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9. Mechanistic insights into consumption of the food additive xanthan gum by the human gut microbiota

Author

Matthew P. Ostrowski, Sabina Leanti La Rosa, Benoit J. Kunath, Andrew Robertson, Gabriel Pereira, Live H. Hagen, Neha J. Varghese, Ling Qiu, Tianming Yao, Gabrielle Flint, James Li, Sean P. McDonald, Duna Buttner, Nicholas A. Pudlo, Matthew K. Schnizlein, Vincent B. Young, Harry Brumer, Thomas M. Schmidt, Nicolas Terrapon, Vincent Lombard, Bernard Henrissat, Bruce Hamaker, Emiley A. Eloe-Fadrosh, Ashootosh Tripathi, Phillip B. Pope, Eric C. Martens, Norwegian University of Life Sciences (NMBU), Luxembourg Centre For Systems Biomedicine (LCSB), University of Luxembourg [Luxembourg], US Department of Energy Joint Genome Institute, Walnut Creek CA, USA, DOE Joint Genome Institute [Walnut Creek], Department of Microbiology and Immunology, University of Michigan Medical School, University of Michigan [Ann Arbor], University of Michigan System-University of Michigan System, University of British Columbia (UBC), Paul Scherrer Institute (PSI), Architecture et fonction des macromolécules biologiques (AFMB), and Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)

Subjects
Dietary Fiber, Microbiology (medical), MESH: Humans, [SDV]Life Sciences [q-bio], Polysaccharides, Bacterial, Immunology, MESH: Food Additives, Cell Biology, Applied Microbiology and Biotechnology, Microbiology, MESH: Gastrointestinal Microbiome, Gastrointestinal Microbiome, Mice, MESH: Dietary Fiber, Genetics, Animals, Humans, Food Additives, MESH: Animals, MESH: Polysaccharides, Bacterial, MESH: Mice
Abstract

International audience; Processed foods often include food additives such as xanthan gum, a complex polysaccharide with unique rheological properties, that has established widespread use as a stabilizer and thickening agent. Xanthan gum's chemical structure is distinct from those of host and dietary polysaccharides that are more commonly expected to transit the gastrointestinal tract, and little is known about its direct interaction with the gut microbiota, which plays a central role in digestion of other dietary fibre polysaccharides. Here we show that the ability to digest xanthan gum is common in human gut microbiomes from industrialized countries and appears contingent on a single uncultured bacterium in the family Ruminococcaceae. Our data reveal that this primary degrader cleaves the xanthan gum backbone before processing the released oligosaccharides using additional enzymes. Some individuals harbour Bacteroides intestinalis that is incapable of consuming polymeric xanthan gum but grows on oligosaccharide products generated by the Ruminococcaceae. Feeding xanthan gum to germfree mice colonized with a human microbiota containing the uncultured Ruminococcaceae supports the idea that the additive xanthan gum can drive expansion of the primary degrader Ruminococcaceae, along with exogenously introduced B. intestinalis. Our work demonstrates the existence of a potential xanthan gum food chain involving at least two members of different phyla of gut bacteria and provides an initial framework for understanding how widespread consumption of a recently introduced food additive influences human microbiomes.

Published
2022
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10. Lipophilicity trends upon fluorination of isopropyl, cyclopropyl and 3-oxetanyl groups

Author

Robert I. Troup, Zhong Wang, Jérôme Graton, Jean-Yves Le Questel, Bruno Linclau, Anaïs Goupille, Benjamin Jeffries, Charlene Fallan, James S. Scott, Elisabetta Chiarparin, DOE Joint Genome Institute [Walnut Creek], Chimie Et Interdisciplinarité : Synthèse, Analyse, Modélisation (CEISAM), Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST), Université de Nantes (UN)-Université de Nantes (UN)-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC), University of Toronto, School of Chemistry [Southampton, UK], and University of Southampton

Subjects
Isostere, Substituent, isopropyl, 010402 general chemistry, Oxetane, 01 natural sciences, Medicinal chemistry, aliphatic fluorination, Full Research Paper, Cyclopropane, lcsh:QD241-441, chemistry.chemical_compound, lcsh:Organic chemistry, isostere, lipophilicity, [CHIM]Chemical Sciences, lcsh:Science, Carbon atom, 010405 organic chemistry, Organic Chemistry, oxetane, 0104 chemical sciences, Chemistry, chemistry, Lipophilicity, cyclopropane, lcsh:Q, Isopropyl
Abstract

International audience; A systematic comparison of lipophilicity modulations upon fluorination of isopropyl, cyclopropyl and 3-oxetanyl substituents, at a single carbon atom, is provided using directly comparable, and easily accessible model compounds. In addition, comparison with relevant linear chain derivatives is provided, as well as lipophilicity changes occurring upon chain extension of acyclic precursors to give cyclopropyl containing compounds. For the compounds investigated, fluorination of the isopropyl substituent led to larger lipophilicity modulation compared to fluorination of the cyclopropyl substituent.

Published
2020
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11. Yaravirus: A novel 80-nm virus infecting Acanthamoeba castellanii

Author

Saïd Azza, Jean-Pierre Baudoin, Philippe Decloquement, Talita Bastos Machado, Anthony Levasseur, Eric Chabrière, Frederik Schulz, Thomas Klose, Philippe Colson, Paulo V. M. Boratto, Ana Cláudia dos Santos Pereira Andrade, Jônatas Santos Abrahão, Bernard La Scola, Graziele Pereira Oliveira, Microbes évolution phylogénie et infections (MEPHI), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Universidade Federal de Minas Gerais, Institut Hospitalier Universitaire Méditerranée Infection (IHU Marseille), Department of Biological Sciences [Lafayette IN], Purdue University [West Lafayette], DOE Joint Genome Institute [Walnut Creek], Lawrence Berkeley National Laboratory [Berkeley] (LBNL), Laboratório de Vírus, and Universidade Federal de Minas Gerais [Belo Horizonte] (UFMG)-Instituto de Ciências Biológicas [Goiânia, Brésil] (ICB)

Subjects
[SDV]Life Sciences [q-bio], Genome, Viral, Biology, Proteomics, Genome, Virus, Viral Proteins, Yaravirus, 03 medical and health sciences, chemistry.chemical_compound, Phylogenetics, capsid, Genetics, 2.2 Factors relating to the physical environment, Viral, Aetiology, Gene, Phylogeny, 030304 developmental biology, Acanthamoeba castellanii, metagenomics, 0303 health sciences, Multidisciplinary, 030306 microbiology, Human Genome, DNA Viruses, ORFan, Genome project, Biological Sciences, chemistry, Metagenomics, NCLDV, Infection, DNA
Abstract

Here we report the discovery of Yaravirus, a lineage of amoebal virus with a puzzling origin and evolution. Yaravirus presents 80-nm-sized particles and a 44,924-bp dsDNA genome encoding for 74 predicted proteins. Yaravirus genome annotation showed that none of its genes matched with sequences of known organ-isms at the nucleotide level; at the amino acid level, six predicted proteins had distant matches in the nr database. Complimentary prediction of three-dimensional structures indicated possible func-tion of 17 proteins in total. Furthermore, we were not able to retrieve viral genomes closely related to Yaravirus in 8,535 publicly available metagenomes spanning diverse habitats around the globe. The Yaravirus genome also contained six types of tRNAs that did not match commonly used codons. Proteomics revealed that Yaravirus particles contain 26 viral proteins, one of which potentially represent-ing a divergent major capsid protein (MCP) with a predicted double jelly-roll domain. Structure-guided phylogeny of MCP suggests that Yaravirus groups together with the MCPs of Pleurochrysis endemic viruses. Yaravirus expands our knowledge of the diversity of DNA viruses. The phylogenetic distance between Yaravirus and all other viruses highlights our still preliminary assessment of the genomic diversity of eukaryotic viruses, reinforcing the need for the isolation of new viruses of protists.

Published
2020
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12. DNA Methylation in Ensifer Species during Free-Living Growth and during Nitrogen-Fixing Symbiosis with Medicago spp

Author

Alessio Mengoni, Nicole Shapiro, Matthew J. Blow, Peter Mergaert, Tanja Woyke, Quentin Nicoud, Emanuele G. Biondi, Benoit Alunni, Janis H.T. Cheng, Lisa Cangioli, George C. diCenzo, Bulgarelli, Davide, Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Queen's University [Kingston, Canada], University of California [Berkeley] (UC Berkeley), University of California (UC), DOE Joint Genome Institute [Walnut Creek], Department of Energy / Joint Genome Institute (DOE), Los Alamos National Laboratory (LANL), Laboratoire de chimie bactérienne (LCB), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Università degli Studi di Firenze = University of Florence (UniFI), ANR-11-EQPX-0029,MORPHOSCOPE 2,Imagerie et reconstruction multiéchelles de la morphogenèse. (Plateforme d'innovation technologique et méthodologique pour l'imagerie in vivo et la reconstruction des dynamiques multiéchelles de la morphogenèse)(2011), ANR-11-IDEX-0003,IPS,Idex Paris-Saclay(2011), ANR-17-CE20-0011,SymbiontCellCyc,Rôle du cycle cellulaire bactérien dans la fixation symbiotique d'azote chez les Légumineuses(2017), Università degli Studi di Firenze = University of Florence [Firenze] (UNIFI), I2BC - Institut de Biologie Intégrative de la Cellule, Institute for Integrative Biology of the Cell [Gif-sur-Yvette] (I2BC), and Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France.

Subjects
symbiotic nitrogen fixation, Methyltransferase, Physiology, [SDV]Life Sciences [q-bio], 1.1 Normal biological development and functioning, Cell, Biology, rhizobia, Biochemistry, Microbiology, DNA sequencing, 03 medical and health sciences, Underpinning research, CcrM, medicine, Genetics, Endoreduplication, 2.2 Factors relating to the physical environment, Replicon, Aetiology, Molecular Biology, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, 0303 health sciences, DNA methylation, 030306 microbiology, Human Genome, fungi, Cell cycle regulation, Rhizobia, Symbiotic nitrogen fixation, food and beverages, Methylation, Cell cycle, Computer Science Applications, medicine.anatomical_structure, Modeling and Simulation, Infection, cell cycle regulation, Research Article
Abstract

Methylation of specific DNA sequences is ubiquitous in bacteria and has known roles in immunity and regulation of cellular processes, such as the cell cycle. Here, we explored DNA methylation in bacteria of the genus Ensifer, including its potential role in regulating terminal differentiation during nitrogen-fixing symbiosis with legumes. Using single-molecule real-time sequencing, six genome-wide methylated motifs were identified across four Ensifer strains, five of which were strain-specific. Only the GANTC motif, recognized by the cell cycle-regulated CcrM methyltransferase, was methylated in all strains. In actively dividing cell cultures, methylation of GANTC motifs increased progressively from the ori to ter regions in each replicon, in agreement with a cell cycle-dependent regulation of CcrM. In contrast, there was near full genome-wide GANTC methylation in the early stage of symbiotic differentiation. This was followed by a moderate decrease in the overall extent of methylation and a progressive decrease in chromosomal GANTC methylation from the ori to ter regions in later stages of differentiation. Based on these observations, we suggest that CcrM activity is dysregulated and constitutive during terminal differentiation, which we hypothesize is a driving factor for endoreduplication of terminally differentiated bacteroids. IMPORTANCE Nitrogen fixation by rhizobia in symbiosis with legumes is economically and ecologically important. The symbiosis can involve a complex bacterial transformation—terminal differentiation—that includes major shifts in the transcriptome and cell cycle. Epigenetic regulation is an important regulatory mechanism in diverse bacteria; however, the roles of DNA methylation in rhizobia and symbiotic nitrogen fixation have been poorly investigated. We show that aside from cell cycle regulation, DNA methyltransferases are unlikely to have conserved roles in the biology of bacteria of the genus Ensifer. However, we present evidence consistent with an interpretation that the cell cycle methyltransferase CcrM is dysregulated during symbiosis, which we hypothesize may be a key factor driving the cell cycle switch in terminal differentiation required for effective symbioses.

Published
2022
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13. Critical Assessment of Metagenome Interpretation: the second round of challenges

Author

Fernando Meyer, Adrian Fritz, Zhi-Luo Deng, David Koslicki, Till Robin Lesker, Alexey Gurevich, Gary Robertson, Mohammed Alser, Dmitry Antipov, Francesco Beghini, Denis Bertrand, Jaqueline J. Brito, C. Titus Brown, Jan Buchmann, Aydin Buluç, Bo Chen, Rayan Chikhi, Philip T. L. C. Clausen, Alexandru Cristian, Piotr Wojciech Dabrowski, Aaron E. Darling, Rob Egan, Eleazar Eskin, Evangelos Georganas, Eugene Goltsman, Melissa A. Gray, Lars Hestbjerg Hansen, Steven Hofmeyr, Pingqin Huang, Luiz Irber, Huijue Jia, Tue Sparholt Jørgensen, Silas D. Kieser, Terje Klemetsen, Axel Kola, Mikhail Kolmogorov, Anton Korobeynikov, Jason Kwan, Nathan LaPierre, Claire Lemaitre, Chenhao Li, Antoine Limasset, Fabio Malcher-Miranda, Serghei Mangul, Vanessa R. Marcelino, Camille Marchet, Pierre Marijon, Dmitry Meleshko, Daniel R. Mende, Alessio Milanese, Niranjan Nagarajan, Jakob Nissen, Sergey Nurk, Leonid Oliker, Lucas Paoli, Pierre Peterlongo, Vitor C. Piro, Jacob S. Porter, Simon Rasmussen, Evan R. Rees, Knut Reinert, Bernhard Renard, Espen Mikal Robertsen, Gail L. Rosen, Hans-Joachim Ruscheweyh, Varuni Sarwal, Nicola Segata, Enrico Seiler, Lizhen Shi, Fengzhu Sun, Shinichi Sunagawa, Søren Johannes Sørensen, Ashleigh Thomas, Chengxuan Tong, Mirko Trajkovski, Julien Tremblay, Gherman Uritskiy, Riccardo Vicedomini, Zhengyang Wang, Ziye Wang, Zhong Wang, Andrew Warren, Nils Peder Willassen, Katherine Yelick, Ronghui You, Georg Zeller, Zhengqiao Zhao, Shanfeng Zhu, Jie Zhu, Ruben Garrido-Oter, Petra Gastmeier, Stephane Hacquard, Susanne Häußler, Ariane Khaledi, Friederike Maechler, Fantin Mesny, Simona Radutoiu, Paul Schulze-Lefert, Nathiana Smit, Till Strowig, Andreas Bremges, Alexander Sczyrba, Alice Carolyn McHardy, Braunschweig Integrated Centre of Systems Biology [Braunschweig] (BRICS), Technische Universität Braunschweig = Technical University of Braunschweig [Braunschweig]-Helmholtz Centre for Infection Research (HZI), Pennsylvania State University (Penn State), Penn State System, German Center for Infection Research - partner site Hannover-Braunschweig (DZIF), Saint Petersburg State University (SPBU), Department of Information Technology and Electrical Engineering [Zürich] (D-ITET), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), Center for Algorithmic Biotechnology [Saint Petersburg], Institute of Translational Biomedicine [Saint-Petersburg], Saint Petersburg University (SPBU)-Saint Petersburg University (SPBU), Centre for Integrative Biology (CIBIO), University of Trento (CIBIO), University of Trento [Trento], Genome Institute of Singapore (GIS), University of Southern California (USC), University of California [Davis] (UC Davis), University of California (UC), Heinrich Heine Universität Düsseldorf = Heinrich Heine University [Düsseldorf], Lawrence Berkeley National Laboratory [Berkeley] (LBNL), Institut Pasteur [Paris] (IP), National Food Institute [Lyngby] (Forside), Drexel University, Robert Koch Institute [Berlin] (RKI), University of Technology Sydney (UTS), DOE Joint Genome Institute [Walnut Creek], University of California [Los Angeles] (UCLA), Intel Corporation [Santa Clara], Intel Corporation [USA], Department of Plant and Environmental Sciences [Frederiksberg], University of Copenhagen = Københavns Universitet (UCPH), Fudan University [Shanghai], Beijing Genomics Institute [Shenzhen] (BGI), Novo Nordisk Foundation Center for Biosustainability, Danmarks Tekniske Universitet = Technical University of Denmark (DTU), Université de Genève = University of Geneva (UNIGE), The Arctic University of Norway [Tromsø, Norway] (UiT), Charité - UniversitätsMedizin = Charité - University Hospital [Berlin], University of California [San Diego] (UC San Diego), University of Wisconsin-Madison, Scalable, Optimized and Parallel Algorithms for Genomics (GenScale), Inria Rennes – Bretagne Atlantique, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-GESTION DES DONNÉES ET DE LA CONNAISSANCE (IRISA-D7), Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT), Centre National de la Recherche Scientifique (CNRS), Centre de Recherche en Informatique, Signal et Automatique de Lille - UMR 9189 (CRIStAL), Centrale Lille-Université de Lille-Centre National de la Recherche Scientifique (CNRS), Hasso Plattner Institute [Potsdam, Germany], The University of Sydney, Inria Lille - Nord Europe, Institut National de Recherche en Informatique et en Automatique (Inria), Amsterdam UMC - Amsterdam University Medical Center, Structural and Computational Biology, European Molecular Biology Laboratory [Heidelberg] (EMBL), DTU Electrical Engineering [Lyngby], National Institutes of Health [Bethesda] (NIH), Department of Biology [ETH Zürich] (D-BIOL), University of Virginia, IT University of Copenhagen (ITU), Freie Universität Berlin, University of Potsdam = Universität Potsdam, Florida International University [Miami] (FIU), National Research Council of Canada (NRC), Phase Genomics [Seattle], Max Planck Institute for Plant Breeding Research (MPIPZ), Helmholtz Centre for Infection Research (HZI), Aarhus University [Aarhus], Center for Biotechnology (CeBiTec), Universität Bielefeld = Bielefeld University, Open access funding provided by Helmholtz-Zentrum für Infektionsforschung GmbH (HZI), ANR-16-CONV-0005,INCEPTION,Institut Convergences pour l'étude de l'Emergence des Pathologies au Travers des Individus et des populatiONs(2016), ANR-19-P3IA-0001,PRAIRIE,PaRis Artificial Intelligence Research InstitutE(2019), and Medical Microbiology and Infection Prevention

Subjects
06 Biological Sciences, 10 Technology, 11 Medical and Health Sciences, Reproducibility of Results, Cell Biology, DNA, Sequence Analysis, DNA, Biochemistry, Archaea, Software, Metagenome, Metagenomics, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], Molecular Biology, Sequence Analysis, Biotechnology, Developmental Biology
Abstract

Evaluating metagenomic software is key for optimizing metagenome interpretation and focus of the Initiative for the Critical Assessment of Metagenome Interpretation (CAMI). The CAMI II challenge engaged the community to assess methods on realistic and complex datasets with long- and short-read sequences, created computationally from around 1,700 new and known genomes, as well as 600 new plasmids and viruses. Here we analyze 5,002 results by 76 program versions. Substantial improvements were seen in assembly, some due to long-read data. Related strains still were challenging for assembly and genome recovery through binning, as was assembly quality for the latter. Profilers markedly matured, with taxon profilers and binners excelling at higher bacterial ranks, but underperforming for viruses and Archaea. Clinical pathogen detection results revealed a need to improve reproducibility. Runtime and memory usage analyses identified efficient programs, including top performers with other metrics. The results identify challenges and guide researchers in selecting methods for analyses., Nature Methods, 19 (8), ISSN:1548-7105, ISSN:1548-7091

Published
2022
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15. Diversity, taxonomy, and evolution of archaeal viruses of the class Caudoviricetes

Author

Liu, Ying, Demina, Tatiana, Roux, Simon, Aiewsakun, Pakorn, Kazlauskas, Darius M., Simmonds, Peter, Prangishvili, David, Oksanen, Hanna, Krupovic, Mart, Virologie des archées - Archaeal Virology, Institut Pasteur [Paris], University of Helsinki, DOE Joint Genome Institute [Walnut Creek], University of Oxford [Oxford], Mahidol University [Bangkok], Vilnius University [Vilnius], Ivane Javakhishvili Tbilisi State University (TSU), This work was supported by l’Agence Nationale de la Recherche grant ANR-20-CE20-0009-02 (to M.K.) and the European Union’s Horizon 2020 research and innovation program under grant agreement 685778, project VIRUS X (to D.P.). Y.L. is a recipient of the Pasteur-Roux-Cantarini Fellowship from Institut Pasteur. The Ella and Georg Ehrnrooth Foundation and the Finnish Cultural Foundation are sincerely acknowledged (grants to T.D.). The work conducted by the U.S. Department of Energy Joint Genome Institute (S.R.) is supported by the Office of Science of the U.S. Department of Energy under contract no. DE-AC02-05CH11231. The development and application of GRAViTy analysis was supported by a grant to PS from the Wellcome Trust (WT108418AIA). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript., We thank Sari Korhonen, Matti Ylänne, and Carlos Lapedriza for skillful technical assistance. We are also grateful to Marc Monot (Biomics Platform, Institut Pasteur) for help with the sequencing of viral genomes. The facilities and expertise of the HiLIFE Biocomplex unit at the University of Helsinki, a member of Instruct-ERIC Centre Finland, FINStruct, and Biocenter Finland are gratefully acknowledged., ANR-20-CE20-0009,VIROMET,Devoiler le virome des archées methanogenes(2020), European Project: 685778,H2020,H2020-LEIT-BIO-2015-1,Virus-X(2016), Université Paris Cité (UPCité)-Microbiologie Intégrative et Moléculaire (UMR6047), Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Helsingin yliopisto = Helsingfors universitet = University of Helsinki, University of Oxford, Suttle, Curtis, Department of Microbiology, Molecular and Integrative Biosciences Research Programme, Faculty Common Matters (Faculty of Biology and Environmental Sciences), and Molecular Principles of Viruses

Subjects
Archaeal Viruses, FEATURES, Pathology and Laboratory Medicine, Medical and Health Sciences, Biochemistry, Microbial Physiology, Medicine and Health Sciences, TOOL, Viral, Bacterial Physiology, Biology (General), Archaean Biology, Phylogeny, Data Management, Protein Metabolism, 11832 Microbiology and virology, Viral Genomics, Genome, Archaeal Evolution, taxonomy, archaeal viruses, Caudoviricetes, Phylogenetic Analysis, Genomics, Biological Sciences, Biological Evolution, Adhesins, SUBUNITS, Phylogenetics, Infectious Diseases, 1181 Ecology, evolutionary biology, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Pathogens, PHI-CH1, Infection, Research Article, Computer and Information Sciences, GENES, Archaeal virus, QH301-705.5, Virulence Factors, GENOMES, Genome, Viral, Microbial Genomics, SEQUENCE, Microbiology, Host Specificity, Viral Evolution, Viral Proteins, Virology, Genetics, Evolutionary Systematics, Taxonomy, Evolutionary Biology, COMPLEX, Agricultural and Veterinary Sciences, Virus taxonomy, Organisms, Genetic Variation, Biology and Life Sciences, Bacteriology, DNA, Virus evolution, Archaea, Organismal Evolution, Metabolism, Prokaryotic Cells, DNA, Viral, Mutation, Microbial Evolution, TAILED VIRUSES, Developmental Biology
Abstract

The archaeal tailed viruses (arTV), evolutionarily related to tailed double-stranded DNA (dsDNA) bacteriophages of the class Caudoviricetes, represent the most common isolates infecting halophilic archaea. Only a handful of these viruses have been genomically characterized, limiting our appreciation of their ecological impacts and evolution. Here, we present 37 new genomes of haloarchaeal tailed virus isolates, more than doubling the current number of sequenced arTVs. Analysis of all 63 available complete genomes of arTVs, which we propose to classify into 14 new families and 3 orders, suggests ancient divergence of archaeal and bacterial tailed viruses and points to an extensive sharing of genes involved in DNA metabolism and counterdefense mechanisms, illuminating common strategies of virus–host interactions with tailed bacteriophages. Coupling of the comparative genomics with the host range analysis on a broad panel of haloarchaeal species uncovered 4 distinct groups of viral tail fiber adhesins controlling the host range expansion. The survey of metagenomes using viral hallmark genes suggests that the global architecture of the arTV community is shaped through recurrent transfers between different biomes, including hypersaline, marine, and anoxic environments., Comparative genomics and host range analysis reveals the remarkable diversity and evolution of tailed archaeal viruses of the order Caudoviricetes, which together with their bacterial relatives arguably represent the most abundant and widespread virus group on our planet.

