taxonomically diverse group of organisms less than 2 micrometers in diameter. Photosynthetic marine picoeukaryotes in the genus Micromonas thrive in ecosystems ranging from tropical to polar and could serve as sentinel organisms for biogeochemical fluxes of modern oceans during climate change. These broadly distributed primary producers belong to an anciently diverged sister clade to land plants. Although Micromonas isolates have high 18 S ribosomal RNA gene identity, we found that genomes from two isolates shared only 90% of their predicted genes. Their independent evolutionary paths were emphasized by distinct riboswitch arrangements as well as the discovery of intronic repeat elements in one isolate, and in metagenomic data, but not in other genomes. Divergence appears to have been facilitated by selection and acquisition processes that actively shape the repertoire of genes that are mutually exclusive between the two isolates differently than the core genes. Analyses of the Micromonas genomes offer valuable insights into ecological differentiation and the dynamic nature of early plant evolution.
Published: 2009

42. Small-scale gene duplications played a major role in the recent evolution of wheat chromosome 3B

Author: Catherine Feuillet, Josquin Daron, Frédéric Choulet, Klaas Vandepoele, Etienne Paux, Natasha Glover, Lise Pingault, Génétique Diversité et Ecophysiologie des Céréales (GDEC), Institut National de la Recherche Agronomique (INRA)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP), Center for Plant Systems Biology (PSB Center), Vlaams Instituut voor Biotechnologie [Ghent, Belgique] (VIB), Department of Plant Biotechnology and Bioinformatics, Universiteit Gent = Ghent University [Belgium] (UGENT), French National Research Agency ANR-09-GENM-025 3BSEQ, France Agrimer, European Commission, French Ministry of Research, Region Auvergne, Ghent University Multidisciplinary Research Partnership ('Bioinformatics: from nucleotides to networks') 01MR0310W, VIB Department of Plant Systems Biology, Ghent University [Belgium] (UGENT), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Institut National de la Recherche Agronomique (INRA), and Universiteit Gent = Ghent University (UGENT)
Subjects: résistance aux maladies, Genome evolution, blé hexaploïde, BARLEY, RECOMBINATION, ORGANIZATION, Genes, Plant, Poaceae, SEQUENCE, Genome, Chromosomes, Plant, GRASSES, Evolution, Molecular, blé, duplication de gènes, Gene Duplication, Gene duplication, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, RICE, Triticeae, Gene, Triticum, Synteny, 2. Zero hunger, Genetics, GENOME EVOLUTION, chromosome 3B, Vegetal Biology, biology, Research, Biology and Life Sciences, food and beverages, 15. Life on land, biology.organism_classification, ALIGNMENT, Evolutionary biology, TRANSPOSABLE ELEMENTS, Brachypodium distachyon, PLANT GENOMES, Biologie végétale, Reference genome
Abstract: Background Bread wheat is not only an important crop, but its large (17 Gb), highly repetitive, and hexaploid genome makes it a good model to study the organization and evolution of complex genomes. Recently, we produced a high quality reference sequence of wheat chromosome 3B (774 Mb), which provides an excellent opportunity to study the evolutionary dynamics of a large and polyploid genome, specifically the impact of single gene duplications. Results We find that 27 % of the 3B predicted genes are non-syntenic with the orthologous chromosomes of Brachypodium distachyon, Oryza sativa, and Sorghum bicolor, whereas, by applying the same criteria, non-syntenic genes represent on average only 10 % of the predicted genes in these three model grasses. These non-syntenic genes on 3B have high sequence similarity to at least one other gene in the wheat genome, indicating that hexaploid wheat has undergone massive small-scale interchromosomal gene duplications compared to other grasses. Insertions of non-syntenic genes occurred at a similar rate along the chromosome, but these genes tend to be retained at a higher frequency in the distal, recombinogenic regions. The ratio of non-synonymous to synonymous substitution rates showed a more relaxed selection pressure for non-syntenic genes compared to syntenic genes, and gene ontology analysis indicated that non-syntenic genes may be enriched in functions involved in disease resistance. Conclusion Our results highlight the major impact of single gene duplications on the wheat gene complement and confirm the accelerated evolution of the Triticeae lineage among grasses. Electronic supplementary material The online version of this article (doi:10.1186/s13059-015-0754-6) contains supplementary material, which is available to authorized users.
Published: 2015

