NystedtStreetWetterbomEtAl2013

Référence

Nystedt, B., Street, N. R., Wetterbom, A., Zuccolo, A., Lin, Y. C., Scofield, D. G., Vezzi, F., Delhomme, N., Giacomello, S., Alexeyenko, A., Vicedomini, R., Sahlin, K., Sherwood, E., Elfstrand, M., Gramzow, L., Holmberg, K., Hallman, J., Keech, O., Klasson, L., Koriabine, M., Kucukoglu, M., Kaller, M., Luthman, J., Lysholm, F., Niittyla, T., Olson, A., Rilakovic, N., Ritland, C., Rossello, J. A., Sena, J., Svensson, T., Talavera-Lopez, C., Theiszen, G., Tuominen, H., Vanneste, K., Wu, Z. Q., Zhang, B., Zerbe, P., Arvestad, L., Bhalerao, R., Bohlmann, J., Bousquet, J., Garcia G. R., Hvidsten, T. R., de Jong, P., MacKay, J., Morgante, M., Ritland, K., Sundberg, B., Lee Thomson, S., Van de Peer, Y., Andersson, B., Nilsson, O., Ingvarsson, P. K., Lundeberg, J. and Jansson, S. (2013) The Norway spruce genome sequence and conifer genome evolution. Nature, 497:579-584. (URL )

Résumé

Conifers have dominated forests for more than 200 million years and are of huge ecological and economic importance. Here we present the draft assembly of the 20-gigabase genome of Norway spruce (Picea abies), the first available for any gymnosperm. The number of well-supported genes (28,354) is similar to the >100 times smaller genome of Arabidopsis thaliana, and there is no evidence of a recent whole-genome duplication in the gymnosperm lineage. Instead, the large genome size seems to result from the slow and steady accumulation of a diverse set of long-terminal repeat transposable elements, possibly owing to the lack of an efficient elimination mechanism. Comparative sequencing of Pinus sylvestris, Abies sibirica, Juniperus communis, Taxus baccata and Gnetum gnemon reveals that the transposable element diversity is shared among extant conifers. Expression of 24-nucleotide small RNAs, previously implicated in transposable element silencing, is tissue-specific and much lower than in other plants. We further identify numerous long (>10,000 base pairs) introns, gene-like fragments, uncharacterized long non-coding RNAs and short RNAs. This opens up new genomic avenues for conifer forestry and breeding.

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@ARTICLE { NystedtStreetWetterbomEtAl2013,
    AUTHOR = { Nystedt, B. and Street, N. R. and Wetterbom, A. and Zuccolo, A. and Lin, Y. C. and Scofield, D. G. and Vezzi, F. and Delhomme, N. and Giacomello, S. and Alexeyenko, A. and Vicedomini, R. and Sahlin, K. and Sherwood, E. and Elfstrand, M. and Gramzow, L. and Holmberg, K. and Hallman, J. and Keech, O. and Klasson, L. and Koriabine, M. and Kucukoglu, M. and Kaller, M. and Luthman, J. and Lysholm, F. and Niittyla, T. and Olson, A. and Rilakovic, N. and Ritland, C. and Rossello, J. A. and Sena, J. and Svensson, T. and Talavera-Lopez, C. and Theiszen, G. and Tuominen, H. and Vanneste, K. and Wu, Z. Q. and Zhang, B. and Zerbe, P. and Arvestad, L. and Bhalerao, R. and Bohlmann, J. and Bousquet, J. and Garcia G. R. and Hvidsten, T. R. and de Jong, P. and MacKay, J. and Morgante, M. and Ritland, K. and Sundberg, B. and Lee Thomson, S. and Van de Peer, Y. and Andersson, B. and Nilsson, O. and Ingvarsson, P. K. and Lundeberg, J. and Jansson, S. },
    TITLE = { The Norway spruce genome sequence and conifer genome evolution },
    JOURNAL = { Nature },
    YEAR = { 2013 },
    VOLUME = { 497 },
    PAGES = { 579-584 },
    MONTH = { may },
    ABSTRACT = { Conifers have dominated forests for more than 200 million years and are of huge ecological and economic importance. Here we present the draft assembly of the 20-gigabase genome of Norway spruce (Picea abies), the first available for any gymnosperm. The number of well-supported genes (28,354) is similar to the >100 times smaller genome of Arabidopsis thaliana, and there is no evidence of a recent whole-genome duplication in the gymnosperm lineage. Instead, the large genome size seems to result from the slow and steady accumulation of a diverse set of long-terminal repeat transposable elements, possibly owing to the lack of an efficient elimination mechanism. Comparative sequencing of Pinus sylvestris, Abies sibirica, Juniperus communis, Taxus baccata and Gnetum gnemon reveals that the transposable element diversity is shared among extant conifers. Expression of 24-nucleotide small RNAs, previously implicated in transposable element silencing, is tissue-specific and much lower than in other plants. We further identify numerous long (>10,000 base pairs) introns, gene-like fragments, uncharacterized long non-coding RNAs and short RNAs. This opens up new genomic avenues for conifer forestry and breeding. },
    ISSN = { 1476-4687 },
    OWNER = { nafon9 },
    PUBLISHER = { Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved. },
    TIMESTAMP = { 2013.05.22 },
    URL = { http://dx.doi.org/10.1038/nature12211 },
}

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