LangUllrichMuratEtAl2018

Référence

Lang, D., Ullrich, K.K., Murat, F., Fuchs, J., Jenkins, J., Haas, F.B., Piednoel, M., Gundlach, H., Van Bel, M., Meyberg, R., Vives, C., Morata, J., Symeonidi, A., Hiss, M., Muchero, W., Kamisugi, Y., Saleh, O., Blanc, G., Decker, E.L., Gessel, N., Grimwood, J., Hayes, R.D., Graham, S.W., Gunter, L.E., McDaniel, S.F., Hoernstein, S.N.W., Larsson, A., Li, F.-W., Perroud, P.-F., Phillips, J., Ranjan, P., Rokshar, D.S., Rothfels, C.J., Schneider, L., Shu, S., Stevenson, D.W., Thümmler, F., Tillich, M., Villarreal, J.C., Widiez, T., Wong, G.K.-S., Wymore, A., Zhang, Y., Zimmer, A.D., Quatrano, R.S., Mayer, K.F.X., Goodstein, D., Casacuberta, J.M., Vandepoele, K., Reski, R., Cuming, A.C., Tuskan, G.A., Maumus, F., Salse, J., Schmutz, J. and Rensing, S.A. (2018) The Physcomitrella patens chromosome-scale assembly reveals moss genome structure and evolution. The Plant Journal, 93(3):515-533. (URL )

Résumé

Summary 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.

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@ARTICLE { LangUllrichMuratEtAl2018,
    AUTHOR = { Lang, D. and Ullrich, K.K. and Murat, F. and Fuchs, J. and Jenkins, J. and Haas, F.B. and Piednoel, M. and Gundlach, H. and Van Bel, M. and Meyberg, R. and Vives, C. and Morata, J. and Symeonidi, A. and Hiss, M. and Muchero, W. and Kamisugi, Y. and Saleh, O. and Blanc, G. and Decker, E.L. and Gessel, N. and Grimwood, J. and Hayes, R.D. and Graham, S.W. and Gunter, L.E. and McDaniel, S.F. and Hoernstein, S.N.W. and Larsson, A. and Li, F.-W. and Perroud, P.-F. and Phillips, J. and Ranjan, P. and Rokshar, D.S. and Rothfels, C.J. and Schneider, L. and Shu, S. and Stevenson, D.W. and Thümmler, F. and Tillich, M. and Villarreal, J.C. and Widiez, T. and Wong, G.K.-S. and Wymore, A. and Zhang, Y. and Zimmer, A.D. and Quatrano, R.S. and Mayer, K.F.X. and Goodstein, D. and Casacuberta, J.M. and Vandepoele, K. and Reski, R. and Cuming, A.C. and Tuskan, G.A. and Maumus, F. and Salse, J. and Schmutz, J. and Rensing, S.A. },
    TITLE = { The Physcomitrella patens chromosome-scale assembly reveals moss genome structure and evolution },
    JOURNAL = { The Plant Journal },
    YEAR = { 2018 },
    VOLUME = { 93 },
    NUMBER = { 3 },
    PAGES = { 515-533 },
    ABSTRACT = { Summary 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. },
    DOI = { 10.1111/tpj.13801 },
    EPRINT = { https://onlinelibrary.wiley.com/doi/pdf/10.1111/tpj.13801 },
    KEYWORDS = { evolution, genome, chromosome, plant, moss, methylation, duplication, synteny, Physcomitrella patens },
    URL = { https://onlinelibrary.wiley.com/doi/abs/10.1111/tpj.13801 },
}

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