43. A Repressor Protein Complex Regulates Leaf Growth in Arabidopsis

Author: Gonzalez, Nathalie, Pauwels, Laurens, Baekelandt, Alexandra, De Milde, Liesbeth, Van Leene, Jelle, Besbrugge, Nienke, Heyndrickx, Ken S., Perez, Amparo Cuellar, Durand, Astrid Nagels, De Clercq, Rebecca, Van De Slijke, Eveline, Bossche, Robin Vanden, Eeckhout, Dominique, Gevaert, Kris, Vandepoele, Klaas, De Jaeger, Geert, Goossens, Alain, Inze, Dirk, Center for Plant Systems Biology (PSB Center), and Vlaams Instituut voor Biotechnologie [Ghent, Belgique] (VIB)
Subjects: [SDV]Life Sciences [q-bio], fungi, food and beverages
Abstract: A Repressor Protein Complex Regulates Leaf Growth in Arabidopsis. A Repressor Protein Complex Regulates Leaf Growth in Arabidopsis
Published: 2015

44. Caractérisation des mécanismes moléculaires régulant la croissance des organes chez les plantes

Author: Gonzalez, Nathalie, Universiteit Gent = Ghent University [Belgium] (UGENT), Center for Plant Systems Biology (PSB Center), and Vlaams Instituut voor Biotechnologie [Ghent, Belgique] (VIB)
Subjects: [SDV]Life Sciences [q-bio], hdr
Published: 2015

45. Field trials with genetically engineered forest trees: past experiences and future prospects

Author: Pilate, Gilles, Allona, Isabel, Boerjan, Wout, Dejardin, Annabelle, Fladung, Matthias, Gallardo, Fernando, Häggman, Hely, Jansson, Stefan, Van Acker, Rebecca, Halpin, Claire, Unité de recherche Amélioration, Génétique et Physiologie Forestières (AGPF), Institut National de la Recherche Agronomique (INRA), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria = National Institute for Agricultural and Food Research and Technology (INIA), Universidad Politécnica de Madrid (UPM), Department of plant systems biology, Flanders Institute for Biotechnology, Universiteit Gent = Ghent University [Belgium] (UGENT), Johann Heinrich von Thünen Institut, Universidad de Málaga [Málaga] = University of Málaga [Málaga], University of Oulu, Department of Plant Physiology, Umea Plant Science Centre, Umeå University-Umeå University, Umeå University, Center for Plant Systems Biology (PSB Center), Vlaams Instituut voor Biotechnologie [Ghent, Belgique] (VIB), Division of Plant Sciences, College of Life Sciences, University of Dundee, and IUFRO.
Subjects: [SDV.BIO]Life Sciences [q-bio]/Biotechnology, caractérisation phénotypique, expression de transgène, arbre transgénique, plante transgénique, essai en plein champ, résultat expérimental, Biotechnologies, organisme génétiquement modifié
Abstract: International audience; It is a common agronomic practice to evaluate new varieties under natural field conditions. This applies to GM plants and for more than 25 years, numerous field trials were set up throughout the world to assess GM trees modified for an array of different traits. In this talk, I will stress some of the knowledge, we gained from these experiments. While recently a few GM tree events have been authorized for commercial release, in Europe, GM tree field trials remain limited in numbers, mainly because it is becoming increasingly difficult to obtain authorization for a GM tree field trial. This is in sharp contrast with all the experimental results issued from GM tree field trial experiments: 1) phenotypic effects resulting from transgene expression in GM trees grown in the field appear to be stable, albeit variable 2) most field studies have validated earlier observations made under greenhouse conditions, although in some cases the modification of target traits was less obvious in fluctuating field environments, and in a few cases, GM trees had severe growth and developmental penalties 3) non-target effects were consistently within the range of natural variation. Overall, the European GM tree field trials failed to identify any significant tangible risks. Based on this evidence, it seems appropriate that Europe should now move forward beyond small confined trials to larger scale experiments better fitted to a broader context of evaluation and environmental assessment.
Published: 2015

