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

Daniel Lang, Kristian K. Ullrich, Florent Murat, Joerg Fuchs, Jerry Jenkins, Fabian B. Haas, Mathieu Piednoel, Heidrun Gundlach, Michiel Van Bel UGent, Rabea Meyberg, et al. (2018) PLANT JOURNAL. 93(3). p.515-533
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.
Please use this url to cite or link to this publication:
author
organization
year
type
journalArticle (original)
publication status
published
subject
keyword
ARABIDOPSIS-THALIANA, TRANSPOSABLE ELEMENTS, SEXUAL REPRODUCTION, RECOMBINATION RATE, DNA METHYLATION, SPECIES COMPLEX, LAND PLANTS, RNA-SEQ, GENE, SEQUENCE, evolution, genome, chromosome, plant, moss, methylation, duplication, synteny, Physcomitrella patens
journal title
PLANT JOURNAL
Plant J.
volume
93
issue
3
pages
19 pages
publisher
Wiley
place of publication
Hoboken
Web of Science type
Article
Web of Science id
000426265400009
ISSN
0960-7412
1365-313X
DOI
10.1111/tpj.13801
project
Bioinformatics: from nucleotids to networks (N2N)
language
English
UGent publication?
yes
classification
U
id
8558114
handle
http://hdl.handle.net/1854/LU-8558114
date created
2018-04-03 12:23:33
date last changed
2018-04-03 12:23:33
@article{8558114,
  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.},
  author       = {Lang, Daniel and Ullrich, Kristian K. and Murat, Florent and Fuchs, Joerg and Jenkins, Jerry and Haas, Fabian B. and Piednoel, Mathieu and Gundlach, Heidrun and Van Bel, Michiel and Meyberg, Rabea and Vives, Cristina and Morata, Jordi and Symeonidi, Aikaterini and Hiss, Manuel and Muchero, Wellington and Kamisugi, Yasuko and Saleh, Omar and Blanc, Guillaume and Decker, Eva L. and van Gessel, Nico and Grimwood, Jane and Hayes, Richard D. and Graham, Sean W. and Gunter, Lee E. and McDaniel, Stuart F. and Hoernstein, Sebastian N. W. and Larsson, Anders and Li, Fay-Wei and Perroud, Pierre-Francois and Phillips, Jeremy and Ranjan, Priya and Rokshar, Daniel S. and Rothfels, Carl J. and Schneider, Lucas and Shu, Shengqiang and Stevenson, Dennis W. and Thummler, Fritz and Tillich, Michael and Aguilar, Juan C. Villarreal and Widiez, Thomas and Wong, Gane Ka-Shu and Wymore, Ann and Zhang, Yong and Zimmer, Andreas D. and Quatrano, Ralph S. and Mayer, Klaus F. X. and Goodstein, David and Casacuberta, Josep M. and Vandepoele, Klaas and Reski, Ralf and Cuming, Andrew C. and Tuskan, Gerald A. and Maumus, Florian and Salse, Jerome and Schmutz, Jeremy and Rensing, Stefan A.},
  issn         = {0960-7412},
  journal      = {PLANT JOURNAL},
  keyword      = {ARABIDOPSIS-THALIANA,TRANSPOSABLE ELEMENTS,SEXUAL REPRODUCTION,RECOMBINATION RATE,DNA METHYLATION,SPECIES COMPLEX,LAND PLANTS,RNA-SEQ,GENE,SEQUENCE,evolution,genome,chromosome,plant,moss,methylation,duplication,synteny,Physcomitrella patens},
  language     = {eng},
  number       = {3},
  pages        = {515--533},
  publisher    = {Wiley},
  title        = {The Physcomitrella patens chromosome-scale assembly reveals moss genome structure and evolution},
  url          = {http://dx.doi.org/10.1111/tpj.13801},
  volume       = {93},
  year         = {2018},
}

Chicago
Lang, Daniel, Kristian K. Ullrich, Florent Murat, Joerg Fuchs, Jerry Jenkins, Fabian B. Haas, Mathieu Piednoel, et al. 2018. “The Physcomitrella Patens Chromosome-scale Assembly Reveals Moss Genome Structure and Evolution.” Plant Journal 93 (3): 515–533.
APA
Lang, D., Ullrich, K. K., Murat, F., Fuchs, J., Jenkins, J., Haas, F. B., Piednoel, M., et al. (2018). The Physcomitrella patens chromosome-scale assembly reveals moss genome structure and evolution. PLANT JOURNAL, 93(3), 515–533.
Vancouver
1.
Lang D, Ullrich KK, Murat F, Fuchs J, Jenkins J, Haas FB, et al. The Physcomitrella patens chromosome-scale assembly reveals moss genome structure and evolution. PLANT JOURNAL. Hoboken: Wiley; 2018;93(3):515–33.
MLA
Lang, Daniel, Kristian K. Ullrich, Florent Murat, et al. “The Physcomitrella Patens Chromosome-scale Assembly Reveals Moss Genome Structure and Evolution.” PLANT JOURNAL 93.3 (2018): 515–533. Print.