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

Daniel Lang (1) , Kristian Ullrich , Florent Murat (2) , Jörg Fuchs , Jerry Jenkins (3) , Fabian Haas , Carl Li , Guillaume Blanc (4) , Heidrun H. Gundlach (5) , Michiel van Bel , Rabea Meyberg , Cristina Vives (6) , Jordi Morata , Aikaterini Symeonidi (7) , Manuel Hiss , Wellington Muchero , Lee Kamisugi , Omar A. Saleh (8) , Eva Decker , Nico van Gessel , Jane Grimwood (9) , Richard Hayes (10) , Sean Graham , Lee Gunter , Daniel Mcdaniel , Sebastian N.W. Hoernstein , Anders Larsson (11) , Fay-Wei Li , Pierre-François Perroud , Jeremy Phillips , Priya Ranjan (12) , Daniel Rokshar , Carl Rothfels , Lucas Schneider , Shengqiang Shu , Dennis Stevenson , Fritz Thümmler , Michael Tillich , Juan Villarreal Aguilar , Thomas Widiez (13) , Gane Ka-Shu Wong (14) , Ann Wymore , Yong Zhang (15) , Andreas Zimmer (16) , Ralph Quatrano , Klaus F.X. Mayer , David Goodstein (9) , Josep Casacuberta , Klaas Vandepoele (17) , Ralf Reski (18) , Andrew Cuming , Gerald Tuskan (12) , Florian Maumus (19) , Jérôme Salse (2) , Jeremy Schmutz (3) , Stefan Rensing

1 Fakultät für Biologie = Faculty of Biology [Freiburg]
2 GDEC - Génétique Diversité et Ecophysiologie des Céréales
3 United States Department of Energy
4 MIO - Institut méditerranéen d'océanologie
5 Inst Bioinformat & Syst Biol, Munich Informat Ctr Prot Sequences
6 Center for Research in Agricultural Genomics
7 Freiburg Initiative in Systems Biology
8 LPS - Laboratoire de Physique Statistique de l'ENS
9 DOE - Department of Energy / Joint Genome Institute
10 LSHTM - London School of Hygiene and Tropical Medicine
11 LUT - Luleå University of Technology
12 BioSciences Division [Oak Ridge]
13 RDP - Reproduction et développement des plantes
14 Department of Biological Sciences [Edmonton]
15 WPI - Wolfgang Pauli Institute
16 Department of Molecular Psychiatry
17 PSB Center - Center for Plant Systems Biology
18 Plant Biotechnology, Faculty of Biology
19 URGI - Unité de Recherche Génomique Info

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.

Keywords: genome; chromosome; moss; methylation; Physcomitrella patens

Keywords: evolution; plant; duplication; synteny

Domains: Life Sciences [q-bio]; Vegetal Biology

Daniel Lang, Kristian Ullrich, Florent Murat, Jörg Fuchs, Jerry Jenkins, et al.. The Physcomitrella patens chromosome-scale assembly reveals moss genome structure and evolution. Plant Journal, 2018, 93 (3), pp.515 - 533. ⟨10.1111/tpj.13801⟩. ⟨hal-01760352⟩