Published
2021
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16. Morphological and Genomic Features of the New Klosneuvirinae Isolate Fadolivirus IHUMI-VV54

Author

Frederik Schulz, Fabrizio Di Pinto, Tanja Woyke, Julien Andreani, Bernard La Scola, Anthony Levasseur, Microbes évolution phylogénie et infections (MEPHI), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), DOE Joint Genome Institute [Walnut Creek], Department of Energy / Joint Genome Institute (DOE), and Los Alamos National Laboratory (LANL)

Subjects
Microbiology (medical), Environmental Science and Management, Klosneuvirus, Computational biology, Nucleocytoplasmic large DNA viruses, Microbiology, Genome, Vermamoeba vermiformis, translation components, boats, 03 medical and health sciences, [SDV.MHEP.CSC]Life Sciences [q-bio]/Human health and pathology/Cardiology and cardiovascular system, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Genetics, 2.2 Factors relating to the physical environment, Mimiviridae, Giant Virus, [SDV.MP.PAR]Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology, Aetiology, Gene, giant virus, Original Research, 030304 developmental biology, ATPase subunits, 0303 health sciences, Mimivirus, [SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases, biology, 030306 microbiology, Human Genome, boats.ship_type, Klosneuvirinae, biology.organism_classification, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, QR1-502, 3. Good health, Infectious Diseases, Metagenomics, Soil Sciences, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Infection, Biotechnology, Fadolivirus
Abstract

Since the discovery of Mimivirus, viruses with large genomes encoding components of the translation machinery and other cellular processes have been described as belonging to the nucleocytoplasmic large DNA viruses. Recently, genome-resolved metagenomics led to the discovery of more than 40 viruses that have been grouped together in a proposed viral subfamily named Klosneuvirinae. Members of this group had genomes of up to 2.4Mb in size and featured an expanded array of translation system genes. Yet, despite the large diversity of the Klosneuvirinae in metagenomic data, there are currently only two isolates available. Here, we report the isolation of a novel giant virus known as Fadolivirus from an Algerian sewage site and provide morphological data throughout its replication cycle in amoeba and a detailed genomic characterization. The Fadolivirus genome, which is more than 1.5Mb in size, encodes 1,452 predicted proteins and phylogenetic analyses place this viral isolate as a near relative of the metagenome assembled Klosneuvirus and Indivirus. The genome encodes for 66 tRNAs, 23 aminoacyl-tRNA synthetases and a wide range of transcription factors, surpassing Klosneuvirus and other giant viruses. The Fadolivirus genome also encodes putative vacuolar-type proton pumps with the domains D and A, potentially constituting a virus-derived system for energy generation. The successful isolation of Fadolivirus will enable future hypothesis-driven experimental studies providing deeper insights into the biology of the Klosneuvirinae.

Published
2021
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17. Minimum Information about an Uncultivated Virus Genome (MIUViG)

Author

Seth R. Bordenstein, Frederik Schulz, Pelin Yilmaz, Rebecca Vega Thurber, Natalia Ivanova, Christelle Desnues, Shinichi Sunagawa, Karyna Rosario, Simon Roux, Steven W. Wilhelm, Nicole S. Webster, Mart Krupovic, Lisa Zeigler Allen, Catherine Putonti, K. Eric Wommack, Tanja Woyke, Eugene V. Koonin, Joanne B. Emerson, Jed A. Fuhrman, Hiroyuki Ogata, Ramy K. Aziz, Arvind Varsani, Marie-Agnès Petit, Bonnie L. Hurwitz, Evelien M. Adriaenssens, Andrew M. Kropinski, Katrine Whiteson, Thomas Rattei, Kyung Bum Lee, Peer Bork, David Paez-Espino, Mark J. Young, Jens H. Kuhn, Ben Temperton, Rebecca A. Daly, Natalya Yutin, Emiley A. Eloe-Fadrosh, Manuel Martinez-Garcia, Curtis A. Suttle, Susannah G. Tringe, Alejandro Reyes, Bas E. Dutilh, Nikos C. Kyrpides, Rex R. Malmstrom, Ilene Karsch Mizrachi, Kelly C. Wrighton, Rob Lavigne, Mya Breitbart, Lynn M. Schriml, Philip Hugenholtz, Melissa B. Duhaime, François Enault, Pascal Hingamp, Francisco Rodriguez-Valera, Clara Amid, Matthew B. Sullivan, Jessica M. Labonté, Grieg F. Steward, J. Rodney Brister, Takashi Yoshida, Guy Cochrane, DOE Joint Genome Institute [Walnut Creek], University of Liverpool, Theoretical Biology & Bioinformatics [Utrecht], University Medical Center [Utrecht], Radboud University Medical Center [Nijmegen], National Center for Biotechnology Information (NCBI), University of Guelph, Biologie Moléculaire du Gène chez les Extrêmophiles (BMGE), Institut Pasteur [Paris] (IP), National Institute of Allergy and Infectious Diseases [Bethesda] (NIAID-NIH), National Institutes of Health [Bethesda] (NIH), Catholic University of Leuven - Katholieke Universiteit Leuven (KU Leuven), Arizona State University [Tempe] (ASU), University of Cape Town, European Bioinformatics Institute [Hinxton] (EMBL-EBI), EMBL Heidelberg, Cairo University, Vanderbilt University [Nashville], European Molecular Biology Laboratory [Heidelberg] (EMBL), University of South Florida [Tampa] (USF), Colorado State University [Fort Collins] (CSU), Microbes évolution phylogénie et infections (MEPHI), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), University of Michigan [Ann Arbor], University of Michigan System, University of California [Davis] (UC Davis), University of California (UC), Laboratoire Microorganismes : Génome et Environnement (LMGE), Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Centre National de la Recherche Scientifique (CNRS), University of Southern California (USC), 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)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), University of Queensland [Brisbane], University of Arizona, Texas A&M University [Galveston], National Institute of Genetics (NIG), Universidad de Alicante, Kyoto University, MICrobiologie de l'ALImentation au Service de la Santé (MICALIS), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, University of Chicago, Department of Microbiology and Ecosystem Science [Vienna], University of Vienna [Vienna], Universidad de los Andes [Bogota] (UNIANDES), Universidad Miguel Hernández [Elche] (UMH), University of Maryland School of Medicine, University of Maryland System, University of Hawai‘i [Mānoa] (UHM), Ohio State University [Columbus] (OSU), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), University of British Columbia (UBC), University of Exeter, Oregon State University (OSU), Australian Institute of Marine Science [Townsville] (AIMS Townsville), Australian Institute of Marine Science (AIMS), University of California [Irvine] (UC Irvine), The University of Tennessee [Knoxville], University of Delaware [Newark], Max Planck Institute for Marine Microbiology, Max-Planck-Gesellschaft, Montana State University (MSU), J. Craig Venter Institute, University of California [San Diego] (UC San Diego), This work was supported by the Laboratory Directed Research and Development Program of Lawrence Berkeley National Laboratory under US Department of Energy Contract No. DE-AC02-05CH11231 for S.R., the Netherlands Organization for Scientific Research (NWO) Vidi grant 864.14.004 for B.E.D., the Intramural Research Program of the National Library of Medicine, National Institutes of Health for E.V.K., I.K.M., J.R.B. and N.Y., the Virus-X project (EU Horizon 2020, No. 685778) for F.E. and M.K., Battelle Memorial Institute's prime contract with the US National Institute of Allergy and Infectious Diseases (NIAID) under Contract No. HHSN272200700016I for J.H.K., the GOA grant 'Bacteriophage Biosystems' from KU Leuven for R.L., the European Molecular Biology Laboratory for C.A. and G.R.C., Cairo University Grant 2016-57 for R.K.A., National Science Foundation award 1456778, National Institutes of Health awards R01 AI132581 and R21 HD086833, and The Vanderbilt Microbiome Initiative award for S.R.B., National Science Foundation awards DEB-1239976 for M.B. and K.R. and DEB-1555854 for M.B., the NSF Early Career award DEB-1555854 and NSF Dimensions of Biodiversity #1342701 for K.C.W. and R.A.D., the Agence Nationale de la Recherche JCJC grant ANR-13-JSV6-0004 and Investissements d'Avenir Méditerranée Infection 10-IAHU-03 for C.D., the Gordon and Betty Moore Foundation Marine Microbiology Initiative No. 3779 and the Simons Foundation for J.A.F., the French government 'Investissements d'Avenir' program OCEANOMICS ANR-11-BTBR-0008 and European FEDER Fund 1166-39417 for P. Hingamp, Australian Research Council Laureate Fellowship FL150100038 to P. Hugenholtz the National Science Foundation award 1801367 and C-DEBI Research Grant for J.M.L., the Gordon and Betty Moore Foundation grant 5334 and Ministry of Economy and Competitivity refs. CGL2013-40564-R and SAF2013-49267-EXP for M.M.-G., the Grant-in-Aid for Scientific Research on Innovative Areas from the Ministry of Education, Culture, Science, Sports, and Technology (MEXT) of Japan No. 16H06429, 16K21723, and 16H06437 for H.O. and T.Y., National Science Foundation award DBI-1661357 to C.P., the Ministry of Economy and Competitivity ref CGL2016-76273-P (cofunded with FEDER funds) for F.R.-V., the Gordon and Betty Moore Foundation awards 3305 and 3790 and NSF Biological Oceanography OCE 1536989 for M.B.S., the ETH Zurich and Helmut Horten Foundation and the Novartis Foundation for Medical-Biological Research (17B077) for S.S., a BIOS-SCOPE award from Simons Foundation International and NERC award NE/P008534/1 to B.T., NSF Biological Oceanography Grant 1635913 for R.V.T., the Australian Research Council Future Fellowship FT120100480 for N.S.W., a Gilead Sciences Cystic Fibrosis Research Scholarship for K.L.W., Gordon and Better Moore Foundation Grant 4971 for S.W.W., the NSF EPSCoR grant 1736030 for K.E.W., the National Science Foundation award DEB-4W4596 and National Institutes of Health award R01 GM117361 for M.J.Y., the Gordon and Betty Moore Foundation No. 7000 and the National Oceanic and Atmospheric Administration (NOAA) under award NA15OAR4320071 for L.Z.A. DDBJ is supported by ROIS and MEXT. 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. The views and conclusions contained in this document are those of the authors and should not be interpreted as necessarily representing the official policies, either expressed or implied, of the US Department of Health and Human Services or of the institutions and companies affiliated with the authors. B.E.D., A.K., M.K., J.H.K., R.L. and A.V. are members of the ICTV Executive Committee, but the views and opinions expressed are those of the authors and not those of the ICTV., Universidad de Alicante. Departamento de Fisiología, Genética y Microbiología, Ecología Microbiana Molecular, Institut Pasteur [Paris], University of South Florida (USF), University of California, Laboratoire Microorganismes : Génome et Environnement - Clermont Auvergne (LMGE), Université Clermont Auvergne (UCA)-Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), Kyoto University [Kyoto], Universidad de los Andes [Bogota], Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology in Zürich [Zürich] (ETH Zürich), University of California [Irvine] (UCI), J Craig Venter Institute, 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), Centre National de la Recherche Scientifique (CNRS)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Sub Bioinformatics, and Theoretical Biology and Bioinformatics

Subjects
[SDV]Life Sciences [q-bio], Microbiología, 2.2 Factors relating to physical environment, Applied Microbiology and Biotechnology, Genome, 0302 clinical medicine, Databases, Genetic, Tumours of the digestive tract Radboud Institute for Molecular Life Sciences [Radboudumc 14], phage, Viral, 0303 health sciences, Genetic Databases, Environmental microbiology, pipeline, Genome project, dynamics, Genomics, annotation, Viruses, Molecular Medicine, tacomony, Infection, Genetic databases, Biotechnology, Virus Cultivation, In silico, Biomedical Engineering, Phage biology, Bioengineering, Computational biology, Genome, Viral, Biology, Virus, dna viruses, Article, Uncultivated virus genomes, Databases, 03 medical and health sciences, Annotation, Genetic, Virology, MD Multidisciplinary, Genetics, 030304 developmental biology, Human Genome, Biological classification, commitee, prediction, Metagenomics, Minimum Information about any (x) Sequence (MIxS), 030217 neurology & neurosurgery, discovery
Abstract

We present an extension of the Minimum Information about any (x) Sequence (MIxS) standard for reporting sequences of uncultivated virus genomes. Minimum Information about an Uncultivated Virus Genome (MIUViG) standards were developed within the Genomic Standards Consortium framework and include virus origin, genome quality, genome annotation, taxonomic classification, biogeographic distribution and in silico host prediction. Community-wide adoption of MIUViG standards, which complement the Minimum Information about a Single Amplified Genome (MISAG) and Metagenome-Assembled Genome (MIMAG) standards for uncultivated bacteria and archaea, will improve the reporting of uncultivated virus genomes in public databases. In turn, this should enable more robust comparative studies and a systematic exploration of the global virosphere., Nature Biotechnology, 37 (1), ISSN:1546-1696, ISSN:1087-0156

Published
2018
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18. Intra‐species genetic variability drives carbon metabolism and symbiotic host interactions in the ectomycorrhizal fungus Pisolithus microcarpus

Author

Vivian Ng, Igor V. Grigoriev, Diane Bauer, Jonathan M. Plett, Francis Martin, Krista L. Plett, Vasanth R. Singan, Guifen He, Teresa Lebel, Ian C. Anderson, Annegret Kohler, Hawkesbury Institute for the Environment [Richmond] (HIE), Western Sydney University, Interactions Arbres-Microorganismes (IAM), Université de Lorraine (UL)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Royal Botanic Gardens Victoria, Department of Energy / Joint Genome Institute (DOE), Los Alamos National Laboratory (LANL), DOE Joint Genome Institute [Walnut Creek], U.S. Department of Energy [Washington] (DOE), Lawrence Berkeley National Laboratory [Berkeley] (LBNL), and ANR-11-LABX-0002,ARBRE,Recherches Avancées sur l'Arbre et les Ecosytèmes Forestiers(2011)

Subjects
Range (biology), [SDV]Life Sciences [q-bio], Fungus, Plant Roots, Microbiology, 03 medical and health sciences, Mycorrhizae, Genetic variation, Humans, Genetic variability, Ecosystem, Ecology, Evolution, Behavior and Systematics, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, Regulation of gene expression, Eucalyptus, 0303 health sciences, biology, 030306 microbiology, Host (biology), Ecology, Basidiomycota, 15. Life on land, biology.organism_classification, Carbon, [SDE]Environmental Sciences, Function (biology)
Abstract

Ectomycorrhizal (ECM) fungi are integral to boreal and temperate forest ecosystem functioning and nutrient cycling. ECM fungi, however, originate from diverse saprotrophic lineages and the impacts of genetic variation across species, and especially within a given ECM species, on function and interactions with the environment is not well understood. Here, we explore the extent of intra-species variation between four isolates of the ECM fungus Pisolithus microcarpus, in terms of gene regulation, carbon metabolism and growth, and interactions with a host, Eucalyptus grandis. We demonstrate that, while a core response to the host is maintained by all of the isolates tested, they have distinct patterns of gene expression and carbon metabolism, resulting in the differential expression of isolate-specific response pathways in the host plant. Together, these results highlight the importance of using a wider range of individuals within a species to understand the broader ecological roles of ECM fungi and their host interactions.

Published
2021
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23. Biological Soil Crusts as Modern Analogues for the Archean Continental Biosphere: Insights from Carbon and Nitrogen Isotopes

Author

Martin Homann, Estelle Couradeau, Ferran Garcia-Pichel, Stefan V. Lalonde, Pierre Sansjofre, Anna Giraldo-Silva, Johanna Marin-Carbonne, Christophe Thomazo, Arnaud Brayard, Biogéosciences [UMR 6282] [Dijon] (BGS), Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Centre National de la Recherche Scientifique (CNRS), Lawrence Berkeley National Laboratory [Berkeley] (LBNL), Center for Fundamental and Applied Microbiomics, Arizona State University [Tempe] (ASU)-Biodesign Institute, Institut des sciences de la terre [Lausanne] (ISTE), Université de Lausanne (UNIL), Department of Earth Sciences [UCL London], University College of London [London] (UCL), Laboratoire Géosciences Océan (LGO), Institut Français de Recherche pour l'Exploitation de la Mer - Brest (IFREMER Centre de Bretagne), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Bretagne Sud (UBS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS), Biogéosciences [UMR 6282] (BGS), Université de Bourgogne (UB)-Centre National de la Recherche Scientifique (CNRS), DOE Joint Genome Institute [Walnut Creek], Université de Lausanne = University of Lausanne (UNIL), Université de Bretagne Sud (UBS)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS), Institut de minéralogie, de physique des matériaux et de cosmochimie (IMPMC), Muséum national d'Histoire naturelle (MNHN)-Institut de recherche pour le développement [IRD] : UR206-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), and Work supported by the Programme National de Planétologie (PNP) of the CNRS INSU, cofunded by CNES, and by the EU’s Horizon H2020 research and innovation program ERC (STROMATA, grant agreement 759289).

Subjects
Archean, 010504 meteorology & atmospheric sciences, Earth, Planet, Earth science, Origin of Life, Cyanobacteria, Geologic record, 01 natural sciences, Early life, Soil, [SDU.STU.GC]Sciences of the Universe [physics]/Earth Sciences/Geochemistry, Nitrogen isotope, 0103 physical sciences, Ecosystem, Microbial mat, 010303 astronomy & astrophysics, Nitrogen cycle, Agricultural and Biological Sciences (miscellaneous), Space and Planetary Science, Soil Microbiology, ComputingMilieux_MISCELLANEOUS, 0105 earth and related environmental sciences, Carbon Isotopes, Nitrogen Isotopes, Fossils, Carbon isotope, Biosphere, Nitrogen Cycle, 15. Life on land, Early Earth, Isotope biosignature, [SDU]Sciences of the Universe [physics], 13. Climate action, Isotopes of carbon, Geology
Abstract

5 pages; International audience; Stable isotope signatures of elements related to life such as carbon and nitrogen can be powerful biomarkers that provide key information on the biological origin of organic remains and their paleoenvironments. Marked advances have been achieved in the last decade in our understanding of the coupled evolution of biological carbon and nitrogen cycling and the chemical evolution of the early Earth thanks, in part, to isotopic signatures preserved in fossilized microbial mats and organic matter of marine origin. However, the geologic record of the early continental biosphere, as well as its evolution and biosignatures, is still poorly constrained. Following a recent report of direct fossil evidence of life on land at 3.22 Ga, we compare here the carbon and nitrogen isotopic signals of this continental Archean biosphere with biosignatures of cyanobacteria biological soil crusts (cyanoBSCs) colonizing modern arid environments. We report the first extended δ13C and δ15N data set from modern cyanoBSCs and show that these modern communities harbor specific isotopic biosignatures that compare well with continental Archean organic remains. We therefore suggest that cyanoBSCs are likely relevant analogs for the earliest continental ecosystems. As such, they can provide key information on the timing, extent, and possibly mechanism of colonization of the early Earth's emergent landmasses.

