@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}},
  keywords     = {{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}},
  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}},
}

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