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The Norway spruce genome sequence and conifer genome evolution

(2013) NATURE. 497(7451). p.579-584
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Bioinformatics: from nucleotids to networks (N2N)
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
GENE FAMILY, SEED PLANTS, ORYZA-SATIVA, SIZE VARIATION, LONG NONCODING RNAS, TRANSPOSABLE ELEMENTS, RECOMBINATION, LINEAGE, PINUS, RICE

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Citation

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MLA
Nystedt, Björn et al. “The Norway Spruce Genome Sequence and Conifer Genome Evolution.” NATURE 497.7451 (2013): 579–584. Print.
APA
Nystedt, B., Street, N. R., Wetterbom, A., Zuccolo, A., Lin, Y.-C., Scofield, D. G., Vezzi, F., et al. (2013). The Norway spruce genome sequence and conifer genome evolution. NATURE, 497(7451), 579–584.
Chicago author-date
Nystedt, Björn, Nathaniel R Street, Anna Wetterbom, Andrea Zuccolo, Yao-Cheng Lin, Douglas G Scofield, Francesco Vezzi, et al. 2013. “The Norway Spruce Genome Sequence and Conifer Genome Evolution.” Nature 497 (7451): 579–584.
Chicago author-date (all authors)
Nystedt, Björn, Nathaniel R Street, Anna Wetterbom, Andrea Zuccolo, Yao-Cheng Lin, Douglas G Scofield, Francesco Vezzi, Nicolas Delhomme, Stefania Giacomello, Andrey Alexeyenko, Riccardo Vicedomini, Kristoffer Sahlin, Ellen Sherwood, Malin Elfstrand, Lydia Gramzow, Kristina Holmberg, Jimmie Hällman, Olivier Keech, Lisa Klasson, Maxim Koriabine, Melis Kucukoglu, Max Käller, Johannes Luthman, Fredrik Lysholm, Totte Niittylä, Åke Olson, Nemanja Rilakovic, Carol Ritland, Josep A Rosselló, Juliana Sena, Thomas Svensson, Carlos Talavera-López, Günter Theißen, Hannele Tuominen, Kevin Vanneste, Zhi-Qiang Wu, Bo Zhang, Philipp Zerbe, Lars Arvestad, Rishikesh Bhalerao, Joerg Bohlmann, Jean Bousquet, Rosario Garcia Gil, Torgeir R Hvidsten, Pieter de Jong, John MacKay, Michele Morgante, Kermit Ritland, Björn Sundberg, Stacey Lee Thompson, Yves Van de Peer, Björn Andersson, Ove Nilsson, Pär K Ingvarsson, Joakim Lundeberg, and Stefan Jansson. 2013. “The Norway Spruce Genome Sequence and Conifer Genome Evolution.” Nature 497 (7451): 579–584.
Vancouver
1.
Nystedt B, Street NR, Wetterbom A, Zuccolo A, Lin Y-C, Scofield DG, et al. The Norway spruce genome sequence and conifer genome evolution. NATURE. 2013;497(7451):579–84.
IEEE
[1]
B. Nystedt et al., “The Norway spruce genome sequence and conifer genome evolution,” NATURE, vol. 497, no. 7451, pp. 579–584, 2013.
@article{4110028,
  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.},
  author       = {Nystedt, Björn 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 Hällman, Jimmie and Keech, Olivier and Klasson, Lisa and Koriabine, Maxim and Kucukoglu, Melis and Käller, Max and Luthman, Johannes and Lysholm, Fredrik and Niittylä, Totte and Olson, Åke and Rilakovic, Nemanja and Ritland, Carol and Rosselló, Josep A and Sena, Juliana and Svensson, Thomas and Talavera-López, Carlos and Theißen, Günter 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 Gil, Rosario Garcia and Hvidsten, Torgeir R and de Jong, Pieter and MacKay, John and Morgante, Michele and Ritland, Kermit and Sundberg, Björn and Thompson, Stacey Lee and Van de Peer, Yves and Andersson, Björn and Nilsson, Ove and Ingvarsson, Pär K and Lundeberg, Joakim and Jansson, Stefan},
  issn         = {0028-0836},
  journal      = {NATURE},
  keywords     = {GENE FAMILY,SEED PLANTS,ORYZA-SATIVA,SIZE VARIATION,LONG NONCODING RNAS,TRANSPOSABLE ELEMENTS,RECOMBINATION,LINEAGE,PINUS,RICE},
  language     = {eng},
  number       = {7451},
  pages        = {579--584},
  title        = {The Norway spruce genome sequence and conifer genome evolution},
  url          = {http://dx.doi.org/10.1038/nature12211},
  volume       = {497},
  year         = {2013},
}

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