Published
2020
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24. Running Title: Cross-species multi-omics and conserved gene regulations

Author

Miyauchi, Shingo, Hage, Hayat, Drula, Elodie, Lesage-Meessen, Laurence, Berrin, Jean-Guy, Navarro, David, Favel, Anne, Chaduli, Delphine, Grisel, Sacha, Haon, Mireille, Piumi, François, Levasseur, Anthony, Lomascolo, Anne, Ahrendt, Steven, Barry, Kerrie, LaButti, Kurt M, Chevret, Didier, Daum, Chris, Mariette, Jérôme, Klopp, Christophe, Cullen, Daniel, de Vries, Ronald P, Gathman, Allen C, Hainaut, Matthieu, Henrissat, Bernard, Hildén, Kristiina S, Kües, Ursula, Lilly, Walt, Lipzen, Anna, Mäkelä, Miia R, Martinez, Angel T, Morel-Rouhier, Mélanie, Morin, Emmanuelle, Pangilinan, Jasmyn, Ram, Arthur F J, Wösten, Han A B, Ruiz-Dueñas, Francisco J, Riley, Robert, Record, Eric, Grigoriev, Igor V, Rosso, Marie-Noëlle, Molecular Microbiology, Sub Molecular Plant Physiology, Sub Molecular Microbiology, Molecular Plant Physiology, Department of Microbiology, Department of Food and Nutrition, Fungal Genetics and Biotechnology, Helsinki Institute of Sustainability Science (HELSUS), Westerdijk Fungal Biodiversity Institute - Fungal Physiology, Westerdijk Fungal Biodiversity Institute, Biodiversité et Biotechnologie Fongiques (BBF), Aix Marseille Université (AMU)-École Centrale de Marseille (ECM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Interactions Arbres-Microorganismes (IAM), Université de Lorraine (UL)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Imagine - Institut des maladies génétiques (IHU) (Imagine - U1163), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPCité), Microbes évolution phylogénie et infections (MEPHI), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Institut Hospitalier Universitaire Méditerranée Infection (IHU Marseille), U.S. Department of Energy [Washington] (DOE), MICrobiologie de l'ALImentation au Service de la Santé (MICALIS), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Unité de Mathématiques et Informatique Appliquées de Toulouse (MIAT INRAE), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), USDA Forest Service Rocky Mountain Forest and Range Experiment Station, United States Department of Agriculture (USDA), Westerdijk Fungal Biodiversity Institute [Utrecht] (WI), Royal Netherlands Academy of Arts and Sciences (KNAW), Helsingin yliopisto = Helsingfors universitet = University of Helsinki, Missouri Southern State University (MSSU), Architecture et fonction des macromolécules biologiques (AFMB), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Department of Molecular Cell Biology [Göttingen], Max Planck Institute for Biophysical Chemistry (MPI-BPC), Max-Planck-Gesellschaft-Max-Planck-Gesellschaft, Department of Energy / Joint Genome Institute (DOE), Los Alamos National Laboratory (LANL), Centro de Investigaciones Biológicas (CSIC), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), DOE Joint Genome Institute [Walnut Creek], Department of Molecular Microbiology and Biotechnology, Tel Aviv University (TAU), Utrecht University [Utrecht], Department of Plant Pathology & Microbiology [Riverside], University of California [Riverside] (UC Riverside), University of California (UC)-University of California (UC), Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231Ministerio de Ciencias, Innovación y Universidades de España (BIO2017-86559-R), ANR-14-CE06-0020,FUNTUNE,Cocktails enzymatiques inspirés de modèles fongiques pour la déconstruction contrôlée de la biomasse végétale(2014), Molecular Microbiology, Sub Molecular Plant Physiology, Sub Molecular Microbiology, Molecular Plant Physiology, Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Paris (UP), Unité de Mathématiques et Informatique Appliquées de Toulouse (MIAT INRA), Westerdijk Fungal Biodiversity Insitute [Utrecht] (WI), University of Helsinki, Tel Aviv University [Tel Aviv], University of California [Riverside] (UCR), University of California-University of California, COMBE, Isabelle, Appel à projets générique - Cocktails enzymatiques inspirés de modèles fongiques pour la déconstruction contrôlée de la biomasse végétale - - FUNTUNE2014 - ANR-14-CE06-0020 - Appel à projets générique - VALID, Agence Nationale de la Recherche (France), Department of Energy (US), Ministerio de Ciencia, Innovación y Universidades (España), Miyauchi, Shingo [0000-0002-0620-5547], Hage, Hayat [0000-0003-4118-1816], Drula, Elodie [0000-0002-9168-5214], Lesage-Meessen, Laurence [0000-0003-2275-2978], Berrin, Jean-Guy [0000-0001-7570-3745], Navarro, David [0000-0002-3266-8270], Favel, Anne [0000-0003-2255-3637], Haon, Mireille [0000-0002-5669-5177], Levasseur, Anthony [0000-0003-2989-7539], Lomascolo, Anne [0000-0003-3829-8503], Ahrendt, Steven [0000-0002-3029-2126], LaButti, Kurt M. [0000-0002-5838-1972], Chevret, Didier [0000-0001-9531-7657], Daum, Chris [0000-0003-3895-5892], Klopp, Christophe [0000-0001-7126-5477], Vries, Ronald P. de [0000-0002-4363-1123], Hainaut, Matthieu [0000-0002-7567-657X], Henrissat, Bernard [0000-0002-3434-8588], Hildén, Kristiina S. [0000-0002-0126-8186], Kües, Ursula [0000-0001-9180-4079], Lipzen, Anna [0000-0003-2293-9329], Mäkelä, Miia [0000-0003-0771-2329], Martínez, Ángel T. [0000-0002-1584-2863], Morel-Rouhier, Mélanie [0000-0001-5149-0474], Morin, Emmanuelle [0000-0002-7268-972X], Ram, Arthur [0000-0002-2487-8016], Wösten, Han [0000-0002-0399-3648], Ruiz-Dueñas, F. J. [0000-0002-9837-5665], Record, Éric [0000-0002-7545-9997], Grigoriev, Igor V. [0000-0002-3136-8903], Rosso, Marie-Noëlle [0000-0001-8317-7220], Miyauchi, Shingo, Hage, Hayat, Drula, Elodie, Lesage-Meessen, Laurence, Berrin, Jean-Guy, Navarro, David, Favel, Anne, Haon, Mireille, Levasseur, Anthony, Lomascolo, Anne, Ahrendt, Steven, LaButti, Kurt M., Chevret, Didier, Daum, Chris, Klopp, Christophe, Vries, Ronald P. de, Hainaut, Matthieu, Henrissat, Bernard, Hildén, Kristiina S., Kües, Ursula, Lipzen, Anna, Mäkelä, Miia, Martínez, Ángel T., Morel-Rouhier, Mélanie, Morin, Emmanuelle, Ram, Arthur, Wösten, Han, Ruiz-Dueñas, F. J., Record, Éric, Grigoriev, Igor V., and Rosso, Marie-Noëlle

Subjects
AcademicSubjects/SCI01140, SELECTION, Cellobiose, Lignin, ANNOTATION, chemistry.chemical_compound, lignocellulose, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Phylogeny, [SDV.MP.VIR] Life Sciences [q-bio]/Microbiology and Parasitology/Virology, [SDV.MHEP.ME] Life Sciences [q-bio]/Human health and pathology/Emerging diseases, 11832 Microbiology and virology, 0303 health sciences, [SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases, Genome, Full Paper, Basidiomycota, General Medicine, PHANEROCHAETE-CHRYSOSPORIUM, Wood, Pycnoporus, [SDV.MHEP.CSC] Life Sciences [q-bio]/Human health and pathology/Cardiology and cardiovascular system, GENOME, Fungal, Biochemistry, CAZyme, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, [SDV.MHEP.MI] Life Sciences [q-bio]/Human health and pathology/Infectious diseases, lytic polysaccharide monooxygenase, Genome, Fungal, ENZYMES, CAZymes, [SDV.MP.PAR] Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology, Biotechnology, DATABASE, 1.1 Normal biological development and functioning, Plant Biology & Botany, AcademicSubjects/MED00774, Biology, CLASSIFICATION, Fungal Proteins, CERIPORIOPSIS-SUBVERMISPORA, 03 medical and health sciences, [SDV.MHEP.CSC]Life Sciences [q-bio]/Human health and pathology/Cardiology and cardiovascular system, Underpinning research, Oxidative enzyme, Genetics, [SDV.MP.PAR]Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology, Cellulose, Molecular Biology, Gene, 030304 developmental biology, Lytic Polysaccharide Monooxygenase (LPMO), Comparative genomics, Lytic Polysaccharide Monooxygenase, 030306 microbiology, 15. Life on land, DEGRADATION, biology.organism_classification, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, chemistry, Class II Peroxidase, wood decay, Carbohydrate Dehydrogenases, SECRETOME, [SDV.MP.BAC] Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology
Abstract

14 p.-8 fig.-1 tab., White-rot (WR) fungi are pivotal decomposers of dead organic matter in forest ecosystems and typically use a large array of hydrolytic and oxidative enzymes to deconstruct lignocellulose. However, the extent of lignin and cellulose degradation may vary between species and wood type. Here we combined comparative genomics,transcriptomics and secretome proteomics to identify conserved enzymatic signatures at the onset of wood decaying activity within the Basidiomycota genus Pycnoporus. We observed strong conservation in the genome structures and the repertoires of protein coding genes across the four Pycnoporus species described to date,despite the species having distinct geographic distributions. We further analyzed the early response of P. cinnabarinus, P. coccineus and P. sanguineus to diverse (ligno)-cellulosic substrates. We identified a conserved set of enzymes mobilized by the three species for breaking down cellulose, hemicellulose and pectin.The co-occurrence in the exo-proteomes of H2O2 producing enzymes with H2O2 consuming enzymes was a common feature of the three species, although each enzymatic partner displayed independent transcriptional regulation. Finally, cellobiose dehydrogenase-coding genes were systematically co-regulated with at least one AA9 LPMO gene, indicative of enzymatic synergy in vivo. This study highlights a conserved core white-rot fungal enzymatic mechanism behind the wood decaying process., This work was supported by The French National Agency for Research (ANR-14-CE06-0020). The work conducted by the U.S. Department of Energy Joint Genome Institute, a DOE Office of Science User Facility, is supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231. The work by CSIC was supported by the Ministerio de Ciencias, Innovación y Universidades de España (BIO2017-86559-R).

Published
2020
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25. Inorganic nitrogen availability alters Eucalyptus grandis receptivity to the ectomycorrhizal fungus Pisolithus albus but not symbiotic nitrogen transfer

Author

Francis Martin, Igor V. Grigoriev, Vivian Ng, Krista L. Plett, Vasanth R. Singan, Mei Wang, Jonathan M. Plett, Ian C. Anderson, Hawkesbury Institute for the Environment [Richmond] (HIE), Western Sydney University, DOE Joint Genome Institute [Walnut Creek], Interactions Arbres-Microorganismes (IAM), and Université de Lorraine (UL)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)

Subjects
0106 biological sciences, 0301 basic medicine, Physiology, Nitrogen, [SDV]Life Sciences [q-bio], Plant Biology & Botany, chemistry.chemical_element, Plant Science, Fungus, 01 natural sciences, Plant Roots, 03 medical and health sciences, Human fertilization, Nutrient, Mycorrhizae, Botany, Genetics, Colonization, Symbiosis, transcriptomic analysis, Mutualism (biology), Eucalyptus, biology, nutrient trading, Agricultural and Veterinary Sciences, Basidiomycota, 15. Life on land, Biological Sciences, biology.organism_classification, nitrogen deposition, 030104 developmental biology, chemistry, ectomycorrhizal (ECM) fungi, stable isotope tracing, Soil water, [SDE]Environmental Sciences, 010606 plant biology & botany
Abstract

International audience; Forest trees are able to thrive in nutrient‐poor soils in part because they obtain growth‐limiting nutrients, especially nitrogen (N), through mutualistic symbiosis with ectomycorrhizal (ECM) fungi. Addition of inorganic N into these soils is known to disrupt this mutualism and reduce the diversity of ECM fungi. Despite its ecological impact, the mechanisms governing the observed effects of elevated inorganic N on mycorrhizal communities remain unknown. We address this by using a compartmentalized in vitro system to independently alter nutrients to each symbiont. Using stable isotopes, we traced the nutrient flux under different nutrient regimes between Eucalyptus grandis and its ectomycorrhizal symbiont, Pisolithus albus. We demonstrate that giving E. grandis independent access to N causes a significant reduction in root colonization by P. albus. Transcriptional analysis suggests that the observed reduction in colonization may be caused, in part, by altered transcription of microbe perception genes and defence genes. We show that delivery of N to host leaves is not increased by host nutrient deficiency but by fungal nutrient availability instead. Overall, this advances our understanding of the effects of N fertilization on ECM fungi and the factors governing nutrient transfer in the E. grandis–P. microcarpus interaction.

Published
2020
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26. Fungal ecological strategies reflected in gene transcription - a case study of two litter decomposers

Author

Florian Barbi, Preetisri Baskaran, Björn D. Lindahl, Alan Kuo, Anna Lipzen, Igor V. Grigoriev, Kurt LaButti, Laure Fauchery, Emmanuelle Morin, Chris Daum, Bernard Henrissat, Kerrie Barry, Annegret Kohler, Katarina Ihrmark, Francis Martin, Swedish University of Agricultural Sciences (SLU), LabEx ARBRE : Advanced Research on the Biology of Tree and Forest Ecosystems ([LabEx ARBRE]), AgroParisTech-Office National des Forêts (ONF)-Université de Lorraine (UL)-Centre National de la Propriété Forestière-CRITT Bois-European Forest Institute = Institut Européen de la Forêt = Euroopan metsäinstituutti (EFI)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Interactions Arbres-Microorganismes (IAM), Institut National de la Recherche Agronomique (INRA)-Université de Lorraine (UL), Ecologie fonctionnelle et écotoxicologie des agroécosystèmes (ECOSYS), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), DOE Joint Genome Institute [Walnut Creek], US Department of Energy Joint Genome Institute, U.S Department of Energy, U.S. Department of Energy [Washington] (DOE)-U.S. Department of Energy [Washington] (DOE), United States Department of Energy, Department of Energy / Joint Genome Institute (DOE), Los Alamos National Laboratory (LANL), Architecture et fonction des macromolécules biologiques (AFMB), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Beijing Forestry University, Office of Science of the U.S. Department of Energy. Grant Number: DE‐AC02‐05CH11231,Région Lorraine Research Council and the European Fund for Regional Development, University of Lorraine, Institut National de la Recherche Agronomique, Office of Science, US Department of Energy, Genomic Science Program, The Swedish Research Council FORMAS. Grant Number: 2011‐1747, ANR-11-LABX-0002,ARBRE,Recherches Avancées sur l'Arbre et les Ecosytèmes Forestiers(2011), and Institut National de la Recherche Agronomique (INRA)-AgroParisTech-CRITT Bois-Office national des forêts (ONF)-Université de Lorraine (UL)-Centre National de la Propriété Forestière-European Forest Institute = Institut Européen de la Forêt = Euroopan metsäinstituutti (EFI)

Subjects
Transcription, Genetic, Glycoside Hydrolases, [SDV]Life Sciences [q-bio], Biology, Microbiology, Decomposer, 03 medical and health sciences, Ascomycota, Genetic, Gene Expression Regulation, Fungal, Genetics, Gene family, Ecosystem, Gene, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, Regulation of gene expression, 0303 health sciences, Evolutionary Biology, Genome, 030306 microbiology, Ecology, Microbiota, Human Genome, Fungal genetics, Fungi, 15. Life on land, Plant Leaves, Fungal, Gene Expression Regulation, Adaptation, Genome, Fungal, Microcosm, Transcription
Abstract

International audience; Microbial communities interplay with their environment through their functional traits that can be a response or an effect on the environment. Here, we explore how a functional trait—the decomposition of organic matter, can be addressed based on genetic markers and how the expression of these markers reflect ecological strategies of two fungal litter decomposer Gymnopus androsaceus and Chalara longipes. We sequenced the genomes of these two fungi, as well as their transcriptomes at different steps of Pinus sylvestris needles decomposition in microcosms. Our results highlighted that if the gene content of the two species could indicate similar potential decomposition abilities, the expression levels of specific gene families belonging to the glycoside hydrolase category reflected contrasting ecological strategies. Actually, C. longipes, the weaker decomposer in this experiment, turned out to have a high content of genes involved in cell wall polysaccharides decomposition but low expression levels, reflecting a versatile ecology compare to the more competitive G. androsaceus with high expression levels of keystone functional genes. Thus, we established that sequential expression of genes coding for different components of the decomposer machinery indicated adaptation to chemical changes in the substrate as decomposition progressed.

Published
2020
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27. A systematic investigation of lipophilicity modulation by aliphatic fluorination motifs

Author

Bruno Linclau, Benjamin Jeffries, Jean-Yves Le Questel, Hannah R Felstead, James S. Scott, Elisabetta Chiarparin, Zhong Wang, Jérôme Graton, DOE Joint Genome Institute [Walnut Creek], Chimie Et Interdisciplinarité : Synthèse, Analyse, Modélisation (CEISAM), Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST), Université de Nantes (UN)-Université de Nantes (UN)-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC), University of Toronto, School of Chemistry [Southampton, UK], and University of Southampton

Subjects
0303 health sciences, Halogenation, Hydrocarbons, Fluorinated, Chemistry, Drug discovery, Molecular Conformation, 01 natural sciences, Combinatorial chemistry, Molecular conformation, 0104 chemical sciences, 010404 medicinal & biomolecular chemistry, 03 medical and health sciences, 1-Butanol, Pentanols, Drug Discovery, Lipophilicity, Molecular Medicine, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, MESH: 1-Butanol / chemistry Halogenation Hydrocarbons, Fluorinated / chemistry* Hydrophobic and Hydrophilic Interactions* Molecular Conformation Pentanols / chemistry, Hydrophobic and Hydrophilic Interactions, 030304 developmental biology
Abstract

International audience; Optimization of compound lipophilicity is a key aspect of drug discovery. The aim of this work was to compare the lipophilicity modulations induced by 16 distinct known and novel fluoroalkyl motifs on three parent models. Fifty fluorinated compounds, with 28 novel experimental aliphatic log P values, are involved in discussing various lipophilicity trends. As well as confirming known trends, a number of novel lipophilicity-reducing motifs are introduced. Tactics to reduce lipophilicity are discussed, such as "motif extensions" and "motif rearrangements", including with concomitant extension of the carbon chain, as well as one- and two-fluorine 'deletions' within perfluoroalkyl groups. Quantum chemical log P calculations (SMD-MN15) based on solvent-dependent three-dimensional (3D) conformational analysis gave excellent correlations with experimental values, superior to Clog P predictions based on 2D structural motifs. The availability of a systematic collection of data based on a small number of parent molecules illustrates the relative lipophilicity modulations of aliphatic fluorination motifs.

Published
2020
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28. Advantages and Limits of Metagenomic Assembly and Binning of a Giant Virus

Author

Tanja Woyke, Bernard La Scola, Julien Andreani, Frederik Schulz, Rania Francis, Hadjer Boudjemaa, Jacques Yaacoub Bou Khalil, Janey Lee, DOE Joint Genome Institute [Walnut Creek], Lawrence Berkeley National Laboratory [Berkeley] (LBNL), Microbes évolution phylogénie et infections (MEPHI), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU), Université Hassiba Ben Bouali de Chlef (UHBC), Institut Hospitalier Universitaire Méditerranée Infection (IHU Marseille), Department of Energy / Joint Genome Institute (DOE), Los Alamos National Laboratory (LANL), Cristea, Ileana M, and Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Physiology, Cellular organisms, [SDV]Life Sciences [q-bio], lcsh:QR1-502, Biology, Nucleocytoplasmic large DNA viruses, Biochemistry, Genome, Microbiology, lcsh:Microbiology, 03 medical and health sciences, Data sequences, Genetics, 2.2 Factors relating to the physical environment, Giant Virus, Aetiology, Novel Systems Biology Techniques, Molecular Biology, giant viruses, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, 0303 health sciences, metagenomics, 030306 microbiology, Human Genome, ncldv, biology.organism_classification, QR1-502, Computer Science Applications, Metagenomics, Evolutionary biology, Modeling and Simulation, NCLDV, Infection, Research Article
Abstract

The discovery of large and giant nucleocytoplasmic large DNA viruses (NCLDV) with genomes in the megabase range and equipped with a wide variety of features typically associated with cellular organisms was one of the most unexpected, intriguing, and spectacular breakthroughs in virology. Recent studies suggest that these viruses are highly abundant in the oceans, freshwater, and soil, impact the biology and ecology of their eukaryotic hosts, and ultimately affect global nutrient cycles. Genome-resolved metagenomics is becoming an increasingly popular tool to assess the diversity and coding potential of giant viruses, but this approach is currently lacking validation., Giant viruses have large genomes, often within the size range of cellular organisms. This distinguishes them from most other viruses and demands additional effort for the successful recovery of their genomes from environmental sequence data. Here, we tested the performance of genome-resolved metagenomics on a recently isolated giant virus, Fadolivirus, by spiking it into an environmental sample from which two other giant viruses were isolated. At high spike-in levels, metagenome assembly and binning led to the successful genomic recovery of Fadolivirus from the sample. A complementary survey of the major capsid protein indicated the presence of other giant viruses in the sample matrix but did not detect the two isolated from this sample. Our results indicate that genome-resolved metagenomics is a valid approach for the recovery of near-complete giant virus genomes given that sufficient clonal particles are present. However, our data also underline that a vast majority of giant viruses remain currently undetected, even in an era of terabase-scale metagenomics. IMPORTANCE The discovery of large and giant nucleocytoplasmic large DNA viruses (NCLDV) with genomes in the megabase range and equipped with a wide variety of features typically associated with cellular organisms was one of the most unexpected, intriguing, and spectacular breakthroughs in virology. Recent studies suggest that these viruses are highly abundant in the oceans, freshwater, and soil, impact the biology and ecology of their eukaryotic hosts, and ultimately affect global nutrient cycles. Genome-resolved metagenomics is becoming an increasingly popular tool to assess the diversity and coding potential of giant viruses, but this approach is currently lacking validation.

