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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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Chicago
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.
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.
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.
MLA
Nystedt, Björn, Nathaniel R Street, Anna Wetterbom, et al. “The Norway Spruce Genome Sequence and Conifer Genome Evolution.” NATURE 497.7451 (2013): 579–584. Print.
@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 {\textrangle}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 ({\textrangle}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, Bj{\"o}rn 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 H{\"a}llman, Jimmie and Keech, Olivier and Klasson, Lisa and Koriabine, Maxim and Kucukoglu, Melis and K{\"a}ller, Max and Luthman, Johannes and Lysholm, Fredrik and Niittyl{\"a}, Totte and Olson, {\AA}ke and Rilakovic, Nemanja and Ritland, Carol and Rossell{\'o}, Josep A and Sena, Juliana and Svensson, Thomas and Talavera-L{\'o}pez, Carlos and Thei{\ss}en, G{\"u}nter 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, Bj{\"o}rn and Thompson, Stacey Lee and Van de Peer, Yves and Andersson, Bj{\"o}rn and Nilsson, Ove and Ingvarsson, P{\"a}r K and Lundeberg, Joakim and Jansson, Stefan},
  issn         = {0028-0836},
  journal      = {NATURE},
  keyword      = {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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