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

Lang, D., Ullrich, K. K., Murat, F., Fuchs, J., Jenkins, J., Haas, F. B., et al. (2018). The Physcomitrella patens chromosome-scale assembly reveals moss genome structure and evolution. The Plant Journal, 93(3), 515-533. doi:10.1111/tpj.13801.

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Lang, Daniel, Author
Ullrich, Kristian K.1, Author              
Murat, Florent, Author
Fuchs, Jörg, Author
Jenkins, Jerry, Author
Haas, Fabian B., Author
Piednoel, Mathieu, Author
Gundlach, Heidrun, Author
Bel, Michiel Van, 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, AuthorHayes, Richard D., AuthorGraham, Sean W., AuthorGunter, Lee E., AuthorMcDaniel, Stuart F., AuthorHoernstein, Sebastian N.W., AuthorLarsson, Anders, AuthorLi, Fay-Wei, AuthorPerroud, Pierre-François, AuthorPhillips, Jeremy, AuthorRanjan, Priya, AuthorRokshar, Daniel S., AuthorRothfels, Carl J., AuthorSchneider, Lucas, AuthorShu, Shengqiang, AuthorStevenson, Dennis W., AuthorThümmler, Fritz, AuthorTillich, Michael, AuthorAguilar, Juan C. Villarreal, AuthorWidiez, Thomas, AuthorWong, Gane Ka-Shu, AuthorWymore, Ann, AuthorZhang, Yong, AuthorZimmer, Andreas D., AuthorQuatrano, Ralph S., AuthorMayer, Klaus F.X., AuthorGoodstein, David, AuthorCasacuberta, Josep M., AuthorVandepoele, Klaas, AuthorReski, Ralf, AuthorCuming, Andrew C., AuthorTuskan, Gerald A., AuthorMaumus, Florian, AuthorSalse, Jérome, AuthorSchmutz, Jeremy, AuthorRensing, Stefan A., Author more..
Affiliations:
1Department Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, Max Planck Society, ou_1445635              

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Free keywords: Alkylation; Chromosomes; Gene encoding; Gene expression; Methylation; Seed; Viruses, duplication; evolution; moss; Physcomitrella patens; plant; Synteny, Genes
 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. © 2017 The Authors The Plant Journal © 2017 John Wiley Sons Ltd

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Language(s): eng - English
 Dates: 2017-11-202017-10-112017-11-242018-01-192018
 Publication Status: Published in print
 Pages: -
 Publishing info: -
 Table of Contents: -
 Rev. Type: -
 Identifiers: DOI: 10.1111/tpj.13801
 Degree: -

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Project name : Office of Science of the US Department of Energy
Grant ID : DEAC02-05CH11231
Funding program : -
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Title: The Plant Journal
  Other : Plant J.
Source Genre: Journal
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Publ. Info: Oxford : Blackwell Science
Pages: - Volume / Issue: 93 (3) Sequence Number: - Start / End Page: 515 - 533 Identifier: ISSN: 0960-7412
CoNE: https://pure.mpg.de/cone/journals/resource/954925579095_1