46. Aging in Legume Symbiosis. A Molecular View on Nodule Senescence in Medicago truncatula

Author: Eva Kondorosi, Sofie Goormachtig, Peter Mergaert, Willem Van de Velde, Juan Carlos Pérez Guerra, Marcelle Holsters, Riet De Rycke, Stephane Rombauts, Nicolas Maunoury, Annick De Keyser, Institut des sciences du végétal (ISV), Centre National de la Recherche Scientifique (CNRS), Center for Plant Systems Biology (PSB Center), and Vlaams Instituut voor Biotechnologie [Ghent, Belgique] (VIB)
Subjects: 0106 biological sciences, Nodule (geology), Root nodule, Physiology, ALFALFA NODULES, MESH: Plant Roots, Plant Science, MESH: Research Support, Non-U.S. Gov't, Plant Roots, 01 natural sciences, Transcriptome, MESH: Reverse Transcriptase Polymerase Chain Reaction, Medicago, Cluster Analysis, GENE-EXPRESSION, 0303 health sciences, MESH: Symbiosis, biology, Reverse Transcriptase Polymerase Chain Reaction, food and beverages, Fabaceae, Medicago truncatula, Nitrogen fixation, Research Article, MESH: Medicago, Senescence, DNA, Complementary, PROTEASE, DATABASE, Molecular Sequence Data, ARABIDOPSIS LEAF SENESCENCE, engineering.material, Rhizobia, 03 medical and health sciences, Symbiosis, Botany, Genetics, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, PLANTS, ROOT-NODULES, 030304 developmental biology, MESH: Molecular Sequence Data, CYSTEINE PROTEINASE, Biology and Life Sciences, MESH: DNA, Complementary, GENOME-WIDE EXPRESSION, biology.organism_classification, MESH: Cluster Analysis, engineering, NITROGEN-FIXATION, MESH: Fabaceae, 010606 plant biology & botany
Abstract: Rhizobia reside as symbiosomes in the infected cells of legume nodules to fix atmospheric nitrogen. The symbiotic relation is strictly controlled, lasts for some time, but eventually leads to nodule senescence. We present a comprehensive transcriptomics study to understand the onset of nodule senescence in the legume Medicago truncatula. Distinct developmental stages with characteristic gene expression were delineated during which the two symbiotic partners were degraded consecutively, marking the switch in nodule tissue status from carbon sink to general nutrient source. Cluster analysis discriminated an early expression group that harbored regulatory genes that might be primary tools to interfere with pod filling-related or stress-induced nodule senescence, ultimately causing prolonged nitrogen fixation. Interestingly, the transcriptomes of nodule and leaf senescence had a high degree of overlap, arguing for the recruitment of similar pathways.
Published: 2006

47. Au-Au chemical bonding induced by UV irradiation of dinuclear gold(i) complexes: a computational study with experimental evidence