Published
2020
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29. Editorial: Viruses, Genetic Exchange, and the Tree of Life

Author

Kyrpides, Nikos, Roux, Simon, Nasir, Arshan, Caetano-Anollés, Gustavo, Claverie, Jean-Michel, DOE Joint Genome Institute [Walnut Creek], Laboratoire Microorganismes : Génome et Environnement (LMGE), Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Centre National de la Recherche Scientifique (CNRS), Evolutionary Bioinformatics Laboratory, University of Illinois System, Information génomique et structurale (IGS), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Oppenheimer Fellowship (20180751PRD3), Los Alamos National Laboratory to AN. Grants from the National Science Foundation (OISE-1132791) and the National Institute of Food and Agriculture of the United States Department of Agriculture (ILLU-802-909 and ILLU-483-625), and Centre National de la Recherche Scientifique (CNRS)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020])

Subjects
Microbiology (medical), 0303 health sciences, 030306 microbiology, Tree of life (biology), ORFans, lcsh:QR1-502, Biology, Microbiology, lcsh:Microbiology, origin of nucleus, 03 medical and health sciences, tree of life, Evolutionary biology, Horizontal gene transfer, evolution, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, horizontal gene transfer, Genetic exchange, viruses, 030304 developmental biology
Abstract

International audience; Editorial on the Research Topic Viruses, Genetic Exchange, and the Tree of Life We live in exciting times for microbiology research. The significant technological and scientific advancements in the past decades have now enabled scientists to pursue discovery and description of novel microbial and viral linages from previously uncharted Earth habitats. Two such discoveries are particularly exciting and noteworthy in this regard. First, the discovery of the first "giant virus, " Acanthamoeba polyphaga mimivirus, in 2003, and several others thereafter, posed intriguing questions regarding virus origins, evolution, classification, and their place in the "tree of life." Second, the discoveries of "Lokiarchaeota" and several other closely-related archaeal members that encode several eukaryote-specific proteins challenged the three-domain canonical structure of the tree of life. These discoveries have reopened debates on central questions in evolutionary biology research such as the origin of viruses, the origin of eukaryotes, evolutionary relationship between Archaea and Eukarya, and the structure and topology of the tree of life. In this Research Topic, we received a broad range of contributions addressing these and other related questions. Moelling and Broecker discussed the "virus first" model for the evolution of life on Earth. They provided several examples of virus diversity and abundance in a range of Earth environments and in the mammalian genomes. According to their view, ribozymes and viroids could have started early evolution albeit they also acknowledged competing alternatives such as the "proteins first" and the "metabolism first" scenarios of origins of life. In a separate contribution from the same authors

Published
2019
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30. Taxonomic assignment of uncultivated prokaryotic virus genomes is enabled by gene-sharing networks

Author

Simon Roux, J. Rodney Brister, Ho Bin Jang, Olivier Zablocki, Mart Krupovic, Jens H. Kuhn, Evelien M. Adriaenssens, Matthew B. Sullivan, Andrew M. Kropinski, Rob Lavigne, Dann Turner, Benjamin Bolduc, Ohio State University [Columbus] (OSU), Integrated Research Facility at Fort Detrick (IRF-Frederick), National Institute of Allergy and Infectious Diseases [Bethesda] (NIAID-NIH), National Institutes of Health [Bethesda] (NIH)-National Institutes of Health [Bethesda] (NIH), DOE Joint Genome Institute [Walnut Creek], U.S. Department of Energy [Washington] (DOE), Institute of Integrative Biology [Liverpool, UK], University of Liverpool, Quadram Institute, National Center for Biotechnology Information (NCBI), National Institutes of Health [Bethesda] (NIH), Ontario Veterinary College [Univ. Guelph, Canada], University of Guelph, Biologie Moléculaire du Gène chez les Extrêmophiles (BMGE), Institut Pasteur [Paris], Faculty of BioScience Engineering [KU Leuven, Belgium], Catholic University of Leuven - Katholieke Universiteit Leuven (KU Leuven), University of the West of England [Bristol] (UWE Bristol), High-performance computational support was provided as an award from the Ohio Supercomputer Center to M.B.S. Funding was provided in part by the Department of Energy’s Genome Sciences Program Soil Microbiome Scientific Focus Area award (no. SCW1632) to Lawrence Livermore National Laboratory, NSF Biological Oceanography awards (OCE no. 1536989 and OCE no. 1756314), and a Gordon and Betty Moore Foundation Investigator Award (no. 3790) to M.B.S. Funding was provided to J.R.B. by the Intramural Research Program of the National Institutes of Health (NIH) National Library of Medicine. 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 DE-AC02-05CH11231 to S.R. This work was funded in part through Battelle Memorial Institute’s prime contract with the US National Institute of Allergy and Infectious Diseases (NIAID) under Contract no. HHSN272200700016I to J.H.K. The content of this publication does not necessarily reflect the views or policies of the US Department of Health and Human Services or of the institutions and companies affiliated with the authors., We thank L. Bollinger, G. Trubl and I. Tolstoy for their comments on improving the manuscript, as well as Z.-Q. You for helping push the network analytics., Biotechnology and Biological Sciences Research Council (BBSRC), and Institut Pasteur [Paris] (IP)

Subjects
MESH: Genome, Viral/genetics, Classification and taxonomy, MESH: Viruses/classification, MESH: Gene Regulatory Networks/genetics, Applied Microbiology and Biotechnology, Genome, 0302 clinical medicine, RefSeq, TOOL, Bacteriophages, Gene Regulatory Networks, Viral, MESH: Phylogeny, Phylogeny, 0303 health sciences, MESH: Metagenomics, Classification, MESH: Classification, Viruses, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Molecular Medicine, ICTV BACTERIAL, POPULATIONS, Taxonomy (biology), MESH: Prokaryotic Cells/virology, MESH: Viruses/genetics, Centre for Research in Biosciences, MESH: Bacteriophages/genetics, Life Sciences & Biomedicine, Biotechnology, Biomedical Engineering, Bioengineering, PHAGE, Computational biology, Genome, Viral, Biology, CLASSIFICATION, 03 medical and health sciences, MD Multidisciplinary, Human virome, Virus classification, 030304 developmental biology, virus classification, archaeal and bacterial virus taxonomy, scalable framework, gene-sharing networks, Science & Technology, ARCHAEAL VIRUSES, Hierarchical clustering, Computational biology and bioinformatics, Prokaryotic Cells, MESH: Metagenome/genetics, Biotechnology & Applied Microbiology, Metagenomics, EVOLUTIONARY, Metagenome, UPDATE, ECOGENOMICS, Bacterial virus, 030217 neurology & neurosurgery, Software, GENERATION
Abstract

Microbiomes from every environment contain a myriad of uncultivated archaeal and bacterial viruses, but studying these viruses is hampered by the lack of a universal, scalable taxonomic framework. We present vConTACT v.2.0, a network-based application utilizing whole genome gene-sharing profiles for virus taxonomy that integrates distance-based hierarchical clustering and confidence scores for all taxonomic predictions. We report near-identical (96%) replication of existing genus-level viral taxonomy assignments from the International Committee on Taxonomy of Viruses for National Center for Biotechnology Information virus RefSeq. Application of vConTACT v.2.0 to 1,364 previously unclassified viruses deposited in virus RefSeq as reference genomes produced automatic, high-confidence genus assignments for 820 of the 1,364. We applied vConTACT v.2.0 to analyze 15,280 Global Ocean Virome genome fragments and were able to provide taxonomic assignments for 31% of these data, which shows that our algorithm is scalable to very large metagenomic datasets. Our taxonomy tool can be automated and applied to metagenomes from any environment for virus classification. ispartof: NATURE BIOTECHNOLOGY vol:37 issue:6 pages:632-+ ispartof: location:United States status: published

Published
2019
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31. Synthesis of 2,3,4-Trideoxy-2,3,4-trifluoroglucose

Author

Mark E. Light, Lucas Quiquempoix, Bruno Linclau, Jean-Yves Le Questel, Zhong Wang, Jérôme Graton, Peter G. Latchem, DOE Joint Genome Institute [Walnut Creek], Chimie Et Interdisciplinarité : Synthèse, Analyse, Modélisation (CEISAM), Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST), Université de Nantes (UN)-Université de Nantes (UN)-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC), University of Southampton, and Department of Chemistry [Southampton, UK]

Subjects
[CHIM.THEO]Chemical Sciences/Theoretical and/or physical chemistry, chemistry.chemical_compound, 010405 organic chemistry, Chemistry, Computational chemistry, Hydrogen bond, Biological property, Levoglucosan, Organic Chemistry, Crystal structure, 010402 general chemistry, 01 natural sciences, 0104 chemical sciences
Abstract

There is an increasing interest in investigating how polyfluorination of carbohydrates modifies their physical and biological properties. An example that has caught much attention is 2,3,4-trideoxy-2,3,4-trifluoroglucose. Four syntheses of this compound have been reported, which are either low yielding or long (13 or more steps). We report a 6-step synthesis of 2,3,4-trideoxy-2,3,4-trifluoroglucose starting from levoglucosan. The solution-phase structure of an intermediate, 1,6-anhydro-2,4-dideoxy-2,4-difluoroallose, features a rare example of a bifurcated F center dot center dot center dot H(O)center dot center dot center dot F hydrogen bond and is compared to its crystal structure.

Published
2019
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32. Comparative genomics of Rhizophagus irregularis, R. cerebriforme, R. diaphanus and Gigaspora rosea highlights specific genetic features in Glomeromycotina

Author

Morin, Emmanuelle, Miyauchi, Shingo, San Clemente, Hélène, Chen, Eric C. H., Pelin, Adrian, de la Providencia, Ivan, Ndikumana, Steve, Beaudet, Denis, Hainaut, Mathieu, Drula, Elodie, Kuo, Alan, Tang, Nianwu, Roy, Sébastien, Viala, Julie, Henrissat, Bernard, Grigoriev, Igor V, Corradi, Nicolas, Roux, Christophe, Martin, Francis M., Interactions Arbres-Microorganismes (IAM), Institut National de la Recherche Agronomique (INRA)-Université de Lorraine (UL), 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), University of Ottawa [Ottawa], Architecture et fonction des macromolécules biologiques (AFMB), Institut National de la Recherche Agronomique (INRA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Aix Marseille Université (AMU), Institut National de la Recherche Agronomique (INRA), DOE Joint Genome Institute [Walnut Creek], Agronutrition, Interactions Microbiennes dans la Rhizosphère et les Racines, Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), ANR-11-LABX-0002-01, Université de Lorraine (UL)-Institut National de la Recherche Agronomique (INRA), Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Université de Toulouse, University of Ottawa, United States Department of Energy Joint Genome Institute, Agro-Nutrition, Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU)-Institut National de la Recherche Agronomique (INRA), 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
Transcription, Genetic, Genes, Fungal, Plant Biology & Botany, arbuscular mycorrhizal fungi, champignon mycorhizien, Lignin, rhizophagus irregularis, Genetic, Polysaccharides, gigaspora rosea, interspecific variation, Symbiosis, Glomeromycota, fungal evolution, Phylogeny, Conserved Sequence, [SDV.MP.MYC]Life Sciences [q-bio]/Microbiology and Parasitology/Mycology, protein kinases, Genome, Agricultural and Veterinary Sciences, génomique comparative, Reproduction, Rhizophagus diaphanus, Genomics, Biological Sciences, Up-Regulation, Fungal, Genes, Multigene Family, carbohydrate-active enzymes, Rhizophagus cerebriforme, DNA Transposable Elements, Genome, Fungal, transposable elements, Transcription
Abstract

Glomeromycotina is a lineage of early diverging fungi that establish arbuscular mycorrhizal (AM) symbiosis with land plants. Despite their major ecological role, the genetic basis of their obligate mutualism remains largely unknown, hindering our understanding of their evolution and biology. We compared the genomes of Glomerales (Rhizophagus irregularis, Rhizophagus diaphanus, Rhizophagus cerebriforme) and Diversisporales (Gigaspora rosea) species, together with those of saprotrophic Mucoromycota, to identify gene families and processes associated with these lineages and to understand the molecular underpinning of their symbiotic lifestyle. Genomic features in Glomeromycotina appear to be very similar with a very high content in transposons and protein-coding genes, extensive duplications of protein kinase genes, and loss of genes coding for lignocellulose degradation, thiamin biosynthesis and cytosolic fatty acid synthase. Most symbiosis-related genes in R. irregularis and G. rosea are specific to Glomeromycotina. We also confirmed that the present species have a homokaryotic genome organisation. The high interspecific diversity of Glomeromycotina gene repertoires, affecting all known protein domains, as well as symbiosis-related orphan genes, may explain the known adaptation of Glomeromycotina to a wide range of environmental settings. Our findings contribute to an increasingly detailed portrait of genomic features defining the biology of AM fungi.

Published
2019
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33. Leveraging single-cell genomics to expand the fungal tree of life

Author

Asaf Salamov, C. Alisha Quandt, Tanja Woyke, Bernard Henrissat, Timothy Y. James, Bill Andreopoulos, Steven R. Ahrendt, Gerald L. Benny, Igor V. Grigoriev, Alicia Clum, Doina Ciobanu, Adrian Pelin, Jan Fang Cheng, Matthew E. Smith, Nicole K. Reynolds, Lawrence Berkeley National Laboratory [Berkeley] (LBNL), University of Michigan [Ann Arbor], University of Michigan System, Oregon State University (OSU), DOE Joint Genome Institute [Walnut Creek], Department of Energy / Joint Genome Institute (DOE), Los Alamos National Laboratory (LANL), United States Department of Energy, Biotechnology Center [Dresden] (BIOTEC), Technische Universität Dresden (TUD), Ottawa Hospital Research Institute [Ottawa] (OHRI), Architecture et fonction des macromolécules biologiques (AFMB), Institut National de la Recherche Agronomique (INRA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), University of Florida [Gainesville], Technische Universität Dresden = Dresden University of Technology (TU Dresden), Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU)-Institut National de la Recherche Agronomique (INRA), and University of Florida [Gainesville] (UF)

Subjects
0301 basic medicine, zoopagomycotina, Tree of life (biology), 18S, Secondary Metabolism, Applied Microbiology and Biotechnology, Genome, 2.2 Factors relating to physical environment, 2.2 Factors relating to the physical environment, Environmental DNA, Fungal genomics, Aetiology, Phylogeny, superfamily, Multiple sequence alignment, biology, syncephalis zoopagales, Genomics, Biodiversity, Fungal, classification, annotation, Sequence annotation, Medical Microbiology, multiple sequence alignment, Genome, Fungal, Sequence Analysis, Metabolic Networks and Pathways, Biotechnology, Microbiology (medical), Heterozygote, 030106 microbiology, Immunology, DNA, Ribosomal, Microbiology, Article, 03 medical and health sciences, Genetic, Phylogenetics, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], evolution, RNA, Ribosomal, 18S, Genetics, Polymorphism, gene, Symbiosis, Gene, Ribosomal, Zoopagomycotina, Life Cycle Stages, Polymorphism, Genetic, Human Genome, Fungi, Genetic Variation, Cell Biology, Sequence Analysis, DNA, DNA, biology.organism_classification, Evolutionary biology, RNA, discovery
Abstract

Environmental DNA surveys reveal that most fungal diversity represents uncultured species. We sequenced the genomes of eight uncultured species across the fungal tree of life using a new single-cell genomics pipeline. We show that, despite a large variation in genome and gene space recovery from each single amplified genome (SAG), ≥90% can be recovered by combining multiple SAGs. SAGs provide robust placement for early-diverging lineages and infer a diploid ancestor of fungi. Early-diverging fungi share metabolic deficiencies and show unique gene expansions correlated with parasitism and unculturability. Single-cell genomics holds great promise in exploring fungal diversity, life cycles and metabolic potential., Single-cell genome sequencing of eight uncultured fungal species provides insights into the phylogenetic placement of early-diverging lineages, highlights metabolic deficiencies and identifies gene expansions correlated with parasitism and unculturability.

Published
2018
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34. Draft Genome Sequence of the Basidiomycete White-Rot Fungus Phlebia centrifuga

Author

Steven R. Ahrendt, Zoraide Granchi, Thomas Chin-A-Woeng, Igor V. Grigoriev, Matthieu Hainaut, Mao Peng, Bernard Henrissat, Robert Riley, Sake van Pelt, Ronald P. de Vries, Kristiina Hildén, Rosa Hegi, Miia R. Mäkelä, University of Helsinki, Utrecht University [Utrecht], GenomeScan B.V., GenomeScan BV, Leiden University, DOE Joint Genome Institute [Walnut Creek], Joint Genome Institute, United States Department of Energy, Architecture et fonction des macromolécules biologiques (AFMB), Institut National de la Recherche Agronomique (INRA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Department of Energy / Joint Genome Institute (DOE), Los Alamos National Laboratory (LANL), Westerdijk Fungal Biodiversity Center [Utrecht], European Project: 613868,EC:FP7:KBBE,FP7-KBBE-2013-7-single-stage,OPTIBIOCAT(2013), Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU)-Institut National de la Recherche Agronomique (INRA), Westerdijk Fungal Biodiversity Insitute [Utrecht] (WI), Royal Netherlands Academy of Arts and Sciences (KNAW), Helsingin yliopisto = Helsingfors universitet = University of Helsinki, Universiteit Leiden, Westerdijk Fungal Biodiversity Institute [Utrecht] (WI), Hilden, Kristiina S., Westerdijk Fungal Biodiversity Institute, and Westerdijk Fungal Biodiversity Institute - Fungal Physiology

Subjects
0301 basic medicine, Whole genome sequencing, Phlebia centrifuga, biology, Eukaryotes, Strain (biology), fungi, technology, industry, and agriculture, lignin, food and beverages, Picea abies, Fungus, biology.organism_classification, Genome, complex mixtures, 03 medical and health sciences, 030104 developmental biology, rna, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Botany, Genetics, White rot fungus, Molecular Biology, Gene
Abstract

Here, we report the genome sequence of wood-decaying white-rot fungus Phlebia centrifuga strain FBCC195, isolated from Norway spruce ( Picea abies ) in Finnish Lapland. The 34.66-Mb genome containing 13,785 gene models is similar to the genome length reported for other saprobic white-rot species.

Published
2018
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35. Cultivation and sequencing of rumen microbiome members from the Hungate1000 Collection

Author

Seshadri, Rekha, Leahy, Sinead, Attwood, Graeme, Teh, Koon Hoong, Lambie, Suzanne, Cookson, Adrian, Eloe-Fadrosh, Emiley, Pavlopoulos, Georgios, Hadjithomas, Michalis, Varghese, Neha, Páez-Espino, David, Perry, Rechelle, Henderson, Gemma, Creevey, Christopher, Terrapon, Nicolas, Lapébie, Pascal, Drula, Elodie, Lombard, Vincent, Rubin, Edward, Kyrpides, Nikos, Henrissat, Bernard, Woyke, Tanja, Ivanova, Natalia, Kelly, William, Palevich, Nikola, Janssen, Peter, Ronimus, Ron, Noel, Samantha, Soni, Priya, Reilly, Kerri, Atherly, Todd, Ziemer, Cherie, Wright, Andre-Denis, Ishaq, Suzanne, Cotta, Michael, Thompson, Stephanie, Crosley, Katie, McKain, Nest, Wallace, R John, Flint, Harry, Martin, Jennifer, Forster, Robert, Gruninger, Robert, McAllister, Tim, Gilbert, Rosalind, Ouwerkerk, Diane, Klieve, Athol, Jassim, Rafat Al, Denman, Stuart, McSweeney, Chris, Rosewarne, Carly, Koike, Satoshi, Kobayashi, Yasuo, Mitsumori, Makoto, Shinkai, Takumi, Cravero, Silvio, Cucchi, María Cerón, Creevey, Chris, Seshadri, Rekha, Leahy, Sinead C, Attwood, Graeme T, Teh, Koon Hoong, Rosewarne, Carly, Cerón Cucchi, María, Hungate1000 Project Collaborators, US Department of Energy Joint Genome Institute, Walnut Creek CA, USA, DOE Joint Genome Institute [Walnut Creek], Grasslands Research Centre, AgResearch Ltd, AgResearch Limited, Grasslands Res Ctr, AgResearch, Department of Biology [JHU Baltimore], Johns Hopkins University (JHU), Animal & Grassland Research and Innovation Centre, Teagasc - The Agriculture and Food Development Authority (Teagasc), Aberystwyth University, Architecture et fonction des macromolécules biologiques (AFMB), Institut National de la Recherche Agronomique (INRA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Centre d'océanologie de Marseille (COM), Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de la Méditerranée - Aix-Marseille 2, Biodiversité et Biotechnologie Fongiques (BBF), École Centrale de Marseille (ECM)-Aix Marseille Université (AMU)-Institut National de la Recherche Agronomique (INRA), Department of Energy / Joint Genome Institute (DOE), Los Alamos National Laboratory (LANL), Rowett Inst Nutr & Hlth, Microbial Ecol Grp, University of Aberdeen, Laboratoire de Psycholinguistique Expérimentale (FAPSE), University of Geneva [Switzerland], Tohoku University [Sendai], Animal Bioscience Centre, European Project: 322820,EC:FP7:ERC,ERC-2012-ADG_20120314,HUMAN MICROBIOTA(2013), Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU)-Institut National de la Recherche Agronomique (INRA), Institut National de la Recherche Agronomique (INRA)-Aix Marseille Université (AMU)-École Centrale de Marseille (ECM), New Zealand Government - Livestock Research Group of the Global Research Alliance on Agricultural Greenhouse Gases, US Department of Energy Joint Genome Institute (JGI) through their Community Science Program [CSP 612, DE-AC02-05CH11231], Office of Science of the US Department of Energy, Leahy, Sinead C., Université de la Méditerranée - Aix-Marseille 2-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS), and Université de Genève = University of Geneva (UNIGE)

Subjects
0301 basic medicine, BACTERIAL, Rumen, animal structures, Methanogenesis, DATABASE, Microbial metabolism, DIVERSITY, Biomedical Engineering, Bioengineering, Biology, Lignin, ANNOTATION, Applied Microbiology and Biotechnology, REFERENCE GENOMES, 03 medical and health sciences, Microbial ecology, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], REVEALS, rumen microbiota, Animals, Humans, Microbiome, REDUCING EMISSIONS, 2. Zero hunger, Genetics, Bacteria, Microbiota, Human microbiome, food and beverages, biology.organism_classification, Archaea, EVOLUTION, Gastrointestinal Microbiome, 030104 developmental biology, Metagenomics, greenhouse gas, Biofuels, Molecular Medicine, RUMINANT NUTRITION, DAIRY-CATTLE, Biotechnology
Abstract

Hungate1000 project collaborators: Nikola Palevich, Peter H. Janssen, Ron S. Ronimus, Samantha Noel, Priya Soni, Kerri Reilly, Todd Atherly, Cherie Ziemer, Andre-Denis Wright, Suzanne Ishaq, Michael Cotta, Stephanie Thompson, Katie Crosley, Nest McKain, R. John Wallace, Harry J. Flint, Jennifer C. Martin, Robert J. Forster, Robert J. Gruninger, Tim McAllister, Rosalind Gilbert, Diane Ouwerkerk, Athol Klieve, Rafat Al Jassim, Stuart Denman, Chris McSweeney, Carly Rosewarne, Satoshi Koike, Yasuo Kobayashi, Makoto Mitsumori, Takumi Shinkai, Silvio Cravero & María Cerón Cucchi; International audience; Productivity of ruminant livestock depends on the rumen microbiota, which ferment indigestible plant polysaccharides into nutrients used for growth. Understanding the functions carried out by the rumen microbiota is important for reducing greenhouse gas production by ruminants and for developing biofuels from lignocellulose. We present 410 cultured bacteria and archaea, together with their reference genomes, representing every cultivated rumen-associated archaeal and bacterial family. We evaluate polysaccharide degradation, short-chain fatty acid production and methanogenesis pathways, and assign specific taxa to functions. A total of 336 organisms were present in available rumen metagenomic data sets, and 134 were present in human gut microbiome data sets. Comparison with the human microbiome revealed rumen-specific enrichment for genes encoding de novo synthesis of vitamin B12, ongoing evolution by gene loss and potential vertical inheritance of the rumen microbiome based on underrepresentation of markers of environmental stress. We estimate that our Hungate genome resource represents ∼75% of the genus-level bacterial and archaeal taxa present in the rumen.

