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

Article Article scientifique Article The Physcomitrella patens chromosome-scale assembly reveals moss genome structure and evolution eng 2018 author Lang Daniel author Ullrich Kristian K author Murat Florent author Fuchs Jörg author Jenkins Jerry author Haas Fabian B author Piednoel Mathieu author Gundlach Heidrun author Van Bel Michiel author Meyberg Rabea author Vives Cristina author Morata Jordi author Symeonidi Aikaterini author Hiss Manuel author Muchero Wellington author Kamisugi Yasuko author Saleh Omar author Blanc Guillaume author Decker Eva L author van Gessel Nico author Grimwood Jane author Hayes Richard D author Graham Sean W author Gunter Lee E author McDaniel Stuart F author Hoernstein Sebastian N W author Larsson Anders author Li Fay-Wei author Perroud Pierre-François author Phillips Jeremy author Ranjan Priya author Rokshar Daniel S author Rothfels Carl J author Schneider Lucas author Shu Shengqiang author Stevenson Dennis W author Thümmler Fritz author Tillich Michael author Villarreal Aguilar Juan C author Widiez Thomas 772994 author Wong Gane Ka-Shu author Wymore Ann author Zhang Yong author Zimmer Andreas D author Quatrano Ralph S author Mayer Klaus F X author Goodstein David author Casacuberta Josep M author Vandepoele Klaas author Reski Ralf author Cuming Andrew C author Tuskan Gerald A author Maumus Florian author Salse Jérome author Schmutz Jeremy author Rensing Stefan A 515-533 10.1111/tpj.13801 29237241 1365-313X 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. Dewey 580 45 Département des sciences végétales 163 false The Plant Journal 93 3 821c8989-af23-4cc1-a07d-ff9241b44055 Article (Published version) Restricted Lang_PlantJ_2018.pdf 2632857 application/pdf restrictedAccess Faculté des sciences / Section de biologie / Département des sciences végétales

Title	Published in	Year	Views	Downloads

The Physcomitrella patens chromosome-scale assembly reveals moss genome structure and evolution	The Plant Journal	2018	475	0
The chromatin landscape of the moss Physcomitrella patens and its dynamics during development and drought stress	Plant journal	2014	86	56

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