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