Published
2018
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36. Reducing the Lipophilicity of Perfluoroalkyl Groups by CF2-F/CF2-Me or CF3/CH3 Exchange

Author

Bruno Linclau, James S. Scott, Elisabetta Chiarparin, Ryan Greenwood, Jean-Yves Le Questel, Zhong Wang, Jérôme Graton, Thomasin Brind, Benjamin Jeffries, Simon D. Holland, DOE Joint Genome Institute [Walnut Creek], Chimie Et Interdisciplinarité : Synthèse, Analyse, Modélisation (CEISAM), Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST), Université de Nantes (UN)-Université de Nantes (UN)-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC), Department of Chemistry [Southampton, UK], and University of Southampton

Subjects
Trifluoromethyl, 010405 organic chemistry, Drug candidate, Metabolic stability, 010402 general chemistry, 01 natural sciences, Combinatorial chemistry, 0104 chemical sciences, Partition coefficient, chemistry.chemical_compound, chemistry, Drug Discovery, Lipophilicity, Molecular Medicine, [CHIM]Chemical Sciences, Selectivity, Medical science, Methyl group
Abstract

Fluorination is commonly employed to optimize bioactivity and pharmaco-kinetic properties of drug candidates. Aliphatic fluorination often reduces the lipophilicity (log P), but polyfluoroalkylation typically increases lipophilicity. Hence, identification of polyfluorinated motifs that nonetheless lead to similar or even reduced lipophilicities is of interest to expand the arsenal of medicinal chemistry tools in tackling properties such as compound metabolic stability or off-target selectivity. We show that changing a CF3-group of a perfluoroalkyl chain to a methyl group leads to a drastic reduction in lipophilicity. We also show that changing a C-F bond of a trifluoromethyl group, including when incorporated as part of a perfluoroalkyl group, to a C-Me group, leads to a reduction in log P, despite the resulting chain elongation. The observed lipophilicity trends were identified in fluorinated alkanol models and reproduced when incorporated in analogues of a drug candidate, and the metabolic stability of these motifs was demonstrated.

Published
2018
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37. Minimum Information about a Biosynthetic Gene cluster

Author

Patrick Caffrey, Renzo Kottmann, Eriko Takano, Sean Doyle, Axel A. Brakhage, Matthew Cummings, Juan Pablo Gomez-Escribano, Yvonne Mast, Ryan F. Seipke, Rob Lavigne, Markus Nett, Hans-Wilhelm Nützmann, Jan Claesen, David H. Sherman, Daniel Petras, Pablo Cruz-Morales, Carl J. Balibar, Anne Osbourn, Oscar P. Kuipers, Leonilde M. Moreira, Xinyu Liu, Marcia S. Osburne, Bohdan Ostash, David P. Fewer, Changsheng Zhang, Pelin Yilmaz, Mohamed S. Donia, Anja Greule, Hyun Uk Kim, Nicholas J. Tobias, Frank Oliver Glöckner, Christoph Geiger, Chia Y. Lee, William H. Gerwick, Philipp Wiemann, Bertolt Gust, Susan E. Jensen, Wilfred A. van der Donk, Jan Kormanec, Ben Shen, Christopher M. Thomas, Jason Micklefield, Srikanth Duddela, R. Cameron Coates, René De Mot, Anthony S. Haines, Neha Garg, Guohui Pan, Roderich D. Süssmuth, Hyung Jin Kwon, Jonathan D. Walton, Lena Gerwick, Jörn Piel, Monika Ehling-Schulz, Zhenhua Tian, Jonathan L. Klassen, Xiaohui Yan, Emily A. Monroe, Yunchang Xie, Russell J. Cox, Keishi Ishida, Grace Yim, Stefano Donadio, Nadine Ziemert, Yuta Tsunematsu, Matthew L. Hillwig, Miroslav Petricek, Sylvie Lautru, Tilmann Weber, Andrew W. Truman, Rainer Breitling, Peter Kötter, Nikos C. Kyrpides, Stephanie Düsterhus, Christian Hertweck, Hideaki Oikawa, Sean F. Brady, Christopher T. Walsh, Adam C. Jones, Marcus A. Moore, Bradley S. Moore, Barrie Wilkinson, Simone M. Mantovani, Nathan A. Moss, Elizabeth E. Wyckoff, Emily P. Balskus, Kapil Tahlan, Fengan Yu, Monica Höfte, Jos M. Raaijmakers, Taifo Mahmud, Yit-Heng Chooi, Yi Tang, Andreas Bechthold, Douglas A. Mitchell, Joanne M. Willey, Helge B. Bode, John B. Biggins, Margherita Sosio, Yi-Qiang Cheng, Carmen Méndez, Leonard Kaysser, Joleen Masschelein, Daniel Krug, Federico Rosconi, Marnix H. Medema, Kaarina Sivonen, Tomohisa Kuzuyama, Mikko Metsä-Ketelä, Esther K. Schmitt, Carsten Kegler, Andriy Luzhetskyy, Gilles P. van Wezel, Bai Linquan, Kai Blin, Jens Nielsen, Bertrand Aigle, Amrita Pati, Harald Gross, Muriel Viaud, Pieter C. Dorrestein, Carla S. Jones, Michael A. Fischbach, Shelley M. Payne, Zhe Rui, Gerard D. Wright, Wen Liu, Alexey V. Melnik, Barry Scott, Brett A. Neilan, Nancy P. Keller, Rainer Borriss, Katrin Jungmann, Michalis Hadjithomas, Evi Stegmann, Daniel J. Edwards, F. Jerry Reen, Alexander Kristian Apel, Wolfgang Wohlleben, Michael J. Smanski, Leonard Katz, Fergal O'Gara, Eric J. N. Helfrich, Sergey B. Zotchev, Olivier Ploux, Arnold J. M. Driessen, Rolf Müller, Jean-Luc Pernodet, K. D. Entian, José A. Salas, Irene de Bruijn, Francisco Barona-Gómez, Jianhua Ju, Jon Clardy, Molecular Microbiology, Molecular Genetics, Jacobs University [Bremen], Microbial genomics and bioinformatics research group, Max Planck Institute for Marine Microbiology, Max-Planck-Gesellschaft-Max-Planck-Gesellschaft, Max-Planck-Gesellschaft, Atmospheric Chemistry Observations and Modeling Laboratory (ACOML), National Center for Atmospheric Research [Boulder] (NCAR), Department of Food and Environmental Sciences, Helsingin yliopisto = Helsingfors universitet = University of Helsinki, Collaborative Mass Spectrometry Innovation Center, University of California [San Diego] (UC San Diego), University of California (UC)-University of California (UC), Heilongjiang Institute of Science and Technology, Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), Merck Stiftungsprofessur fûr Molekulare Biotechnologie Fachbereich Biowissenscharten, Goethe-University Frankfurt am Main, Department of Opto-Mechatronics Engineering and Cogno-Mechatronics Engineering, Pusan National University, University of Liverpool, College of Computer Science and Technology [Zhejiang] (Zhejiang University), University of Florida [Gainesville] (UF), School of Management, University of Science and Technology of China [Hefei] (USTC), State Key Laboratory of Nuclear Physics and Technology (SKL-NPT), Peking University [Beijing], Massachusetts Institute of Technology (MIT), Memorial Sloane Kettering Cancer Center [New York], South China Sea Institute of Oceanology, Chinese Academy of Sciences [Beijing] (CAS), Dynamique des Génomes et Adaptation Microbienne (DynAMic), Institut National de la Recherche Agronomique (INRA)-Université de Lorraine (UL), Institut für Biologie [Berlin] (IFB), Humboldt University Of Berlin, School of Biomolecular and Biomedical Science and Centre for Synthesis and Chemical Biology, University College Dublin [Dublin] (UCD), Parallélisme, Réseaux, Systèmes, Modélisation (PRISM), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Centre National de la Recherche Scientifique (CNRS), Skaggs School of Pharmacy and Pharmaceutical Sciences [San Diego], Grenoble Institut des Neurosciences (GIN), Université Joseph Fourier - Grenoble 1 (UJF)-Institut National de la Santé et de la Recherche Médicale (INSERM), Pixyl Medical [Grenoble], Integrated Optical MicroSystems (IOMS), University of Twente-MESA+ Institute for Nanotechnology, 7Lehrstuhl für Mikrobielle Ökologie, Department für Grundlagen der Biowissenschaften, Technische Universität Munchen - Université Technique de Munich [Munich, Allemagne] (TUM), Service Néphrologie Pédiatrique, CHU Strasbourg-Hôpital de Hautepierre [Strasbourg], Advanced Resources and Risk Technology, Laboratory of Phytopathology (K.C., H.S., B.A., M.H.), Universiteit Gent = Ghent University (UGENT), Trifork Aarhus C, Aalborg University [Denmark] (AAU), Centers for Disease Control and Prevention [Atlanta] (CDC), Centers for Disease Control and Prevention, Groupe d'Etude de la Matière Condensée (GEMAC), Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen [Groningen], DOE Joint Genome Institute [Walnut Creek], Microbiologie Moléculaire des Actinomycètes (ACTINO), Département Microbiologie (Dpt Microbio), Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Institut de génétique et microbiologie [Orsay] (IGM), Université Paris-Sud - Paris 11 (UP11)-Centre National de la Recherche Scientifique (CNRS), Laboratory of Gene Technology, Catholic University of Leuven - Katholieke Universiteit Leuven (KU Leuven), Joint Center for Structural Genomics (JCSG), Stanford University, Centre européen de recherche et d'enseignement des géosciences de l'environnement (CEREGE), Institut de Recherche pour le Développement (IRD)-Institut National de la Recherche Agronomique (INRA)-Aix Marseille Université (AMU)-Collège de France (CdF (institution))-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS), Centre de Recherches et d'Applications Pédagogiques en Langues (CRAPEL), Université Nancy 2, Space Sciences Laboratory [Berkeley] (SSL), University of California [Berkeley] (UC Berkeley), Polytechnic Institute of Leiria, NMR Laboratory, Université de Mons, Université de Mons (UMons), School of Biomedical Science, Curtin University [Perth], Planning and Transport Research Centre (PATREC)-Planning and Transport Research Centre (PATREC), BIOMERIT Research Centre, School of Microbiology, University College Cork (UCC), Department of Engineering Science, University of Oxford, Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Laboratoire Charles Friedel, Ecole Nationale Supérieure de Chimie de Paris - Chimie ParisTech-PSL (ENSCP), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Laboratory of Phytopathology, Wageningen University and Research [Wageningen] (WUR), Department of Microbial Ecology, Netherlands Institute of Ecology, Department of Animal Production, Universidad de Córdoba = University of Córdoba [Córdoba], IMV Technologies, Gulliver (UMR 7083), Ecole Superieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI Paris), Institut für Chemie, Technical University of Berlin / Technische Universität Berlin (TU), Lipides - Nutrition - Cancer (U866) (LNC), Université de Bourgogne (UB)-Institut National de la Santé et de la Recherche Médicale (INSERM)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Ecole Nationale Supérieure de Biologie Appliquée à la Nutrition et à l'Alimentation de Dijon (ENSBANA), Centre de Recherche Paul Pascal (CRPP), Université de Bordeaux (UB)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), DEPARTMENT OF CHEMISTRY, Durham University, Molekulare Ökologie, Joint Attosecond Science Laboratory, University of Ottawa and National Research Council, Department of Mechanical and Aerospace Engineering [Univ California Davis] (MAE - UC Davis), University of California [Davis] (UC Davis), University of Helsinki, University of California-University of California, Université de Lorraine (UL)-Institut National de la Recherche Agronomique (INRA), Humboldt-Universität zu Berlin, University of Twente [Netherlands]-MESA+ Institute for Nanotechnology, Technische Universität München [München] (TUM), Universiteit Gent = Ghent University [Belgium] (UGENT), Department of Biosystems, KU Leuven, Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Collège de France (CdF (institution))-Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA), University of California [Berkeley], NMR and Molecular Imaging Laboratory [Mons], University of Mons [Belgium] (UMONS), University of Oxford [Oxford], Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Supérieure de Chimie de Paris - Chimie ParisTech-PSL (ENSCP), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut de Chimie du CNRS (INC), Universidad de Córdoba [Cordoba], Technische Universität Berlin (TU), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Bourgogne (UB)-Ecole Nationale Supérieure de Biologie Appliquée à la Nutrition et à l'Alimentation de Dijon (ENSBANA)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Department of Mechanical and Aerospace Engineering [Davis], Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology in Zürich [Zürich] (ETH Zürich), University of Florida [Gainesville], Institut für Biologie, Humboldt Universität zu Berlin, Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU Grenoble-Université Joseph Fourier - Grenoble 1 (UJF), Ghent University [Belgium] (UGENT), 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-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-Institut de Biologie Intégrative de la Cellule (I2BC), 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-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, Stanford University [Stanford], Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Collège de France (CdF)-Institut national des sciences de l'Univers (INSU - CNRS)-Aix Marseille Université (AMU)-Institut National de la Recherche Agronomique (INRA), NMR and Molecular Imaging Laboratory, 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, Ecole Nationale Supérieure de Chimie de Paris- Chimie ParisTech-PSL (ENSCP)-Centre National de la Recherche Scientifique (CNRS), Wageningen University and Research Centre [Wageningen] (WUR), Gulliver, ESPCI ParisTech-Centre National de la Recherche Scientifique (CNRS), Technische Universität Berlin (TUB), Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS), Max Planck Society (GERMANY), Max Planck Society (GERMANY)-Max Planck Society (GERMANY), Laboratoire Leprince-Ringuet ( LLR ), Institut National de Physique Nucléaire et de Physique des Particules du CNRS ( IN2P3 ) -École polytechnique ( X ) -Centre National de la Recherche Scientifique ( CNRS ), Atmospheric Chemistry Observations and Modeling Laboratory ( ACOML ), National Center for Atmospheric Research [Boulder] ( NCAR ), University of California [San Diego] ( UC San Diego ), Eidgenössische Technische Hochschule [Zürich] ( ETH Zürich ), University of Science and Technology of China [Hefei] ( USTC ), State Key Laboratory of Nuclear Physics and Technology ( SKL-NPT ), Massachusetts Institute of Technology ( MIT ), Memorial Sloan Kettering Cancer Center ( MSKCC ), Shanghai Ocean University, Dynamique des Génomes et Adaptation Microbienne ( DynAMic ), Institut National de la Recherche Agronomique ( INRA ) -Université de Lorraine ( UL ), University College Dublin [Dublin] ( UCD ), Parallélisme, Réseaux, Systèmes, Modélisation ( PRISM ), Université de Versailles Saint-Quentin-en-Yvelines ( UVSQ ) -Centre National de la Recherche Scientifique ( CNRS ), Grenoble Institut des Neurosciences ( GIN ), Institut National de la Santé et de la Recherche Médicale ( INSERM ) -CHU Grenoble-Université Joseph Fourier - Grenoble 1 ( UJF ), Integrated Optical MicroSystems ( IOMS ), Technische Universität München [München] ( TUM ), Ghent University [Belgium] ( UGENT ), Aalborg University [Denmark] ( AAU ), Centers for Disease Control and Prevention [Atlanta] ( CDC ), Groupe d'Etude de la Matière Condensée ( GEMAC ), Groningen Biomolecular Sciences and Biotechnology Institute ( GBB ), Microbiologie Moléculaire des Actinomycètes ( ACTINO ), Département Microbiologie ( Dpt Microbio ), 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 ) -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 ) -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 ) -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 ), Institut de génétique et microbiologie [Orsay] ( IGM ), Université Paris-Sud - Paris 11 ( UP11 ) -Centre National de la Recherche Scientifique ( CNRS ), Joint Center for Structural Genomics ( JCSG ), Centre européen de recherche et d'enseignement de géosciences de l'environnement ( CEREGE ), Centre National de la Recherche Scientifique ( CNRS ) -Institut de Recherche pour le Développement ( IRD ) -Aix Marseille Université ( AMU ) -Collège de France ( CdF ) -Institut National de la Recherche Agronomique ( INRA ) -Institut national des sciences de l'Univers ( INSU - CNRS ), Centre de Recherches et d'Applications Pédagogiques en Langues ( CRAPEL ), Space Sciences Laboratory [Berkeley] ( SSL ), Université de Mons ( UMons ), Planning and Transport Research Centre ( PATREC ) -Planning and Transport Research Centre ( PATREC ), University College Cork ( UCC ), 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 ), Ecole Nationale Supérieure de Chimie de Paris- Chimie ParisTech-PSL ( ENSCP ) -Centre National de la Recherche Scientifique ( CNRS ), Wageningen University and Research Centre [Wageningen] ( WUR ), ESPCI ParisTech, Technische Universität Berlin ( TUB ), Lipides - Nutrition - Cancer (U866) ( LNC ), Université de Bourgogne ( UB ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ) -AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Ecole Nationale Supérieure de Biologie Appliquée à la Nutrition et à l'Alimentation de Dijon ( ENSBANA ), Centre de recherche Paul Pascal, CNRS, Université de Bordeaux ( UPR8641 ), Centre de Recherche Paul Pascal, CNRS, Université de Bordeaux, University Durham, University of California [Davis] ( UC Davis ), 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)-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)-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)-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), 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), [GIN] Grenoble Institut des Neurosciences (GIN), Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), and Saarland University, Building A4.1, 66123 Saarbruecken, Germany.

Subjects
MESH : Protein Biosynthesis, protein synthesis, Operon, MESH : Polysaccharides, International Cooperation, MESH: Plants, plant, Review, MESH: Terpenes, gene cluster, polyketide, data base, genetic database, Gene cluster, acyltransferase, Databases, Genetic, MESH : Metagenome, MESH : Genetic Markers, genetics, terpene, GeneralLiterature_REFERENCE(e.g.,dictionaries,encyclopedias,glossaries), ComputingMilieux_MISCELLANEOUS, MESH : Peptides, MESH: Peptides, biology, fungus, nonribosomal peptide synthesis, Plants, bacterium, peptide, priority journal, MESH: Protein Biosynthesis, Multigene Family, MESH : Terpenes, MESH: Computational Biology, Genetic Markers, MESH: Terminology as Topic, Bioinformatics, MESH : Multigene Family, biological activity, Article, metagenome, Alkaloids, Manchester Institute of Biotechnology, Terminology as Topic, Bioinformatica, MESH : Bacteria, Peptide Biosynthesis, MESH : Databases, Genetic, Molecular Biology, MESH : Fungi, MESH: Polyketides, standardization, secondary metabolism, [ SDV ] Life Sciences [q-bio], Bacteria, ta1182, Computational Biology, MESH : Terminology as Topic, operon, Laboratorium voor Phytopathologie, MESH: International Cooperation, gene function, Metagenomics, polysaccharide, Laboratory of Phytopathology, chemical structure, Metagenome, MESH: Multigene Family, EPS, biosynthesis, Peptides, MESH : Computational Biology, MESH : International Cooperation, [SDV]Life Sciences [q-bio], MESH: Genetic Markers, information, MESH : Alkaloids, Synthetic biology, MESH: Peptide Biosynthesis, Nucleic Acid-Independent, database, MESH: Databases, Genetic, Genetics, MESH : Polyketides, MESH : Peptide Biosynthesis, Nucleic Acid-Independent, ddc:540, standards, Peptide Biosynthesis, Nucleic Acid-Independent, ComputingMethodologies_DOCUMENTANDTEXTPROCESSING, nomenclature, genetic marker, alkaloid derivative, MESH: Fungi, Biology, MESH : Plants, peptide derivative, Polyketide, MESH: Alkaloids, Polysaccharides, ddc:570, Life Science, 14. Life underwater, Secondary metabolism, enzyme specificity, Gene, nonhuman, Terpenes, Fungi, nucleotide sequence, Cell Biology, MESH: Metagenome, ResearchInstitutes_Networks_Beacons/manchester_institute_of_biotechnology, alkaloid, MESH: Bacteria, MESH: Polysaccharides, 13. Climate action, Polyketides, Protein Biosynthesis, synthetic biology, metabolism
Abstract

M.H.M. was supported by a Rubicon fellowship of the Netherlands Organization for Scientific Research (NWO;Rubicon 825.13.001). The work of R.K. was supported by the European Union’s Seventh Framework Programme(Joint Call OCEAN.2011–2: Marine microbial diversity—new insights into marine ecosystems functioning and its biotechnological potential) under the grant agreement no.287589 (Micro B3). M.C. was supported by a Biotechnology and Biological Sciences Research Council (BBSRC)studentship (BB/J014478/1). The GSC is supported by funding from the Natural Environment Research Council(UK), the National Institute for Energy Ethics and Society(NIEeS; UK), the Gordon and Betty Moore Foundation,the National Science Foundation (NSF; US) and the US Department of Energy. The Manchester Synthetic Biology Research Centre, SYNBIOCHEM, is supported by BBSRC/Engineering and Physical Sciences Research Council(EPSRC) grant BB/M017702/1, Medema, M.H., Kottmann, R., Yilmaz, P., Cummings, M., Biggins, J.B., Blin, K., De Bruijn, I., Chooi, Y.H., Claesen, J., Coates, R.C., Cruz-Morales, P., Duddela, S., Düsterhus, S., Edwards, D.J., Fewer, D.P., Garg, N., Geiger, C., Gomez-Escribano, J.P., Greule, A., Hadjithomas, M., Haines, A.S., Helfrich, E.J.N., Hillwig, M.L., Ishida, K., Jones, A.C., Jones, C.S., Jungmann, K., Kegler, C., Kim, H.U., Kötter, P., Krug, D., Masschelein, J., Melnik, A.V., Mantovani, S.M., Monroe, E.A., Moore, M., Moss, N., Nützmann, H.-W., Pan, G., Pati, A., Petras, D., Reen, F.J., Rosconi, F., Rui, Z., Tian, Z., Tobias, N.J., Tsunematsu, Y., Wiemann, P., Wyckoff, E., Yan, X., Yim, G., Yu, F., Xie, Y., Aigle, B., Apel, A.K., Balibar, C.J., Balskus, E.P., Barona-Gómez, F., Bechthold, A., Bode, H.B., Borriss, R., Brady, S.F., Brakhage, A.A., Caffrey, P., Cheng, Y.Q., Clardy, J., Cox, R.J., De Mot, R., Donadio, S., Donia, M.S., Van Der Donk, W.A., Dorrestein, P.C., Doyle, S., Driessen, A.J.M., Ehling-Schulz, M., Entian, K.-D., Fischbach, M.A., Gerwick, L., Gerwick, W.H., Gross, H., Gust, B., Hertweck, C., Höfte, M., Jensen, S.E., Ju, J., Katz, L., Kaysser, L., Klassen, J.L., Keller, N.P., Kormanec, J., Kuipers, O.P., Kuzuyama, T., Kyrpides, N.C., Kwon, H.-J., Lautru, S., Lavigne, R., Lee, C.Y., Linquan, B., Liu, X., Liu, W., Luzhetskyy, A., Mahmud, T., Mast, Y., Méndez, C., Metsä-Ketelä, M., Micklefield, J., Mitchell, D.A., Moore, B.S., Moreira, L.M., Müller, R., Neilan, B.A., Nett, M., Nielsen, J., O'Gara, F., Oikawa, H., Osbourn, A., Osburne, M.S., Ostash, B., Payne, S.M., Pernodet, J.-L., Petricek, M., Piel, J., Ploux, O., Raaijmakers, J.M., Salas, J.A., Schmitt, E.K., Scott, B., Seipke, R.F., Shen, B., Sherman, D.H., Sivonen, K., Smanski, M.J., Sosio, M., Stegmann, E., Süssmuth, R.D., Tahlan, K., Thomas, C.M., Tang, Y., Truman, A.W., Viaud, M., Walton, J.D., Walsh, C.T., Weber, T., Van Wezel, G.P., Wilkinson, B., Willey, J.M., Wohlleben, W., Wright, G.D., Ziemert, N., Zhang, C., Zotchev, S.B., Breitling, R., Takano, E., Glöckner, F.O.