Author: Chen-Wei Liu, Yan-Ru Lin, Camille Latouche, Yeny A. Tobon, Jean-Yves Saillard, Abdou Boucekkine, Eric Furet, Institut des Sciences Chimiques de Rennes (ISCR), Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Ecole Nationale Supérieure de Chimie de Rennes (ENSCR)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Center for Plant Systems Biology (PSB Center), Vlaams Instituut voor Biotechnologie [Ghent, Belgique] (VIB), Laboratoire Avancé de Spectroscopie pour les Intéractions la Réactivité et l'Environnement - UMR 8516 (LASIRE), Institut de Chimie du CNRS (INC)-Université de Lille-Centre National de la Recherche Scientifique (CNRS), Université européenne de Bretagne - European University of Brittany (UEB), Laboratoire Interdisciplinaire de Physique, Laboratoire Interdisciplinaire de Physique [Saint Martin d’Hères] (LIPhy), Université Joseph Fourier - Grenoble 1 (UJF)-Centre National de la Recherche Scientifique (CNRS)-Université Joseph Fourier - Grenoble 1 (UJF)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Ecole Nationale Supérieure de Chimie de Rennes (ENSCR)-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), Institut de Chimie du CNRS (INC)-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Centrale Lille Institut (CLIL), and Centre National de la Recherche Scientifique (CNRS)-Université Joseph Fourier - Grenoble 1 (UJF)-Centre National de la Recherche Scientifique (CNRS)-Université Joseph Fourier - Grenoble 1 (UJF)
Subjects: 010405 organic chemistry, Chemistry, Ultraviolet Rays, General Physics and Astronomy, Time-dependent density functional theory, 010402 general chemistry, Photochemistry, 01 natural sciences, Spectral line, 0104 chemical sciences, [CHIM.THEO]Chemical Sciences/Theoretical and/or physical chemistry, Crystallography, symbols.namesake, Chemical bond, Excited state, symbols, Quantum Theory, Gold, Physical and Theoretical Chemistry, Absorption (chemistry), Luminescence, Ground state, Raman spectroscopy, Organogold Compounds
Abstract: International audience; Two luminescent dinuclear gold(i) species, namely diselenophosphinate [Au2{μ-Se2P((CH2)2Ph)2}2] and dithiophosphinate [Au2{μ-S2P((CH2)2Ph)2}2], exhibiting interesting structural, absorption and emission properties have been studied. In the solid state, both complexes exist in a dinuclear monomeric form, exhibiting no aurophilic interaction, and display similar photophysical properties. It is shown, using DFT computations, that Au-Au chemical bonding appears in the first excited state of these complexes, whereas such bonding does not exist in their ground state; Raman spectroscopy experiments, which bring to light the stretching of this new bond, confirm the theoretical results. Moreover, TDDFT computations permitted us to assign the observed absorption bands of the UV-visible spectra of the two species to LMCT transitions and to describe the emission.
Published: 2014

48. A Haploid System of Sex Determination in the Brown Alga Ectocarpus sp

Author: Akira F. Peters, John H. F. Bothwell, J. Mark Cock, Denis Roze, Marine Robuchon, Myriam Valero, Susana M. Coelho, Alexandre Cormier, Eugénie Pessia, Yves Van de Peer, Simon M. Dittami, Sophia Ahmed, Lieven Sterck, Remy Luthringer, Gabriel A. B. Marais, Erwan Corre, Jean-Marc Aury, Santé Végétale (SV), Institut National de la Recherche Agronomique (INRA)-École Nationale d'Ingénieurs des Travaux Agricoles - Bordeaux (ENITAB), Végétaux marins et biomolécules, Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-GOEMAR-Centre National de la Recherche Scientifique (CNRS), Sexe et évolution, Département PEGASE [LBBE] (PEGASE), Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-Université Pierre et Marie Curie - Paris 6 (UPMC)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS), Evolutionary Biology and Ecology of Algae (EBEA), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Pontificia Universidad Católica de Chile (UC)-Universidad Austral de Chile-Centre National de la Recherche Scientifique (CNRS), Center for Plant Systems Biology (PSB Center), Vlaams Instituut voor Biotechnologie [Ghent, Belgique] (VIB), Bezhin Rosko, Marine Biological Association Laboratory (MBA Laboratory), Marine Biological Association of the UK, Phophorylation de protéines et Pathologies Humaines (P3H), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-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), Génomique métabolique (UMR 8030), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-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 d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Sorbonne Université (SU), Department of Plant Biotechnology and Bioinformatics, Universiteit Gent = Ghent University (UGENT), Department of Plant Systems Biology, Flanders Institute for Biotechnology, Department of Genetics, Genomics Research Institute, University of Pretoria [South Africa], Belfast e-Science Centre [Belfast] (BESC), Queen's University [Belfast] (QUB), Laboratoire de Biologie Intégrative des Modèles Marins (LBI2M), Biologie Intégrative des Populations, École pratique des hautes études (EPHE)-Centre National de la Recherche Scientifique (CNRS), State University of Ghent, 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)-Centre National de la Recherche Scientifique (CNRS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), Sorbonne Universités, Ghent University [Belgium] (UGENT), Muséum national d'Histoire naturelle (MNHN)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Universidad Austral de Chile-Centre National de la Recherche Scientifique (CNRS)-Pontificia Universidad Católica de Chile (UC), Universiteit Gent = Ghent University [Belgium] (UGENT), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-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)-Université Paris-Saclay, and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE)
Subjects: 0106 biological sciences, Biology, Haploidy, Phaeophyta, 010603 evolutionary biology, 01 natural sciences, Genome, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, Negative selection, Gene, 030304 developmental biology, Genetics, 0303 health sciences, [SDV.GEN]Life Sciences [q-bio]/Genetics, Agricultural and Biological Sciences(all), Biochemistry, Genetics and Molecular Biology(all), [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], Haplotype, Chromosome, Ectocarpus, Sex Determination Processes, biology.organism_classification, Sexual dimorphism, Ploidy, General Agricultural and Biological Sciences
Abstract: Summary Background A common feature of most genetic sex-determination systems studied so far is that sex is determined by nonrecombining genomic regions, which can be of various sizes depending on the species. These regions have evolved independently and repeatedly across diverse groups. A number of such sex-determining regions (SDRs) have been studied in animals, plants, and fungi, but very little is known about the evolution of sexes in other eukaryotic lineages. Results We report here the sequencing and genomic analysis of the SDR of Ectocarpus , a brown alga that has been evolving independently from plants, animals, and fungi for over one giga-annum. In Ectocarpus , sex is expressed during the haploid phase of the life cycle, and both the female (U) and the male (V) sex chromosomes contain nonrecombining regions. The U and V of this species have been diverging for more than 70 mega-annum, yet gene degeneration has been modest, and the SDR is relatively small, with no evidence for evolutionary strata. These features may be explained by the occurrence of strong purifying selection during the haploid phase of the life cycle and the low level of sexual dimorphism. V is dominant over U, suggesting that femaleness may be the default state, adopted when the male haplotype is absent. Conclusions The Ectocarpus UV system has clearly had a distinct evolutionary trajectory not only to the well-studied XY and ZW systems but also to the UV systems described so far. Nonetheless, some striking similarities exist, indicating remarkable universality of the underlying processes shaping sex chromosome evolution across distant lineages.
Published: 2014

