The Physcomitrella patens chromosome-scale assembly reveals moss genome structure and evolution
Lang, Daniel (Helmholtz Center Munich. Plant Genome and Systems Biology)
Ullrich, Kristian K. (University of Marburg. Faculty of Biology)
Murat, Florent (Institut national de la recherche agronomique. UMR 1095 Genetics. Diversity and Ecophysiology of Cereals)
Fuchs, Jorg (Leibniz Institute of Plant Genetics and Crop Plant Research)
Jenkins, Jerry (HudsonAlpha Institute for Biotechnology)
Haas, Fabian B. (University of Marburg. Faculty of Biology)
Piednoel, M. (Max Planck Institute for Plant Breeding Research)
Gundlach, H. (Helmholtz Center Munich. Plant Genome and Systems Biology)
Van Bel, M. (VIB-UGent Center for Plant Systems Biology)
Meyberg, R. (University of Marburg. Faculty of Biology)
Vives, Cristina (Centre de Recerca en Agrigenòmica)
Morata, Jordi (Centre de Recerca en Agrigenòmica)
Symeonidi, Aikaterini (University of Marburg. Faculty of Biology)
Hiss, Manuel (University of Marburg. Faculty of Biology)
Muchero, Wellington (Oak Ridge National Laboratory. Biosciences Division)
Kamisugi, Yasuko (University of Leeds. Centre for Plant Sciences)
Saleh, Omar (University of Freiburg. Faculty of Biology)
Blanc, Guillaume (Aix-Marseille Université. Structural and Genomic Information Laboratory)
Decker, Eva L. (University of Freiburg. Faculty of Biology)
van Gessel, Nico (University of Freiburg. Faculty of Biology)
Grimwood, Jane (HudsonAlpha Institute for Biotechnology)
Hayes, Richard D. (DOE Joint Genome Institute)
Graham, Sean W. (University of British Columbia. Department of Botany)
Gunter, Lee E. (Oak Ridge National Laboratory. Biosciences Division)
McDaniel, Stuart F. (University of Florida. Department of Biology)
Hoernstein, Sebastian N. W. (University of Freiburg. Faculty of Biology)
Larsson, Anders (Uppsala University. Evolutionary Biology Centre)
Li, Fay-Wei (Boyce Thompson Institute)
Perroud, Pierre-François (University of Marburg. Faculty of Biology)
Phillips, Jeremy (DOE Joint Genome Institute)
Ranjan, Priya (Oak Ridge National Laboratory)
Rokshar, Daniel S. (DOE Joint Genome Institute)
Rothfels, Carl J. (University of California. Department of Integrative Biology)
Schneider, Lucas (University of Marburg. Faculty of Biology)
Shu, Shengqiang (DOE Joint Genome Institute)
Stevenson, Dennis W. (New York Botanical Garden)
Thümmler, Fritz (Vertis Biotechnologie AG)
Tillich, Michael (Max Planck Institute of Molecular Plant Physiology)
Villarreal Aguilar, Juan C. (Université Laval. Department of Biology)
Widiez, Thomas (University of Geneva. Department of Plant Biology)
Wong, Gane Ka-Shu (University of Alberta. Department of Biological Sciences)
Wymore, Ann (Oak Ridge National Laboratory)
Zhang, Yong (Shenzhen Huahan Gene Life Technology Co. Ltd)
Zimmer, Aandreas D. (University of Freiburg. Faculty of Biology)
Quatrano, Ralph S. (Washington University. Department of Biology)
Mayer, Klaus F. X. (Technical University Munich)
Goodstein, David (DOE Joint Genome Institute)
Casacuberta i Suñer, Josep M. 1962- (Centre de Recerca en Agrigenòmica)
Vandepoele, Klaas (Ghent University. Department of Plant Biotechnology and Bioinformatics)
Reski, Ralph (University of Freiburg. Faculty of Biology)
Cuming, Andrew C. (University of Leeds. Faculty of Biological Sciences)
Tuskan, Gerald A. (Oak Ridge National Laboratory. Biosciences Division)
Maumus, Florian (Institut National de la Recherche Agronomique (França))
Salse, Jerome (Institut national de la recherche agronomique. UMR 1095 Genetics. Diversity and Ecophysiology of Cereals)
Schmutz, Jeremy (DOE Joint Genome Institute)
Rensing, Stefan A. (University of Freiburg. BIOSS Centre for Biological Signalling Studies)

Date:	2018
Abstract:	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.
Grants:	Ministerio de Economía y Competitividad AGL2013-43244-R European Commission 267146
Rights:	Tots els drets reservats.
Language:	Anglès
Document:	Article ; recerca ; Versió acceptada per publicar
Subject:	Evolution ; Genome ; Chromosome ; Plant ; Moss ; Methylation ; Duplication ; Synteny ; Physcomitrellapatens
Published in:	The Plant journal, Vol. 93, issue 3 (Feb. 2018) , p. 515-533, ISSN 1365-313X

DOI: 10.1111/tpj.13801
PMID: 29237241

Post-print 60 p, 1.6 MB

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