Published
2015
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38. Critical Assessment of Metagenome Interpretation – a benchmark of computational metagenomics software

Author

Alexander Sczyrba, Peter Hofmann, Peter Belmann, David Koslicki, Stefan Janssen, Johannes Dröge, Ivan Gregor, Stephan Majda, Jessika Fiedler, Eik Dahms, Andreas Bremges, Adrian Fritz, Ruben Garrido-Oter, Tue Sparholt Jørgensen, Nicole Shapiro, Philip D. Blood, Alexey Gurevich, Yang Bai, Dmitrij Turaev, Matthew Z. DeMaere, Rayan Chikhi, Niranjan Nagarajan, Christopher Quince, Fernando Meyer, Monika Balvoit, Lars Hestbjerg Hansen, Søren J. Sørensen, Burton K. H. Chia, Bertrand Denis, Jeff L. Froula, Zhong Wang, Robert Egan, Dongwan Don Kang, Jeffrey J. Cook, Charles Deltel, Michael Beckstette, Claire Lemaitre, Pierre Peterlongo, Guillaume Rizk, Dominique Lavenier, Yu-Wei Wu, Steven W. Singer, Chirag Jain, Marc Strous, Heiner Klingenberg, Peter Meinicke, Michael Barton, Thomas Lingner, Hsin-Hung Lin, Yu-Chieh Liao, Genivaldo Gueiros Z. Silva, Daniel A. Cuevas, Robert A. Edwards, Surya Saha, Vitor C. Piro, Bernhard Y. Renard, Mihai Pop, Hans-Peter Klenk, Markus Göker, Nikos C. Kyrpides, Tanja Woyke, Julia A. Vorholt, Paul Schulze-Lefert, Edward M. Rubin, Aaron E. Darling, Thomas Rattei, Alice C. McHardy, Center for Biotechnology (CeBiTec), Universität Bielefeld = Bielefeld University, Technische Fakultät, Universität Bielefeld, Algorithmische Bioinformatik [Düsseldorf], Heinrich Heine Universität Düsseldorf = Heinrich Heine University [Düsseldorf], Computational Biology of Infection Research [Braunschweig], Helmholtz Centre for Infection Research (HZI), Braunschweig Integrated Centre of Systems Biology [Braunschweig] (BRICS), Technische Universität Braunschweig = Technical University of Braunschweig [Braunschweig]-Helmholtz Centre for Infection Research (HZI), Department of Mathematics [Corvallis, Oregon], Oregon State University (OSU), Department of Computer Science and Engineering [Univ California San Diego] (CSE - UC San Diego), University of California [San Diego] (UC San Diego), University of California (UC)-University of California (UC), Department of Pediatrics [Univ California San Diego] (UC San Diego), School of Medicine [Univ California San Diego] (UC San Diego), University of California (UC)-University of California (UC)-University of California [San Diego] (UC San Diego), Max Planck Institute for Informatics [Saarbrücken], Faculty of Biology [Essen], Universität Duisburg-Essen = University of Duisburg-Essen [Essen], German Center for Infection Research - partner site Hannover-Braunschweig (DZIF), Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research (MPIPZ), Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine Universität Düsseldorf = Heinrich Heine University [Düsseldorf]-Max Planck Institute for Plant Breeding Research (MPIPZ)-Universität zu Köln = University of Cologne, Department of Environmental Science [Roskilde] (ENVS), Aarhus University [Aarhus], Section of Microbiology [Copenhagen], Department of Biology [Copenhagen], Faculty of Science [Copenhagen], 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), Department of Science and Environment [Roskilde], Roskilde University, DOE Joint Genome Institute [Walnut Creek], Pittsburgh Supercomputing Center (PSC), Center for Algorithmic Biotechnology [Saint Petersburg], Institute of Translational Biomedicine [Saint-Petersburg], Saint Petersburg University (SPBU)-Saint Petersburg University (SPBU), Centre of Excellence for Plant and Microbial Sciences (CEPAMS), John Innes Centre [Norwich], Biotechnology and Biological Sciences Research Council (BBSRC)-Biotechnology and Biological Sciences Research Council (BBSRC)-Chinese Academy of Agricultural Sciences (CAAS), Department of Microbiology and Ecosystem Science [Vienna], University of Vienna [Vienna], iThree Institute, University of Technology Sydney (UTS), Bioinformatics and Sequence Analysis (BONSAI), Université de Lille, Sciences et Technologies-Inria Lille - Nord Europe, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre de Recherche en Informatique, Signal et Automatique de Lille - UMR 9189 (CRIStAL), Centrale Lille-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Centrale Lille-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Centre de Recherche en Informatique, Signal et Automatique de Lille - UMR 9189 (CRIStAL), Centrale Lille-Université de Lille-Centre National de la Recherche Scientifique (CNRS), Department of Computational and Systems Biology [Singapore], Genome Institute of Singapore (GIS), Department of Microbiology and Infection [Coventry], Warwick Medical School, University of Warwick [Coventry]-University of Warwick [Coventry], Intel Corporation [Hillsboro], Intel Corporation [USA], Scalable, Optimized and Parallel Algorithms for Genomics (GenScale), Inria Rennes – Bretagne Atlantique, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-GESTION DES DONNÉES ET DE LA CONNAISSANCE (IRISA-D7), Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT), Department of Molecular Infection Biology [Braunschweig], Joint BioEnergy Institute [Emeryville], Graduate Institute of Biomedical Informatics [Taipei], Taipei Medical University, Biological Systems and Engineering [LBNL Berkeley], Lawrence Berkeley National Laboratory [Berkeley] (LBNL), Max planck Institute for Biology of Ageing [Cologne], Energy Engineering and Geomicrobiology [Calgary], University of Calgary, Institute of Microbiology and Genetics [Göttingen], Georg-August-University = Georg-August-Universität Göttingen, University Medical Center Göttingen (UMG), Institute of Population Health Sciences [Taiwan], National Health Research Institutes [Taiwan] (NHRI), San Diego State University (SDSU), Boyce Thompson Institute [Ithaca], Robert Koch Institute [Berlin] (RKI), Ministry of Education [Brazil], Center for Bioinformatics and Computational Biology [Maryland] (CBCB), University of Maryland [College Park], University of Maryland System-University of Maryland System, School of Biology [Newcastle upon Tyne], Newcastle University [Newcastle], Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH / Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures (DSMZ), biological sciences department [Jeddah], King Abdulaziz University, Institute of Microbiology [Zurich], Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), Department of Computer Science and Engineering [San Diego] (CSE-UCSD), University of California-University of California, Department of Pediatrics [san Diego], UC San Diego School of Medicine, Universität Duisburg-Essen [Essen], Universität zu Köln-Heinrich Heine Universität Düsseldorf = Heinrich Heine University [Düsseldorf]-Max Planck Institute for Plant Breeding Research (MPIPZ), 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), John Innes Centre [Norwich]-Chinese Academy of Agricultural Sciences (CAAS), Centre National de la Recherche Scientifique (CNRS)-Centre de Recherche en Informatique, Signal et Automatique de Lille - UMR 9189 (CRIStAL), Centrale Lille-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Centrale Lille-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Université de Lille, Sciences et Technologies-Inria Lille - Nord Europe, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria), Université de Bretagne Sud (UBS)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National de Recherche en Informatique et en Automatique (Inria)-École normale supérieure - Rennes (ENS Rennes)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-CentraleSupélec-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Bretagne Sud (UBS)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-École normale supérieure - Rennes (ENS Rennes)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Georg-August-University [Göttingen], Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Rennes 1 (UR1), and Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique)

Subjects
0303 health sciences, Biological data, business.industry, Benchmarking, Biology, Data science, Genome, 03 medical and health sciences, 0302 clinical medicine, Software, Metagenomics, Profiling (information science), Critical assessment, Taxonomic rank, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], business, 030217 neurology & neurosurgery, 030304 developmental biology
Abstract

In metagenome analysis, computational methods for assembly, taxonomic profiling and binning are key components facilitating downstream biological data interpretation. However, a lack of consensus about benchmarking datasets and evaluation metrics complicates proper performance assessment. The Critical Assessment of Metagenome Interpretation (CAMI) challenge has engaged the global developer community to benchmark their programs on datasets of unprecedented complexity and realism. Benchmark metagenomes were generated from ~700 newly sequenced microorganisms and ~600 novel viruses and plasmids, including genomes with varying degrees of relatedness to each other and to publicly available ones and representing common experimental setups. Across all datasets, assembly and genome binning programs performed well for species represented by individual genomes, while performance was substantially affected by the presence of related strains. Taxonomic profiling and binning programs were proficient at high taxonomic ranks, with a notable performance decrease below the family level. Parameter settings substantially impacted performances, underscoring the importance of program reproducibility. While highlighting current challenges in computational metagenomics, the CAMI results provide a roadmap for software selection to answer specific research questions.

Published
2017
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39. Comparative genomics of Mortierella elongata and its bacterial endosymbiont Mycoavidus cysteinexigens

Author

Du, C, Gryganskyi, G, Tschaplinski, R, Misztal, C, Wu, A, Desirò, I, Vande Pol, I, Du, R, Zienkiewicz, R, Zienkiewicz, G, Tisserant, R, Splivallo, G, Hainaut, R, Henrissat, R, Ohm, R., Kuo, G, Yan, G., Lipzen, G, Nolan, G, LaButti, G, Barry, G, Goldstein, G, Labbe, R., Schadt, R, Tuskan, G., Grigoriev, G, Martin, R, Vilgalys, R., Bonito, G., Du, J., Gryganskyi, A., Du, K., Tschaplinski, T., Misztal, K., Wu, S., Desirò, A., Vande Pol, N., Du, Z., Zienkiewicz, A., Zienkiewicz, K., Morin, E., Tisserant, E., Splivallo, R., Hainaut, M., Henrissat, B., Kuo, A., Yan, J., Lipzen, A., Nolan, M., LaButti, K., Barry, K., Goldstein, A., Labbé, J., Schadt, C., Grigoriev, I., Martin, F., Duke University [Durham], BioSciences Division [Oak Ridge], Oak Ridge National Laboratory [Oak Ridge] (ORNL), UT-Battelle, LLC-UT-Battelle, LLC, University of California [Berkeley], University of California, Arizona State University [Tempe] (ASU), Deparment of Plant, Soil and Microbial Sciences, Michigan State University [East Lansing], Michigan State University System-Michigan State University System, MSU-DOE Plant Research Laboratory and Department of Biochemistry and Molecular Biology, Interactions Arbres-Microorganismes (IAM), Institut National de la Recherche Agronomique (INRA)-Université de Lorraine (UL), Goethe-University Frankfurt am Main, 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), Utrecht University [Utrecht], Genomic Science Program, U.S. Department of Energy, Office of Science - Biological and Environmental Research as part of the Plant Microbe Interfaces Scientific Focus Area at Oak Ridge National Laboratory, U.S. Department of Energy DE-AC05- 00OR22725, DOE Joint Genome Institute by the JGI Community sequencing program 570, Office of Science of the US Department of Energy DE-AC02-05CH11231, EU Laboratory of Excellence Advanced Research on the Biology of Tree and Forest Ecosystems (ARBRE) ANR-11-LABX-0002-01, Joint Genome Institute (JGI), Northwest Institute for Nonferrous Metal Research (NIN), Laboratorio de Turbulencia, Universidad de Santiago de Chile [Santiago] (USACH), UT-Battelle, LLC, Centre d'études de chimie métallurgique (CECM), Centre National de la Recherche Scientifique (CNRS), Kansas State University, Université de Lorraine (UL)-Institut National de la Recherche Agronomique (INRA), Institut National de la Recherche Agronomique (INRA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), United States Department of Energy, Center for Human Genetics, University of Leuven School of Medicine, SCHOOL of MEDICINE [Louvain], Université Catholique de Louvain (UCL)-Université Catholique de Louvain (UCL), DOE Joint Genome Institute [Walnut Creek], Lawrence Berkeley National Laboratory [Berkeley] (LBNL), Sub Molecular Microbiology, Molecular Microbiology, Joint Genome Institute ( JGI ), Northwest Institute for Nonferrous Metal Research, Oak Ridge National Laboratory, Duke university [Durham], Centre d'études de chimie métallurgique ( CECM ), Centre National de la Recherche Scientifique ( CNRS ), Interactions Arbres-Microorganismes ( IAM ), Institut National de la Recherche Agronomique ( INRA ) -Université de Lorraine ( UL ), 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 ), UNIVERSITY of LEUVEN SCHOOL of MEDICINE, Institute of Northern Engineering, 455 Duckering Bldg, Lawrence Berkeley National Laboratory [Berkeley] ( LBNL ), Lipides - Nutrition - Cancer (U866) ( LNC ), Université de Bourgogne ( UB ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ) -AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Ecole Nationale Supérieure de Biologie Appliquée à la Nutrition et à l'Alimentation de Dijon ( ENSBANA ), University of California [Berkeley] (UC Berkeley), and University of California (UC)

Subjects
Burkholderiaceae, [SDV.NEU.NB]Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC]/Neurobiology, MESH : Symbiosis, MESH: Base Sequence, MESH: Genome, Bacterial, 2.2 Factors relating to physical environment, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, LAND PLANTS, 2.2 Factors relating to the physical environment, MESH : Metagenome, MESH: Animals, [ SDV.BIBS ] Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], MESH: Phylogeny, Phylogeny, MESH: Lipid Metabolism, [SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases, MESH: Symbiosis, Endosymbiosis, [ SDV.MHEP.ME ] Life Sciences [q-bio]/Human health and pathology/Emerging diseases, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], Bacterial, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], FATTY-ACID BIOSYNTHESIS, [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biomolecules [q-bio.BM], [ SDV.MHEP.MI ] Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Fungal, [ SDV.NEU.NB ] Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC]/Neurobiology, MESH: Genome, Fungal, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Infection, Evolution, 030106 microbiology, MESH : Genome, Bacterial, [ SDV.MP.VIR ] Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Microbiology, GENE-TRANSFER, 03 medical and health sciences, MESH : Burkholderiaceae, Botany, MESH : Evolution, Molecular, Ecology, Evolution, Behavior and Systematics, Comparative genomics, [ SDV.IMM.II ] Life Sciences [q-bio]/Immunology/Innate immunity, MESH : Genome, Fungal, Molecular, ENDOBACTERIA, MESH: Burkholderiaceae, DNA, 15. Life on land, Lipid Metabolism, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, INTRACELLULAR BACTERIA, 030104 developmental biology, MESH: Mortierella, Metagenome, MESH : Sequence Analysis, DNA, 0301 basic medicine, MESH: Sequence Analysis, DNA, [SDV.BIO]Life Sciences [q-bio]/Biotechnology, MESH: Carbohydrate Metabolism, [ SDV.MP.BAC ] Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Genome, GUT MICROBIOME, [SDV.IMM.II]Life Sciences [q-bio]/Immunology/Innate immunity, ARBUSCULAR MYCORRHIZAL FUNGI, [ SDV.BBM.BC ] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biomolecules [q-bio.BM], Mortierella, MESH : Lipid Metabolism, MESH: Evolution, Molecular, 2. Zero hunger, Genetics, biology, Ecology, Fungal genetics, MESH : Carbohydrate Metabolism, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biomolecules [q-bio.BM], ESCHERICHIA-COLI, Carbohydrate Metabolism, Sequence Analysis, Metabolic Networks and Pathways, CANDIDATUS GLOMERIBACTER GIGASPORARUM, Bacterial genome size, Symbiosis, Behavior and Systematics, Lipid biosynthesis, Animals, [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biochemistry [q-bio.BM], Evolutionary Biology, Base Sequence, MESH : Metabolic Networks and Pathways, MESH : Phylogeny, [ SDV.BIO ] Life Sciences [q-bio]/Biotechnology, [ SDV.SP.PHARMA ] Life Sciences [q-bio]/Pharmaceutical sciences/Pharmacology, MESH: Metagenome, biology.organism_classification, MESH: Metabolic Networks and Pathways, [SDV.SP.PHARMA]Life Sciences [q-bio]/Pharmaceutical sciences/Pharmacology, MESH : Base Sequence, BICOLOR S238N, MESH : Animals, MESH : Mortierella, [ SDV.BBM.BS ] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biomolecules [q-bio.BM]
Abstract

International audience; Endosymbiosis of bacteria by eukaryotes is a defining feature of cellular evolution. In addition to well-known bacterial origins for mitochondria and chloroplasts, multiple origins of bacterial endosymbiosis are known within the cells of diverse animals, plants and fungi. Early-diverging lineages of terrestrial fungi harbor endosymbiotic bacteria belonging to the Burkholderiaceae. We sequenced the metagenome of the soil-inhabiting fungus Mortierella elongata and assembled the complete circular chromosome of its endosymbiont, Mycoavidus cysteinexigens, which we place within a lineage of endofungal symbionts that are sister clade to Burkholderia. The genome of M. elongata strain AG77 features a core set of primary metabolic pathways for degradation of simple carbohydrates and lipid biosynthesis, while the M. cysteinexigens (AG77) genome is reduced in size and function. Experiments using antibiotics to cure the endobacterium from the host demonstrate that the fungal host metabolism is highly modulated by presence/absence of M. cysteinexigens. Independent comparative phylogenomic analyses of fungal and bacterial genomes are consistent with an ancient origin for M. elongata - M. cysteinexigens symbiosis, most likely over 350 million years ago and concomitant with the terrestrialization of Earth and diversification of land fungi and plants.

Published
2017
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40. Population genomics of picophytoplankton unveils novel chromosome hypervariability

Author

Blanc-Mathieu, Romain, Krasovec, Marc, Hebrard, Maxime, Yau, Sheree, Desgranges, Elodie, Martin, Joel, Schackwitz, Wendy, Kuo, Alan, Salin, Gerald, Donnadieu, Cecile, Desdevises, Yves, Sanchez-Ferandin, Sophie, Moreau, Hervé, Rivals, Eric, Grigoriev, Igor V., Grimsley, Nigel, Eyre-Walker, Adam, Piganeau, Gwenael, Biologie intégrative des organismes marins (BIOM), Observatoire océanologique de Banyuls (OOB), 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), Méthodes et Algorithmes pour la Bioinformatique (MAB), Laboratoire d'Informatique de Robotique et de Microélectronique de Montpellier (LIRMM), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), DOE Joint Genome Institute [Walnut Creek], Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Génome et Transcriptome - Plateforme Génomique (GeT-PlaGe), Institut National de la Recherche Agronomique (INRA)-Plateforme Génome & Transcriptome (GET), Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Institut de Biologie Computationnelle (IBC), Université de Montpellier (UM)-Institut National de la Recherche Agronomique (INRA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS), School of Life Sciences, University of Sussex, LabEx NUMEV, ATGC bioinformatics platform, ANR-11-BINF-0002,IBC,Institut de biologie Computationnelle(2011), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), GeT PlaGe, Genotoul, Institut National de la Recherche Agronomique (INRA), Institut National de la Recherche Agronomique (INRA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), ANR-11-BINF-0002,IBC,Institut de Biologie Computationnelle de Montpellier(2011), Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-École nationale supérieure agronomique de Toulouse (ENSAT), Université de Toulouse (UT)-Université de Toulouse (UT), Université de Toulouse (UT)-Université de Toulouse (UT)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Centre National de la Recherche Scientifique (CNRS)-Observatoire océanologique de Banyuls (OOB), 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), and Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-École nationale supérieure agronomique de Toulouse [ENSAT]

Subjects
population genomics, Evolution, Population, linkage disequilbrium, prasinovirus, Polymorphism, Single Nucleotide, Chromosomes, Genetic Diversity, Evolution, Molecular, Genetic, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Genetics, QH0359, Polymorphism, standing genetic-variation, alga ostreococcus-tauri, large dna viruse, mammalian genome, sequencing data, photosynthetic eukaryote, evolution, recombination, adaptation, yeast, Selection, Genetic, Selection, Research Articles, Phylogeny, [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], Human Genome, fungi, evolutionary genomics, Molecular, SciAdv r-articles, Genetic Variation, Single Nucleotide, Genomics, mating type locus, picophytoplankton, Genetics, Population, Phenotype, multiple nucleotide mutation events, QH0426, GC content evolution, Mutation, Phytoplankton, chromothripsis, Disease Susceptibility, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], sex evolution, human activities, Biotechnology, Autre (Sciences du Vivant), Research Article
Abstract

Phytoplanktonic eukaryotes form huge panmictic populations and have evolved original hypervariability mechanisms to resist viral attack., Tiny photosynthetic microorganisms that form the picoplankton (between 0.3 and 3 μm in diameter) are at the base of the food web in many marine ecosystems, and their adaptability to environmental change hinges on standing genetic variation. Although the genomic and phenotypic diversity of the bacterial component of the oceans has been intensively studied, little is known about the genomic and phenotypic diversity within each of the diverse eukaryotic species present. We report the level of genomic diversity in a natural population of Ostreococcus tauri (Chlorophyta, Mamiellophyceae), the smallest photosynthetic eukaryote. Contrary to the expectations of clonal evolution or cryptic species, the spectrum of genomic polymorphism observed suggests a large panmictic population (an effective population size of 1.2 × 107) with pervasive evidence of sexual reproduction. De novo assemblies of low-coverage chromosomes reveal two large candidate mating-type loci with suppressed recombination, whose origin may pre-date the speciation events in the class Mamiellophyceae. This high genetic diversity is associated with large phenotypic differences between strains. Strikingly, resistance of isolates to large double-stranded DNA viruses, which abound in their natural environment, is positively correlated with the size of a single hypervariable chromosome, which contains 44 to 156 kb of strain-specific sequences. Our findings highlight the role of viruses in shaping genome diversity in marine picoeukaryotes.

