The Norway Spruce Genome Sequence and Conifer Genome Evolution

The Norway Spruce Genome Sequence and Conifer Genome Evolution. Nystedt, B., Street, N. R., Wetterbom, A., Zuccolo, A., Lin, Y., 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., Zhang, B., Zerbe, P., Arvestad, L., Bhalerao, R., Bohlmann, J., Bousquet, J., Garcia Gil, R., Hvidsten, T. R., de Jong, P., MacKay, J., Morgante, M., Ritland, K., Sundberg, B., Lee Thompson, S., Van de Peer, Y., Andersson, B., Nilsson, O., Ingvarsson, P. K., Lundeberg, J., & Jansson, S. 497(7451):579–584.

Paper doi abstract bibtex

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.

@article{nystedtNorwaySpruceGenome2013,
  title = {The {{Norway}} Spruce Genome Sequence and Conifer Genome Evolution},
  author = {Nystedt, Bjorn and Street, Nathaniel R. and Wetterbom, Anna and Zuccolo, Andrea and Lin, Yao-Cheng and Scofield, Douglas G. and Vezzi, Francesco and Delhomme, Nicolas and Giacomello, Stefania and Alexeyenko, Andrey and Vicedomini, Riccardo and Sahlin, Kristoffer and Sherwood, Ellen and Elfstrand, Malin and Gramzow, Lydia and Holmberg, Kristina and Hallman, Jimmie and Keech, Olivier and Klasson, Lisa and Koriabine, Maxim and Kucukoglu, Melis and Kaller, Max and Luthman, Johannes and Lysholm, Fredrik and Niittyla, Totte and Olson, Ake and Rilakovic, Nemanja and Ritland, Carol and Rossello, Josep A. and Sena, Juliana and Svensson, Thomas and Talavera-Lopez, Carlos and Theiszen, Gunter and Tuominen, Hannele and Vanneste, Kevin and Wu, Zhi-Qiang and Zhang, Bo and Zerbe, Philipp and Arvestad, Lars and Bhalerao, Rishikesh and Bohlmann, Joerg and Bousquet, Jean and Garcia Gil, Rosario and Hvidsten, Torgeir R. and de Jong, Pieter and MacKay, John and Morgante, Michele and Ritland, Kermit and Sundberg, Bjorn and Lee Thompson, Stacey and Van de Peer, Yves and Andersson, Bjorn and Nilsson, Ove and Ingvarsson, Par K. and Lundeberg, Joakim and Jansson, Stefan},
  date = {2013-05},
  journaltitle = {Nature},
  volume = {497},
  pages = {579--584},
  issn = {0028-0836},
  doi = {10.1038/nature12211},
  url = {https://doi.org/10.1038/nature12211},
  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.},
  keywords = {*imported-from-citeulike-INRMM,~INRMM-MiD:c-12358914,forest-resources,picea-abies},
  number = {7451},
  options = {useprefix=true}
}

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