49. The genome of Eucalyptus grandis

Author: Anand Raj Kumar Kullan, Erich Bornberg-Bauer, Christopher M. Sullivan, Florent Murat, Elisson Romanel, Yves Van de Peer, Aaron Liston, Priya Ranjan, Dorothy A. Steane, Justin Elser, Pooja Singh, Victor Carocha, Orzenil B. Silva-Junior, Marçal Soler, Cesar Petroli, Inna Dubchak, Jane Grimwood, Carsten Külheim, Danielle A. Faria, Ida Van Jaarsveld, Chu-Yu Ye, Giancarlo Pasquali, Charles A. Hefer, Desre Pinard, Roberto C. Togawa, Richard D. Hayes, Eshchar Mizrachi, Fourie Joubert, Erika Lindquist, Kevin Vanneste, Philippe Rigault, Jérôme Salse, Karen Van der Merwe, David Kudrna, Palitha Dharmwardhana, Gerald A. Tuskan, Diane Bauer, Alexandre Poliakov, Marcio Alves-Ferreira, Kerrie Barry, Vindhya Amarasinghe, Ting Li, William J. Foley, Georgios J. Pappas, Carolina Sansaloni, René E. Vaillancourt, Marília de Castro Rodrigues Pappas, Uffe Hellsten, Daniel S. Rokhsar, Martin Ranik, Anna R. Kersting, Alexander Andrew Myburg, Hua Cassan-Wang, David Goodstein, Christophe Dunand, Naijib Saidi, Timothy J. Tschaplinski, Sushma Naithani, Dario Grattapaglia, Pankaj Jaiswal, Steven G. Hussey, Jeremy Schmutz, Rajani Raja, Brad M. Potts, Margaret Byrne, Antanas V. Spokevicius, Jorge A. P. Paiva, Jacqueline Grima-Pettenati, Xiaohan Yang, Alexander Boyd, Hope Tice, Joseph W. Spatafora, Lieven Sterck, Jerry Jenkins, Steven H. Strauss, Sérgio Hermínio Brommonschenkel, Josquin Tibbits, Rebecca C. Jones, Kelly J. Vining, Hélène San Clemente, BioSciences Division [Oak Ridge], Oak Ridge National Laboratory [Oak Ridge] (ORNL), UT-Battelle, LLC-UT-Battelle, LLC, DOE Joint Genome Institute [Walnut Creek], Department of Epidemiology & Population Health, London School of Hygiene and Tropical Medicine (LSHTM), Department of Energy / Joint Genome Institute (DOE), Los Alamos National Laboratory (LANL), United States Department of Energy, US Department of Energy Joint Genome Institute, University of California, Embrapa Uva e Vinho (BRAZIL), Technicolor R & I [Cesson Sévigné], Technicolor, Department of Plant Systems Biology, State University of Ghent, Ghent University [Belgium] (UGENT), Génétique Diversité et Ecophysiologie des Céréales (GDEC), Institut National de la Recherche Agronomique (INRA)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP), Laboratoire de Recherche en Sciences Végétales (LRSV), Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Institute for Evolution and Biodiversity (IEB), Westfälische Wilhelms-Universität Münster (WWU), Department of Botany and Plant Pathology, Oregon State University (OSU), RAIZ – Forestry & Paper Research Institut, Laboratory of Plant Cell Biotechnology, ITQB/IBET, Ecology and Evolutionary Biology [Tucson] (EEB), University of Arizona, GYDLE, Agriculture Victoria Research, Department of Economic Development, Jobs, Transport and Resources, AgriBio, Bioinformatics and Computational Biology Unit, Faculty of Natural and Agricultural Sciences-University of Pretoria [South Africa], Institute of Continuing Medical Education of Ioannina, Plastes et différenciation cellulaire (PDC), Université Joseph Fourier - Grenoble 1 (UJF)-Centre National de la Recherche Scientifique (CNRS), Génétique Diversité et Ecophysiologie des Céréales - Clermont Auvergne (GDEC), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne (UCA), Center for Plant Systems Biology (PSB Center), Vlaams Instituut voor Biotechnologie [Ghent, Belgique] (VIB), Universiteit Gent = Ghent University [Belgium] (UGENT), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Régulation et Dynamique de la Formation du Bois, Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Dynamique et Evolution des Parois cellulaires végétales, Office of Science of the US Department of Energy [DE-AC02-05CH11231], Office of Biological and Environmental Research in the US Department of Energy Office of Science, US DOE Bioenergy Center [DE-AC05-00OR22725], Brazilian Ministry of Science, Technology and Innovation (MCTI) through (CNPq), Brazilian Ministry of Science, Technology and Innovation (MCTI) through (FINEP), Brazilian Federal District Research Foundation (FAP-DF), Technology and Human Resources for Industry Programme (THRIP) [UID 80118], South African Department of Science and Technology (DST), National Research Foundation (NRF) [UID 18312, 86936], Laboratoire d'Excellence [LABEX TULIP ANR-10-LABX-41], Agence Nationale pour la Recherche (Project Tree For Joules) [ANR-2010-KBBE-007-01], Fundacao para a Ciencia e Tecnologia (FCT) [P-KBBE/AGR_GPL/0001/2010], Centre National pour la Recherche Scientifique (CNRS), University Paul Sabatier Toulouse III (UPS), Ghent University, Hercules Foundation, Flemish Government-department EWI, Myburg, Alexander A., University of California (UC), Universiteit Gent = Ghent University (UGENT), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), and Westfälische Wilhelms-Universität Münster = University of Münster (WWU)
Subjects: Genome evolution, DATABASE, phylogénomique, [SDV]Life Sciences [q-bio], Biology, Genome, DNA sequencing, Evolution, Molecular, Phylogenomics, Myrtales, Botany, Inbreeding depression, TOOL, Inbreeding, RNA-SEQ, PLANT, NUCLEAR-DNA, Phylogeny, ComputingMilieux_MISCELLANEOUS, Eucalyptus, Multidisciplinary, FOREST TREES, Biology and Life Sciences, Genetic Variation, métabolisme secondaire, 15. Life on land, biology.organism_classification, GENE, EVOLUTION, ALIGNMENT, biocarburant, Biofuels, Eucalyptus globulus, évolution du génome, WHOLE-GENOME, Secondary metabolism, Genome, Plant
Abstract: International audience; Eucalypts are the world's most widely planted hardwood trees. Their outstanding diversity, adaptability and growth have made them a global renewable resource of fibre and energy. We sequenced and assembled >94% of the 640-megabase genome of Eucalyptus grandis. Of 36,376 predicted protein-coding genes, 34% occur in tandem duplications, the largest proportion thus far in plant genomes. Eucalyptus also shows the highest diversity of genes for specialized metabolites such as terpenes that act as chemical defence and provide unique pharmaceutical oils. Genome sequencing of the E. grandis sister species E. globulus and a set of inbred E. grandis tree genomes reveals dynamic genome evolution and hotspots of inbreeding depression. The E. grandis genome is the first reference for the eudicot order Myrtales and is placed here sister to the eurosids. This resource expands our understanding of the unique biology of large woody perennials and provides a powerful tool to accelerate comparative biology, breeding and biotechnology.
Published: 2014