Published
2017
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41. Evolutionary genomics of the cold-adapted diatom Fragilariopsis cylindrus

Author

Beverley R. Green, Gernot Glöckner, Thomas Mock, Remo Sanges, James A. Raymond, Michael G. Janech, Barbara R. Lyon, Kerrie Barry, Florian Leese, Ansgar Gruber, Joel Martin, Erika Lindquist, Matthew D. Clark, Robert Otillar, Ben J. Ward, Alexandra Z. Worden, Christoph Mayer, Antonio Emidio Fortunato, Micaela S. Parker, Christopher L. Dupont, Maria Immacolata Ferrante, Stephan Frickenhaus, Klaus Valentin, Hadi Quesneville, Vincent Moulton, Rachel Hipkin, Angela Falciatore, Igor V. Grigoriev, Christiane Uhlig, Chris Bowler, Cock van Oosterhout, Ruben E. Valas, Asaf Salamov, Jeremy Schmutz, E. Virginia Armbrust, Andrew E. Allen, Alaguraj Veluchamy, Jan Strauss, Peter G. Kroth, Mark McMullan, Taoyang Wu, Andrew Toseland, Pirita Paajanen, Florian Maumus, School of Environmental Sciences [Norwich], University of East Anglia [Norwich] (UEA), Joint Genome Institute, United States Department of Energy, Hudson Alpha Institute, Sezione Ecologia Marina Integrata, Stazione Zoologica Anton Dohrn, School of Physics [NUI Galway], National University of Ireland [Galway] (NUI Galway), Infection et inflammation chronique (2I), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Institut National de la Santé et de la Recherche Médicale (INSERM), Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung (AWI), Unité de Recherche Génomique Info (URGI), Institut National de la Recherche Agronomique (INRA), Technical University of Munich (TUM), Biologie Computationnelle et Quantitative = Laboratory of Computational and Quantitative Biology (LCQB), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut de Biologie Paris Seine (IBPS), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-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), Genomics Institute for Biochemistry I, University of Cologne, University of Innsbruck, Laboratoire Genome Population & Interactions, Université Montpellier 2 - Sciences et Techniques (UM2)-Centre National de la Recherche Scientifique (CNRS)-ORSTOM, Department of Biology, University of Konstanz, Animal Ecology, Evolution and Biodiversity, Ruhr-Universität Bochum [Bochum], Univ Reading, Sch Chem Pharm & Food Biosci, Reading RG6 6AD, Berks, England, Canadian Institute for Advanced Research (CIAR), Université de Montréal [Montréal], Monterey Bay Aquarium Research Institute (MBARI), Monterey Bay Aquarium Research Institute, University of California [Santa Cruz] (UCSC), University of California, School of Oceanography [Seattle], University of Washington [Seattle], Johns Hopkins University School of Medicine [Baltimore], Department of Computer Science, DOE Joint Genome Institute [Walnut Creek], Stazione Zoologica Anton Dohrn (SZN), Infection et inflammation (2I), Technische Universität Munchen - Université Technique de Munich [Munich, Allemagne] (TUM), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-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), Leopold Franzens Universität Innsbruck - University of Innsbruck, Université Montpellier 2 - Sciences et Techniques (UM2)-ORSTOM-Centre National de la Recherche Scientifique (CNRS), Canadian Institute for Advanced Research (CIFAR), University of California [Santa Cruz] (UC Santa Cruz), University of California (UC), ERC Advanced Grant ERC-2011-ADG (Diatomite) - Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231 - NERC under grants NE/I001751/1, NE/K004530/1, MGF (NBAF) grant 197, The Royal Society grant RG090774 and the Earth & Life Systems Alliance in Norwich, European Project: 294823,EC:FP7:ERC,ERC-2011-ADG_20110310,DIATOMITE(2012), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ), Institut de Biologie Paris Seine (IBPS), and Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)

Subjects
0106 biological sciences, 0301 basic medicine, Acclimatization, [SDV]Life Sciences [q-bio], 01 natural sciences, Mutation Rate, Settore BIO/13 - Biologia Applicata, Freezing, Alleles, Carbon Dioxide, Darkness, Diatoms, Gene Expression Profiling, Genetic Drift, Genome, Ice Cover, Iron, Oceans and Seas, Phylogeny, Recombination, Genetic, Transcriptome, Cold Temperature, Evolution, Molecular, Genomics, Multidisciplinary, biology, Ecology, Biologie, Biotechnology, Genome evolution, Evolution, General Science & Technology, 03 medical and health sciences, Genetic drift, Genetic, Cylindrus, Molecular evolution, ddc:570, Genetics, 14. Life underwater, Genome size, Human Genome, fungi, Molecular, biology.organism_classification, Recombination, 030104 developmental biology, Diatom, Adaptation, 010606 plant biology & botany
Abstract

The Southern Ocean houses a diverse and productive community of organisms. Unicellular eukaryotic diatoms are the main primary producers in this environment, where photosynthesis is limited by low concentrations of dissolved iron and large seasonal fluctuations in light, temperature and the extent of sea ice. How diatoms have adapted to this extreme environment is largely unknown. Here we present insights into the genome evolution of a cold-Adapted diatom from the Southern Ocean, Fragilariopsis cylindrus, based on a comparison with temperate diatoms. We find that approximately 24.7 per cent of the diploid F. cylindrus genome consists of genetic loci with alleles that are highly divergent (15.1 megabases of the total genome size of 61.1 megabases). These divergent alleles were differentially expressed across environmental conditions, including darkness, low iron, freezing, elevated temperature and increased CO 2 . Alleles with the largest ratio of non-synonymous to synonymous nucleotide substitutions also show the most pronounced condition-dependent expression, suggesting a correlation between diversifying selection and allelic differentiation. Divergent alleles may be involved in adaptation to environmental fluctuations in the Southern Ocean. © 2017 Macmillan Publishers Limited, part of Springer Nature. All rights reserved.

Published
2017
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42. Structural and Functional Modularity of the Orange Carotenoid Protein: Distinct Roles for the N- and C-Terminal Domains in Cyanobacterial Photoprotection

Author

Richard A. Mathies, Denis Jallet, Cheryl A. Kerfeld, Ryan L. Leverenz, Ming-De Li, Diana Kirilovsky, Department of Plant and Microbial Biology [Berkeley], University of California [Berkeley], University of California-University of California, Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Department of Chemistry [Berkeley], DOE Joint Genome Institute [Walnut Creek], Berkeley Synthetic Biology Institute [Berkeley] (SYNBIO), National Science Foundation [MCB 0851094, MCB1160614], Agence Nationale de la Recherche (Project CYANOPROTECT), CNRS, CEA, HARVEST EU FP7 Marie Curie Research Training Network, University Paris XI, Mathies Royalty Fund, University of California [Berkeley] (UC Berkeley), and University of California (UC)-University of California (UC)

Subjects
0106 biological sciences, Cyanobacteria, [SDV.BIO]Life Sciences [q-bio]/Biotechnology, Plant Science, 01 natural sciences, 03 medical and health sciences, Bacterial Proteins, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Carotenoid, Research Articles, 030304 developmental biology, chemistry.chemical_classification, 0303 health sciences, biology, Orange carotenoid protein, Effector, Cell Biology, Chromophore, biology.organism_classification, Carotenoids, Protein Structure, Tertiary, Light intensity, chemistry, Biochemistry, Photoprotection, Proteolysis, Phycobilisome, Energy Metabolism, 010606 plant biology & botany
Abstract

The orange carotenoid protein (OCP) serves as a sensor of light intensity and an effector of phycobilisome (PB)–associated photoprotection in cyanobacteria. Structurally, the OCP is composed of two distinct domains spanned by a single carotenoid chromophore. Functionally, in response to high light, the OCP converts from a dark-stable orange form, OCPO, to an active red form, OCPR. The C-terminal domain of the OCP has been implicated in the dynamic response to light intensity and plays a role in switching off the OCP's photoprotective response through its interaction with the fluorescence recovery protein. The function of the N-terminal domain, which is uniquely found in cyanobacteria, is unclear. To investigate its function, we isolated the N-terminal domain in vitro using limited proteolysis of native OCP. The N-terminal domain retains the carotenoid chromophore; this red carotenoid protein (RCP) has constitutive PB fluorescence quenching activity comparable in magnitude to that of active, full-length OCPR. A comparison of the spectroscopic properties of the RCP with OCPR indicates that critical protein–chromophore interactions within the C-terminal domain are weakened in the OCPR form. These results suggest that the C-terminal domain dynamically regulates the photoprotective activity of an otherwise constitutively active carotenoid binding N-terminal domain.

Published
2014
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43. Draft genome sequences of gammaproteobacterial methanotrophs isolated from marine ecosystems

Author

Nicole Shapiro, Jeremy D. Semrau, Nikos C. Kyrpides, James D. Flynn, Tanja Woyke, Yasuyoshi Sakai, Claudia Knief, Mike S. M. Jetten, Fran�oise Bringel, Marina G. Kalyuzhnaya, Mette M. Svenning, Martin G. Klotz, Valentina N. Khmelenina, Lisa Y. Stein, Huub J. M. Op den Camp, Hisako Hirayama, Peter F. Dunfield, St�phane Vuilleumier, Alan A. DiSpirito, J. Colin Murrell, Yuri A. Trotsenko, RIKEN - Institute of Physical and Chemical Research [Japon] (RIKEN), Kyoto University [Kyoto], University of Calgary, Laboratoire de Synthèse et Fonctionnalisation de Céramiques (LSFC), Saint Gobain-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), University of Bonn, Department of Microbiology, Institute for Water and Wetland Research, Skryabin Institute of biochemistry and physiology of microorganisms (IBPM/RAS), Russian Academy of Sciences [Moscow] (RAS), Skryabin Institute of Biochemistry and Physiology of Microorganisms (IBPM/RAS), School of Environmental Sciences [Norwich], University of East Anglia [Norwich] (UEA), University of Michigan [Ann Arbor], University of Michigan System, University of Tromsø (UiT), University of Alberta, DOE Joint Genome Institute [Walnut Creek], Laboratoire de Sismologie (IPGP), Institut de Physique du Globe de Paris, Department of Energy / Joint Genome Institute (DOE), Los Alamos National Laboratory (LANL), Génétique moléculaire, génomique, microbiologie (GMGM), Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS), Iowa State University (ISU), and University of Washington [Seattle]

Subjects
0301 basic medicine, Ecology, Methylomarinum vadi, Strain (biology), Human Genome, Biology, Genome, Microbiology, 03 medical and health sciences, 030104 developmental biology, Methylobacter marinus, Ecological Microbiology, Genetics, Marine ecosystem, 14. Life underwater, Biochemistry and Cell Biology, Prokaryotes, GeneralLiterature_REFERENCE(e.g.,dictionaries,encyclopedias,glossaries), Molecular Biology, ComputingMilieux_MISCELLANEOUS, Hydrothermal vent, [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis
Abstract

The genome sequences of Methylobacter marinus A45, Methylobacter sp. strain BBA5.1, and Methylomarinum vadi IT-4 were obtained. These aerobic methanotrophs are typical members of coastal and hydrothermal vent marine ecosystems.

Published
2016
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44. Crowdsourcing and curation: perspectives from biology and natural language processing

Author

Stéphanie Boué, Rezarta Islamaj Dogan, Lynette Hirschman, Nikos C. Kyrpides, Kevin Bretonnel Cohen, Karën Fort, The MITRE corporation, Sens, Texte, Informatique, Histoire (STIH), Université Paris-Sorbonne (UP4), Philip Morris International R&D (PMI), Philip Morris International, DOE Joint Genome Institute [Walnut Creek], National Center for Biotechnology Information, National Institutes of Health, Department of Health and Human Services, Bethesda, Md, National Institutes of Health [Bethesda] (NIH), and University of Colorado [Boulder]

Subjects
0301 basic medicine, Computer science, media_common.quotation_subject, 02 engineering and technology, computer.software_genre, Crowdsourcing, biomedical, General Biochemistry, Genetics and Molecular Biology, Session (web analytics), World Wide Web, 03 medical and health sciences, Library and Information Studies, 020204 information systems, 0202 electrical engineering, electronic engineering, information engineering, Quality (business), Data Curation, media_common, Natural Language Processing, Metadata, business.industry, Panel session, Data science, Data Format, [INFO.INFO-TT]Computer Science [cs]/Document and Text Processing, 030104 developmental biology, Crowdsourcing software development, games with a purpose, Original Article, crowdsourcing, Artificial intelligence, General Agricultural and Biological Sciences, business, computer, Natural language processing, Information Systems
Abstract

Crowdsourcing is increasingly utilized for performing tasks in both natural language processing and biocuration. Although there have been many applications of crowdsourcing in these fields, there have been fewer high-level discussions of the methodology and its applicability to biocuration. This paper explores crowdsourcing for biocuration through several case studies that highlight different ways of leveraging 'the crowd'; these raise issues about the kind(s) of expertise needed, the motivations of participants, and questions related to feasibility, cost and quality. The paper is an outgrowth of a panel session held at BioCreative V (Seville, September 9-11, 2015). The session consisted of four short talks, followed by a discussion. In their talks, the panelists explored the role of expertise and the potential to improve crowd performance by training; the challenge of decomposing tasks to make them amenable to crowdsourcing; and the capture of biological data and metadata through community editing.Database URL: http://www.mitre.org/publications/technical-papers/crowdsourcing-and-curation-perspectives.

Published
2016
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45. CTCF-Mediated Human 3D Genome Architecture Reveals Chromatin Topology for Transcription

Author

Oscar Junhong Luo, Jakub Wlodarczyk, Ping Wang, Emaly Piecuch, Yijun Ruan, Dariusz Plewczynski, May Penrad-Mobayed, Pawel Trzaskoma, Zhonghui Tang, Jacqueline Jufen Zhu, Przemyslaw Szalaj, Edison T. Liu, Adriana Magalska, Guoliang Li, Grzegorz M. Wilczynski, Laurent M. Sachs, Xingwang Li, Paul J. Michalski, Danjuan Wang, Blazej Ruszczycki, Xiaoan Ruan, Chia-Lin Wei, Simon Zhongyuan Tian, Meizhen Zheng, The Jackson Laboratory's research institute, National Key Laboratory of Crop Genetic Improvement, Sichuan University, College of Life Sciences-Huazhong Agricultural University, Department of Genetics and Genome Sciences, University of Connecticut (UCONN), Center for Bioinformatics and Data Analysis, Medical University of Bialystok, I-BioStat, Hasselt University, Centre of New Technologies, Medical University of Warsaw - Poland, Nencki Institute of Experimental Biology, Polska Akademia Nauk (PAN), Institut Jacques Monod (IJM (UMR_7592)), Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique/Muséum National d'Histoire Naturelle, DOE Joint Genome Institute [Walnut Creek], College of Informatics, Huazhong Agricultural University, Director Innovation Fund of Jackson Laboratory, NCI R01 CA186714, NHGRI R25HG007631, NIDDK U54DK107967 (4DN), Roux family, China '111 project' (B07041), Polish National Science Centre [UMO-2012/05/E/NZ4/02997], [2014/15/B/ST6/05082, UMO-2013/09/B/NZ2/00121], [DEC-2012/06/M/NZ3/00163], National Leading Research Centre in Bialystok, European Union under the European Social Fund, The Jackson Laboratory [Bar Harbor] (JAX), Polska Akademia Nauk = Polish Academy of Sciences (PAN), University of Turku, Evolution des régulations endocriniennes (ERE), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), University of Geneva Medical School, Cancer Biology and Pharmacology, Genome Institute of Singapore (GIS), Hasselt University (UHasselt), and Physiologie moléculaire et adaptation (PhyMA)

Subjects
CCCTC-Binding Factor, Transcription, Genetic, Chromosomal Proteins, Non-Histone, RNA polymerase II, Cell Cycle Proteins, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, Topology, Genome, General Biochemistry, Genetics and Molecular Biology, Chromosomes, Article, Cell Line, 03 medical and health sciences, 0302 clinical medicine, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], DNA Packaging, Animals, Humans, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Gene, ChIA-PET, 030304 developmental biology, Genetics, 0303 health sciences, biology, Biochemistry, Genetics and Molecular Biology(all), Genome, Human, Salamandridae, Chromatin, Repressor Proteins, CTCF, biology.protein, Chromatin Loop, Human genome, RNA Polymerase II, 030217 neurology & neurosurgery
Abstract

International audience; Spatial genome organization and its effect on transcription remains a fundamental question. We applied an advanced chromatin interaction analysis by paired-end tag sequencing (ChIA-PET) strategy to comprehensively map higher-order chromosome folding and specific chromatin interactions mediated by CCCTC-binding factor (CTCF) and RNA polymerase II (RNAPII) with haplotype specificity and nucleotide resolution in different human cell lineages. We find that CTCF/cohesin-mediated interaction anchors serve as structural foci for spatial organization of constitutive genes concordant with CTCF-motif orientation, whereas RNAPII interacts within these structures by selectively drawing cell-type-specific genes toward CTCF foci for coordinated transcription. Furthermore, we show that haplotype variants and allelic interactions have differential effects on chromosome configuration, influencing gene expression, and may provide mechanistic insights into functions associated with disease susceptibility. 3D genome simulation suggests a model of chromatin folding around chromosomal axes, where CTCF is involved in defining the interface between condensed and open compartments for structural regulation. Our 3D genome strategy thus provides unique insights in the topological mechanism of human variations and diseases.

Published
2015
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46. Mammalian Systems Biotechnology Reveals Global Cellular Adaptations in a Recombinant CHO Cell Line

Author

Corrine Wan, Hock Chuan Yeo, Sze Wai Ng, Chung Ping Chow, Faraaz N.K. Yusufi, Ai Ping Hiu, Ju Xin Chin, Yuansheng Yang, Xiaoan Ruan, Ken Wing Kin Sung, Bernard Loo, Miranda Gek Sim Yap, Gavin Teo, Say Kong Ng, Wei Shou Hu, Pramila N. Ariyaratne, Gao Song, Dong-Yup Lee, Muriel Bardor, Ying Swan Ho, Shuwen Chen, Tessa Rui Min Tan, Niranjan Nagarajan, Hsueh Lee Lim, Meiyappan Lakshmanan, DOE Joint Genome Institute [Walnut Creek], Laboratoire de Glycobiologie et Matrice Extracellulaire Végétale (Glyco-MEV), Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Normandie Université (NU), Department of Computational and Systems Biology [Singapore], and Genome Institute of Singapore (GIS)

Subjects
0106 biological sciences, 0301 basic medicine, Glycosylation, [SDV.BIO]Life Sciences [q-bio]/Biotechnology, Gene Dosage, [SDV.BC.BC]Life Sciences [q-bio]/Cellular Biology/Subcellular Processes [q-bio.SC], 01 natural sciences, law.invention, Transcriptome, law, [SDV.BC.IC]Life Sciences [q-bio]/Cellular Biology/Cell Behavior [q-bio.CB], Transgenes, Glycomics, ComputingMilieux_MISCELLANEOUS, [SDV.BDD.GAM]Life Sciences [q-bio]/Development Biology/Gametogenesis, Mammals, Genome, Systems Biology, Chinese hamster ovary cell, [SDV.BBM.MN]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular Networks [q-bio.MN], Transfection, Recombinant Proteins, Recombinant DNA, Biotechnology, Histology, Transgene, CHO Cells, Biology, Pathology and Forensic Medicine, 03 medical and health sciences, Cricetulus, Metabolomics, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], 010608 biotechnology, Animals, [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biochemistry [q-bio.BM], business.industry, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, Cell Biology, [SDV.BV.PEP]Life Sciences [q-bio]/Vegetal Biology/Phytopathology and phytopharmacy, [SDV.BV.AP]Life Sciences [q-bio]/Vegetal Biology/Plant breeding, [CHIM.POLY]Chemical Sciences/Polymers, 030104 developmental biology, Cell culture, business
Abstract

Effective development of host cells for therapeutic protein production is hampered by the poor characterization of cellular transfection. Here, we employed a multi-omics-based systems biotechnology approach to elucidate the genotypic and phenotypic differences between a wild-type and recombinant antibody-producing Chinese hamster ovary (CHO) cell line. At the genomic level, we observed extensive rearrangements in specific targeted loci linked to transgene integration sites. Transcriptional re-wiring of DNA damage repair and cellular metabolism in the antibody producer, via changes in gene copy numbers, was also detected. Subsequent integration of transcriptomic data with a genome-scale metabolic model showed a substantial increase in energy metabolism in the antibody producer. Metabolomics, lipidomics, and glycomics analyses revealed an elevation in long-chain lipid species, potentially associated with protein transport and secretion requirements, and a surprising stability of N-glycosylation profiles between both cell lines. Overall, the proposed knowledge-based systems biotechnology framework can further accelerate mammalian cell-line engineering in a targeted manner.

