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. 2018 Feb;93(3):515-533.
doi: 10.1111/tpj.13801.

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

Daniel Lang  1   2 , Kristian K Ullrich  3 , Florent Murat  4 , Jörg Fuchs  5 , Jerry Jenkins  6 , Fabian B Haas  3 , Mathieu Piednoel  7 , Heidrun Gundlach  2 , Michiel Van Bel  8   9 , Rabea Meyberg  3 , Cristina Vives  10 , Jordi Morata  10 , Aikaterini Symeonidi  3 , Manuel Hiss  3 , Wellington Muchero  11 , Yasuko Kamisugi  12 , Omar Saleh  1 , Guillaume Blanc  13 , Eva L Decker  1 , Nico van Gessel  1 , Jane Grimwood  6   14 , Richard D Hayes  14 , Sean W Graham  15 , Lee E Gunter  11 , Stuart F McDaniel  16 , Sebastian N W Hoernstein  1 , Anders Larsson  17 , Fay-Wei Li  18 , Pierre-François Perroud  3 , Jeremy Phillips  14 , Priya Ranjan  11 , Daniel S Rokshar  14   19 , Carl J Rothfels  20 , Lucas Schneider  3 , Shengqiang Shu  14 , Dennis W Stevenson  21 , Fritz Thümmler  22 , Michael Tillich  23 , Juan C Villarreal Aguilar  24 , Thomas Widiez  25   26 , Gane Ka-Shu Wong  27   28   29 , Ann Wymore  11 , Yong Zhang  30 , Andreas D Zimmer  1 , Ralph S Quatrano  31 , Klaus F X Mayer  2   32 , David Goodstein  14 , Josep M Casacuberta  10 , Klaas Vandepoele  8   9 , Ralf Reski  1   33 , Andrew C Cuming  12 , Gerald A Tuskan  11 , Florian Maumus  34 , Jérome Salse  4 , Jeremy Schmutz  6   14 , Stefan A Rensing  3   33
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Free article

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

Daniel Lang et al. Plant J. 2018 Feb.
Free article

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.

Keywords: Physcomitrella patens; chromosome; duplication; evolution; genome; methylation; moss; plant; synteny.

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