50. New strigolactone analogs as plant hormones with low activities in the rhizosphere

Author: Sofie Goormachtig, François-Didier Boyer, Nicolas Frei dit Frey, Jean-Paul Pillot, Catherine Rameau, Danny Geelen, Guillaume Clavé, Christian V. Stevens, Thomas S. A. Heugebaert, Amélie Roux, Jean-Bernard Pouvreau, Alexandre de Saint Germain, Stephen Depuydt, Dominique Lauressergues, Amanda Rasmussen, Institut de Chimie des Substances Naturelles (ICSN), Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC), Department of Plant Production [Ghent], Faculty of Bioscience Engineering [Ghent], Universiteit Gent = Ghent University [Belgium] (UGENT)-Universiteit Gent = Ghent University [Belgium] (UGENT), Center for Plant Systems Biology (PSB Center), Vlaams Instituut voor Biotechnologie [Ghent, Belgique] (VIB), Institut National de la Recherche Agronomique (INRA), Agence Nationale de la Recherche [ANR-12-BSV6-004-01], Marie Curie International Incoming Fellowship, Newton International Fellowship, and Fund for Scientific Research Flanders (FWO Vlaanderen)
Subjects: Hyphal growth, Gigaspora rosea, plant growth regulator, Mutant, Arabidopsis, Strigolactone, Plant Science, strigolactones, Lactones, Plant Growth Regulators, Gene Expression Regulation, Plant, root parasitic plants, Botany, Glomeromycota, Molecular Biology, Pisum sativum, synthetic analogs, Rhizosphere, biology, [CHIM.ORGA]Chemical Sciences/Organic chemistry, fungi, food and beverages, biology.organism_classification, Germination, Plant hormone, Weed
Abstract: International audience; : Strigolactones (SLs) are known not only as plant hormones, but also as rhizosphere signals for establishing symbiotic and parasitic interactions. The design of new specific SL analogs is a challenging goal in understanding the basic plant biology and is also useful to control plant architectures without favoring the development of parasitic plants. Two different molecules (23 (3'-methyl-GR24), 31 (thia-3'-methyl-debranone-like molecule)) already described, and a new one (AR36), for which the synthesis is presented, are biologically compared with the well-known GR24 and the recently identified CISA-1. These different structures emphasize the wide range of parts attached to the D-ring for the bioactivity as a plant hormone. These new compounds possess a common dimethylbutenolide motif but their structure varies in the ABC part of the molecules: 23 has the same ABC part as GR24, while 31 and AR36 carry, respectively, an aromatic ring and an acyclic carbon chain. Detailed information is given for the bioactivity of such derivatives in strigolactone synthesis or in perception mutant plants (pea rms1 and rms4, Arabidopsis max2 and, max4) for different hormonal functions along with their action in the rhizosphere on arbuscular mycorrhizal hyphal growth and parasitic weed germination.
Published: 2014

Catalog

Books, media, physical & digital resources

See catalog results

Searchworks

Select search scope, currently: Articles Catalog books, media & more in Jio Institute collections Articles journal articles & other e-resources

Search

Search Constraints

Refine your results

Search Limiters

Topic

Publication Year Range

Language

Journal

Database

Publisher

98 results on '"Center for Plant Systems Biology (PSB Center)"'

Search Results

Catalog

Select search scope, currently: Articles

Catalog

books, media & more in Jio Institute collections

Articles

journal articles & other e-resources