Published
2017
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47. Genome interplay in the grain transcriptome of hexaploid bread wheat

Author

Pfeifer, Matthias, Kugler, Karl, Sandve, Simen, Zhan, Bujie, Rudi, Heidi, Hvidsten, Torgeir, Mayer, Klaus, Rogers, Jane, Doležel, Jaroslav, Pozniak, Curtis, Eversole, Kellye, Feuillet, Catherine, Gill, Bikram, Friebe, Bernd, Lukaszewski, Adam, Sourdille, Pierre, Endo, Takashi, Kubaláková, Marie, Číhalíková, Jarmila, Dubská, Zdeňka, Vrána, Jan, Šperková, Romana, Šimková, Hana, Febrer, Melanie, Clissold, Leah, Mclay, Kirsten, Singh, Kuldeep, Chhuneja, Parveen, Singh, Nagendra K, Khurana, Jitendra, Akhunov, Eduard, Choulet, Frédéric, Alberti, Adriana, Barbe, Valérie, Wincker, Patrick, Kanamori, Hiroyuki, Kobayashi, Fuminori, Itoh, Takeshi, Matsumoto, Takashi, Sakai, Hiroaki, Tanaka, Tsuyoshi, Wu, Jianzhong, Ogihara, Yasunari, Handa, Hirokazu, Maclachlan, P Ron, Sharpe, Andrew, Klassen, Darrin, Edwards, David, Batley, Jacqueline, Olsen, Odd-Arne, Lien, Sigbjørn, Steuernagel, Burkhard, Wulff, Brande, Caccamo, Mario, Ayling, Sarah, Ramirez-Gonzalez, Ricardo H, Clavijo, Bernardo J, Wright, Jonathan, Spannagl, Manuel, Martis, Mihaela M, Mascher, Martin, Chapman, Jarrod, Poland, Jesse A, Scholz, Uwe, Barry, Kerrie, Waugh, Robbie, Rokhsar, Daniel S, Muehlbauer, Gary J, Stein, Nils, Gundlach, Heidrun, Zytnicki, Matthias, Jamilloux, Véronique, Quesneville, Hadi, Wicker, Thomas, Faccioli, Primetta, Colaiacovo, Moreno, Stanca, Antonio Michele, Budak, Hikmet, Cattivelli, Luigi, Glover, Natasha, Pingault, Lise, Paux, Etienne, Sharma, Sapna, Appels, Rudi, Bellgard, Matthew, Chapman, Brett, Nussbaumer, Thomas, Bader, Kai Christian, Rimbert, Hélène, Wang, Shichen, Knox, Ron, Kilian, Andrzej, Alaux, Michael, Alfama, Françoise, Couderc, Loïc, Guilhot, Nicolas, Viseux, Claire, Loaec, Mikael, Keller, Beat, Praud, Sébastien, Plant Genome and Systems Biology, Helmholtz Diabetes Center at Helmholtz Zentrum, Norwegian University of Life Sciences (NMBU), University of Norway, Génétique Diversité et Ecophysiologie des Céréales (GDEC), Institut National de la Recherche Agronomique (INRA)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP), Unité de Recherche Génomique Info (URGI), Institut National de la Recherche Agronomique (INRA), Norwegian Research Council 199387, Deutsche Forschungsgemeinschaft (DFG) SFB924, German Federal Ministry of Education and Research (BMBF), European Commission's 7th Framework Program, Plant Genome and Systems Biology (PGSB), Helmholtz Zentrum München = German Research Center for Environmental Health, Centre for Integrative Genetics, Department of Chemistry, Biotechnology and Food Science, Eversole Associates, Centre of Plant Structural and Functional Genomics, Institute of Experimental Botany of the Czech Academy of Sciences (IEB / CAS), Czech Academy of Sciences [Prague] (CAS)-Czech Academy of Sciences [Prague] (CAS), University of Saskatchewan [Saskatoon] (U of S), Bayer Crop Science, Kansas State Univ, Dept Plant Pathol, Manhattan, KS 66506 USA, Partenaires INRAE, Department of Botany and Plant Sciences [Riverside], University of California [Riverside] (UC Riverside), University of California (UC)-University of California (UC), Graduate School of Agriculture, Kyoto University, Kyoto, Japan, Centre of the Region Haná for Biotechnological and Agricultural Research [Univ Palacký] (CRH), Faculty of Science [Univ Palacký], Palacky University Olomouc-Palacky University Olomouc-Institute of Experimental Botany of the Czech Academy of Sciences (IEB / CAS), Centre of the Region Haná for Biotechnological and Agricultural Research, Fraunhofer Institute for Intelligent Analysis and Information Systems (Fraunhofer IAIS), Fraunhofer (Fraunhofer-Gesellschaft), National Research Centre Plant Biotechnology, Dept Plant Pathol, Kansas State University, 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), Bayer Cropscience, Institute of Crop Sciences of CAAS [Beijing] (ICS CAAS), Chinese Academy of Agricultural Sciences (CAAS), National Institute of Agrobiological Sciences (NIAS), National Institute of Agrobiological Sciences, Natl Inst Agrobiol Sci, JST-CREST, Japan Science and Technology Agency, Global Institute of Food Security, School of Agriculture and Food Sciences, Australian Centre for Plant Functional Genomics, University of Queensland [Brisbane], Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences, The Sainsbury Laboratory [Norwich] (TSL), Genome Analysis Centre, John Innes Centre [Norwich], Biotechnology and Biological Sciences Research Council (BBSRC), European Synchrotron Radiation Facility (ESRF), German Research Center for Environmental Health - Helmholtz Center München (GmbH), MIPS/IBIS, Leibniz Institute of Plant Genetics and Crop Plant Research [Gatersleben] (IPK-Gatersleben), DOE Joint Genome Institute [Walnut Creek], United States Department of Energy, The James Hutton Institute, Inst Bioinformat & Syst Biol, Munich Informat Ctr Prot Sequences, Unité de Mathématiques et Informatique Appliquées de Toulouse (MIAT INRA), Institute of Plant Biology, Universität Zürich [Zürich] = University of Zurich (UZH), Fac Engn & Nat Sci, Sabanci University [Istanbul], Genomics Research Centre, Consiglio per la Ricerca e Sperimentazione in Agricoltura, York University, Agriculture Victoria Research, Department of Economic Development, Jobs, Transport and Resources, AgriBio, Centre for Comparative Genomics, Murdoch University, CUBE Division of Computational Systems Biology, University of Vienna [Vienna], Department of Plant Pathology, Shizuoka University, Diversity Arrays Technology Pty Ltd (DArT P/L), Centre de Recherche de Chappes, BIOGEMMA, Research Council of Norway [199387], German Research Foundation (DFG) [SFB924], German Federal Ministry of Education and Research (BMBF), European Project: 283496,EC:FP7:INFRA,FP7-INFRASTRUCTURES-2011-2,TRANSPLANT(2011), Helmholtz-Zentrum München (HZM), Univ Saskatchewan, Dept Plant Sci, Saskatoon, SK, Canada, University of California [Riverside] (UCR), University of California-University of California, 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, University of Saskatchewan, John Innes Centre, and University of Zurich

Subjects
MESH: Genome, Plant, [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, 0106 biological sciences, [SDV]Life Sciences [q-bio], Gene Dosage, 01 natural sciences, Genome, MESH: Gene Dosage, Endosperm, Transcriptome, Gene Expression Regulation, Plant, Triticum, Cancer, Plant Proteins, International Wheat Genome Sequencing Consortium, 2. Zero hunger, Genetics, 0303 health sciences, Multidisciplinary, MESH: Plant Proteins, food and beverages, alignment, Bread, MESH: Edible Grain, starchy endosperm, reveals, Genome, Plant, Biotechnology, profiles, General Science & Technology, Cereals, MESH: Triticum, Biology, Gene dosage, MESH: Endosperm, Polyploidy, MESH: Bread, 03 medical and health sciences, Polyploid, MESH: Polyploidy, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], MD Multidisciplinary, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Gene family, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, MESH: Gene Expression Regulation, Plant, Gene, Metabolic and endocrine, 030304 developmental biology, Whole genome sequencing, triticum, MESH: Transcriptome, Human Genome, Plant, Gene Expression Regulation, germination, gene expression, RNA, identification, Edible Grain, protein, 010606 plant biology & botany
Abstract

Allohexaploid bread wheat ( Triticum aestivum L.) provides approximately 20% of calories consumed by humans. Lack of genome sequence for the three homeologous and highly similar bread wheat genomes (A, B, and D) has impeded expression analysis of the grain transcriptome. We used previously unknown genome information to analyze the cell type–specific expression of homeologous genes in the developing wheat grain and identified distinct co-expression clusters reflecting the spatiotemporal progression during endosperm development. We observed no global but cell type– and stage-dependent genome dominance, organization of the wheat genome into transcriptionally active chromosomal regions, and asymmetric expression in gene families related to baking quality. Our findings give insight into the transcriptional dynamics and genome interplay among individual grain cell types in a polyploid cereal genome.

Published
2014
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48. Sequencing of diverse mandarin, pummelo and orange genomes reveals complex history of admixture during citrus domestication

Author

William G. Farmerie, Chunxian Chen, Marcos A. Machado, Daniel Ramón, Jarrod Chapman, Patrick Wincker, Dominique Brunel, Jerry Jenkins, Juan V. Munoz-Sanz, Mohammed Mohiuddin, Javier Terol, Victoria Ibanez, Simone Scalabrin, Giuseppe Reforgiato, Amparo Herrero-Ortega, Cristian Del Fabbro, Xavier Perrier, Jeremy Schmutz, Simon E. Prochnik, Jérôme Salse, Kamel Jabbari, Uffe Hellsten, Julie Poulain, Daniel S. Rokhsar, Alexandre Lomsadze, Karin M. Fredrikson, Andrea Zuccolo, Francisco R. Tadeo, Leandro H. Estornell, Luis Navarro, Olivier Jaillon, Brian Desany, Frederick G. Gmitter, François Luro, Federica Cattonaro, G Albert Wu, Paul Burns, Francis Quetier, Marco Aurélio Takita, Mark Borodovsky, Manuel Talon, Tim Harkins, Julián Pérez-Pérez, Jane Grimwood, Pablo Aleza, Florent Murat, Mikeal L. Roose, Patrick Ollitrault, Michele Morgante, Karine Labadie, Arnaud Couloux, Sara Pinosio, Juliana Freitas-Astúa, Manuel Ruiz, Chinnappa D. Kodira, United States Department of Energy, Génétique Diversité et Ecophysiologie des Céréales (GDEC), Institut National de la Recherche Agronomique (INRA)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP), DOE Joint Genome Institute [Walnut Creek], Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Applied Genomics Institute (IGA), Instituto Valenciano de Investigaciones Agrarias - Institut Valencià d'Investigacions Agraries - Valencian Institute for agricultural Research (IVIA), 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), Institut Jacques Monod (IJM (UMR_7592)), Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), Institute of Applied Genomics [Udine] (IGA), Institute of Applied Genomics, Plant Genetics Institute, Consiglio Nazionale delle Ricerche [Roma] (CNR), Ecology and Evolutionary Biology [Tucson] (EEB), University of Arizona, Department of Energy / Joint Genome Institute (DOE), Los Alamos National Laboratory (LANL), Centro de Genómica - Centre de Genòmica [IVIA], Department of Food Biotechnology, Biopolis, Universitat de València (UV), Etude du Polymorphisme des Génomes Végétaux (EPGV), Institut National de la Recherche Agronomique (INRA), Génétique et Ecophysiologie de la qualité des agrumes (GEQA), Broad Institute of MIT and Harvard (BROAD INSTITUTE), Harvard Medical School [Boston] (HMS)-Massachusetts Institute of Technology (MIT)-Massachusetts General Hospital [Boston], Institut de Génomique d'Evry (IG), Institut de Biologie François JACOB (JACOB), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, Dipartimento di Produzione Vegetale e Tecnologie Agrarie, Università degli Studi di Udine - University of Udine [Italie], National Science and Technology Institute of Genomics for Citrus Breeding, Brazil [FAPESP 08/57909-2, CNPq 573848/08-4], Brazilian Agricultural Research Corporation (Embrapa), Embrapa-Monsanto Agreement, Agence Nationale de la Recherche (ANR) [CITRUSSEQ PCS-08-GENO], program ANR Blanc-PAGE [ANR-2011-BSV6-00801], US National Institutes of Health [HG00783], Generalitat Valenciana, Spain [PrometeoII/2013/008], Ministry of Economy and Innovation-Fondo Europeo de Desarrollo Regional (FEDER), Spain [AGL2011-26490], Conselleria de Agricultura, Pesca, Alimentacion y Agua from the Generalitat Valenciana, Ministerio de Economia e Innovacion [PSE-060000-2009-8, IPT-010000-2010-43], Citruseq-Citrusgenn consortium company (Anecoop S. Coop., Eurosemillas S.A.), Citruseq-Citrusgenn consortium company (Fundacion Ruralcaja Valencia), Citruseq-Citrusgenn consortium company (GCM Variedades Vegetales A.I.E.), Citruseq-Citrusgenn consortium company ( Investigacion Citricola Castellon S.A.), Citruseq-Citrusgenn consortium company (Source Citrus Genesis-Special New Fruit Licensing, Ltd.), Florida Citrus Production Research Advisory Council (FCPRAC), Florida Department of Agriculture and Consumer Services [013646], Florida Department of Citrus (FDOC), Citrus Research and Development Foundation [71], Ministero delle Politiche Agricole Alimentari e Forestali, Project Citrustart, Ministero dell'Istruzione, dell'Universita e della Ricerca (MIUR), Programma Operativo Nazionale 'Ricerca e Competitivita', Project IT-Citrus Genomics [PON_01623], Office of Science of the US Department of Energy [DE-AC02-05CH11231], Génétique Diversité et Ecophysiologie des Céréales - Clermont Auvergne (GDEC), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne (UCA), 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), Instituto Valenciano de Investigaciones Agrarias, 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), Centro de Genomica, Valencian Institute of Agrarian Research (IVIA), 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), National Research Council of Italy | Consiglio Nazionale delle Ricerche (CNR), Université Paris-Saclay-Institut de Biologie François JACOB (JACOB), 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), and 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)

Subjects
Germplasm, Phylogénie, Citrus, [SDV]Life Sciences [q-bio], Plant genetics, Orange (colour), Breeding, Applied Microbiology and Biotechnology, F30 - Génétique et amélioration des plantes, Domestication, Citrus clementina, Conserved Sequence, ComputingMilieux_MISCELLANEOUS, Genome, food and beverages, F70 - Taxonomie végétale et phytogéographie, séquençage du génome, Molecular Medicine, Ploidy, Sequence Analysis, Citrus × sinensis, Genome, Plant, Biotechnology, Citrus sinensis, Crops, Agricultural, Séquence nucléotidique, Evolution, Molecular Sequence Data, Biomedical Engineering, Bioengineering, Agrume, Crops, Biology, Article, Evolution, Molecular, Citrus maxima, Species Specificity, Phylogenetics, Botany, Hybrid, Génie génétique, Agricultural, Génome, Base Sequence, Molecular, Genetic Variation, Taxonomie, Sequence Analysis, DNA, DNA, Plant, next-generation sequencing, Citrus reticulata
Abstract

Cultivated citrus are selections from, or hybrids of, wild progenitor species whose identities and contributions to citrus domestication remain controversial. Here we sequence and compare citrus genomes-a high-quality reference haploid clementine genome and mandarin, pummelo, sweet-orange and sour-orange genomes- and show that cultivated types derive from two progenitor species. Although cultivated pummelos represent selections from one progenitor species, Citrus maxima, cultivated mandarins are introgressions of C. maxima into the ancestral mandarin species Citrus reticulata. The most widely cultivated citrus, sweet orange, is the offspring of previously admixed individuals, but sour orange is an F1 hybrid of pure C. maxima and C. reticulata parents, thus implying that wild mandarins were part of the early breeding germplasm. A Chinese wild 'mandarin' diverges substantially from C. reticulata, thus suggesting the possibility of other unrecognized wild citrus species. Understanding citrus phylogeny through genome analysis clarifies taxonomic relationships and facilitates sequence-directed genetic improvement., 栽培されている柑橘類は、野生祖先種から選択されたもの、またはその交雑種であるが、その祖先種の正体、および柑橘類栽培化に対する寄与には依然として議論がある。今回、柑橘類ゲノム（クレメンタインの高精度標準ハプロイドゲノム、ならびにマンダリン、パメロ、スイートオレンジ、およびサワーオレンジのゲノム）の配列解読および比較を行ったところ、栽培種が2つの祖先種に由来することが明らかにされた。栽培パメロは単一祖先種 Citrus maxima から選択されたことがわかったが、栽培マンダリンは祖先マンダリン種 Citrus reticulata に C. maxima から遺伝子移入が行われたものであった。最も広く栽培されている柑橘類であるスイートオレンジは過去に混種した個体の子孫であるが、サワーオレンジは純粋な C. maxima と C. reticulata とのF1雑種であり、このことは、野生のマンダリンが初期の育種生殖系列の要素であったことを意味している。中国の野生「マンダリン」は C. reticulata とは大きく異なっており、別の未確認の野生柑橘種である可能性が示唆される。ゲノム解析で柑橘類の系統発生を理解することにより、分類学的な関係が解明され、配列本位の遺伝的改良が促進される。

Published
2014
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49. Functional genomics of novel secondary metabolites from diverse cyanobacteria using untargeted metabolomics

Author

Ferran Garcia-Pichel, Nikos C. Kyrpides, Nicholas A. Jose, Richard Baran, Trent R. Northen, Muriel Gugger, Natalia Ivanova, Lawrence Berkeley National Laboratory [Berkeley] (LBNL), DOE Joint Genome Institute [Walnut Creek], School of Life Sciences [ASU], Arizona State University [Tempe] (ASU), Collection des Cyanobactéries, Institut Pasteur [Paris], This work was supported by the U.S Department of Energy under Contract No. DE-AC02-05CH11231 and the Institut Pasteur., and Institut Pasteur [Paris] (IP)

Subjects
Metabolite, Pharmaceutical Science, Oligosaccharides, Genomics, Biology, Tandem mass spectrometry, Mass spectrometry, Cyanobacteria, Article, 03 medical and health sciences, chemistry.chemical_compound, Metabolomics, Tandem Mass Spectrometry, Drug Discovery, Metabolome, MS/MS, cyanobacteria, metabolomics, mass spectrometry, betaines, oligosaccharides, Human Metabolome Database, lcsh:QH301-705.5, Pharmacology, Toxicology and Pharmaceutics (miscellaneous), 030304 developmental biology, 0303 health sciences, 030306 microbiology, Betaine, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, lcsh:Biology (General), chemistry, Biochemistry, Functional genomics, Chromatography, Liquid
Abstract

International audience; Mass spectrometry-based metabolomics has become a powerful tool for the detection of metabolites in complex biological systems and for the identification of novel metabolites. We previously identified a number of unexpected metabolites in the cyanobacterium Synechococcus sp. PCC 7002, such as histidine betaine, its derivatives and several unusual oligosaccharides. To test for the presence of these compounds and to assess the diversity of small polar metabolites in other cyanobacteria, we profiled cell extracts of nine strains representing much of the morphological and evolutionary diversification of this phylum. Spectral features in raw metabolite profiles obtained by normal phase liquid chromatography coupled to mass spectrometry (MS) were manually curated so that chemical formulae of metabolites could be assigned. For putative identification, retention times and MS/MS spectra were cross-referenced with those of standards or available sprectral library records. Overall, we detected 264 distinct metabolites. These included indeed different betaines, oligosaccharides as well as additional unidentified metabolites with chemical formulae not present in databases of metabolism. Some of these metabolites were detected only in a single strain, but some were present in more than one. Genomic OPEN ACCESS Mar. Drugs 2013, 11 3618 interrogation of the strains revealed that generally, presence of a given metabolite corresponded well with the presence of its biosynthetic genes, if known. Our results show the potential of combining metabolite profiling and genomics for the identification of novel biosynthetic genes.

Published
2013
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50. Genome Sequence of the Obligate Gammaproteobacterial Methanotroph Methylomicrobium album Strain BG8

Author

Mike S. M. Jetten, Ahmet Zeytun, J. Colin Murrell, Lynne Goodwin, K. Dimitri Kits, Alex Copeland, Loren Hauser, Samuel Pitluck, Françoise Bringel, Susan Lucas, Huub J. M. Op den Camp, Alla Lapidus, David Bruce, Marina G. Kalyuzhnaya, Aurélie Lajus, Claudine Médigue, Martin G. Klotz, Jan Fang Cheng, Miriam Land, Lisa Y. Stein, Stéphane Vuilleumier, Alan A. DiSpirito, Tanja Woyke, University of Alberta, University of Washington [Seattle], University of North Carolina [Charlotte] (UNC), University of North Carolina System (UNC), Department of Aquatic Ecology & Environmental Biology, Radboud University [Nijmegen], Génétique moléculaire, génomique, microbiologie (GMGM), Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS), Iowa State University (ISU), School of Environmental Sciences [Norwich], University of East Anglia [Norwich] (UEA), Los Alamos National Laboratory (LANL), DOE Joint Genome Institute [Walnut Creek], Department of Energy / Joint Genome Institute (DOE), Oak Ridge National Laboratory [Oak Ridge] (ORNL), UT-Battelle, LLC, 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)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Groupe d'Etudes des Matériaux Hétérogènes (GEMH), Université de Limoges (UNILIM)-Institut des Procédés Appliqués aux Matériaux (IPAM), Université de Limoges (UNILIM)-Université de Limoges (UNILIM), Department of Molecular and Cell Biology, University of Connecticut (UCONN), Radboud university [Nijmegen], and 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)

Subjects
Whole genome sequencing, 0303 health sciences, Obligate, Methanotroph, 030306 microbiology, Strain (biology), Biology, 03 medical and health sciences, Fixation (population genetics), Ecological Microbiology, Botany, Genetics, Methylomicrobium album, Prokaryotes, GeneralLiterature_REFERENCE(e.g.,dictionaries,encyclopedias,glossaries), Molecular Biology, Gene, [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis, 030304 developmental biology
Abstract

The complete genome sequence of Methylomicrobium album strain BG8, a methane-oxidizing gammaproteobacterium isolated from freshwater, is reported. Aside from a conserved inventory of genes for growth on single-carbon compounds, M. album BG8 carries a range of gene inventories for additional carbon and nitrogen transformations but no genes for growth on multicarbon substrates or for N fixation.

Published
2013
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