WarrenKeelingYuenEtAl2015

Référence

Warren, R.L., Keeling, C.I., Yuen, M.M.S., Raymond, A., Taylor, G.A., Vandervalk, B.P., Mohamadi, H., Paulino, D., Chiu, R., Jackman, S.D., Robertson, G., Yang, C., Boyle, B., Hoffmann, M., Weigel, D., Nelson, D.R., Ritland, C., Isabel, N., Jaquish, B., Yanchuk, A., Bousquet, J., Jones, S.J.M., MacKay, J., Birol, I. and Bohlmann, J. (2015) Improved white spruce (Picea glauca) genome assemblies and annotation of large gene families of conifer terpenoid and phenolic defense metabolism. Plant Journal, 83(2):189-212. (Scopus )

Résumé

Summary White spruce (Picea glauca), a gymnosperm tree, has been established as one of the models for conifer genomics. We describe the draft genome assemblies of two white spruce genotypes, PG29 and WS77111, innovative tools for the assembly of very large genomes, and the conifer genomics resources developed in this process. The two white spruce genotypes originate from distant geographic regions of western (PG29) and eastern (WS77111) North America, and represent elite trees in two Canadian tree-breeding programs. We present an update (V3 and V4) for a previously reported PG29 V2 draft genome assembly and introduce a second white spruce genome assembly for genotype WS77111. Assemblies of the PG29 and WS77111 genomes confirm the reconstructed white spruce genome size in the 20 Gbp range, and show broad synteny. Using the PG29 V3 assembly and additional white spruce genomics and transcriptomics resources, we performed MAKER-P annotation and meticulous expert annotation of very large gene families of conifer defense metabolism, the terpene synthases and cytochrome P450s. We also comprehensively annotated the white spruce mevalonate, methylerythritol phosphate and phenylpropanoid pathways. These analyses highlighted the large extent of gene and pseudogene duplications in a conifer genome, in particular for genes of secondary (i.e. specialized) metabolism, and the potential for gain and loss of function for defense and adaptation. © 2015 The Authors The Plant Journal © 2015 John Wiley & Sons Ltd.

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@ARTICLE { WarrenKeelingYuenEtAl2015,
    AUTHOR = { Warren, R.L. and Keeling, C.I. and Yuen, M.M.S. and Raymond, A. and Taylor, G.A. and Vandervalk, B.P. and Mohamadi, H. and Paulino, D. and Chiu, R. and Jackman, S.D. and Robertson, G. and Yang, C. and Boyle, B. and Hoffmann, M. and Weigel, D. and Nelson, D.R. and Ritland, C. and Isabel, N. and Jaquish, B. and Yanchuk, A. and Bousquet, J. and Jones, S.J.M. and MacKay, J. and Birol, I. and Bohlmann, J. },
    TITLE = { Improved white spruce (Picea glauca) genome assemblies and annotation of large gene families of conifer terpenoid and phenolic defense metabolism },
    JOURNAL = { Plant Journal },
    YEAR = { 2015 },
    VOLUME = { 83 },
    PAGES = { 189-212 },
    NUMBER = { 2 },
    NOTE = { cited By 0 },
    ABSTRACT = { Summary White spruce (Picea glauca), a gymnosperm tree, has been established as one of the models for conifer genomics. We describe the draft genome assemblies of two white spruce genotypes, PG29 and WS77111, innovative tools for the assembly of very large genomes, and the conifer genomics resources developed in this process. The two white spruce genotypes originate from distant geographic regions of western (PG29) and eastern (WS77111) North America, and represent elite trees in two Canadian tree-breeding programs. We present an update (V3 and V4) for a previously reported PG29 V2 draft genome assembly and introduce a second white spruce genome assembly for genotype WS77111. Assemblies of the PG29 and WS77111 genomes confirm the reconstructed white spruce genome size in the 20 Gbp range, and show broad synteny. Using the PG29 V3 assembly and additional white spruce genomics and transcriptomics resources, we performed MAKER-P annotation and meticulous expert annotation of very large gene families of conifer defense metabolism, the terpene synthases and cytochrome P450s. We also comprehensively annotated the white spruce mevalonate, methylerythritol phosphate and phenylpropanoid pathways. These analyses highlighted the large extent of gene and pseudogene duplications in a conifer genome, in particular for genes of secondary (i.e. specialized) metabolism, and the potential for gain and loss of function for defense and adaptation. © 2015 The Authors The Plant Journal © 2015 John Wiley & Sons Ltd. },
    AUTHOR_KEYWORDS = { ABySS; Bloom filter; conifer genomes; genome finishing; genome scaffolding; whole-genome shotgun assembly },
    DOCUMENT_TYPE = { Article },
    DOI = { 10.1111/tpj.12886 },
    KEYWORDS = { Forestry; Metabolism; Physiology; Scaffolds, ABySS; Bloom filters; Conifer genome; Expert annotations; Genome assembly; Phenylpropanoid pathways; Transcriptomics; Whole-genome shotgun, Genes, Coniferophyta; Gymnospermae; Picea glauca },
    SOURCE = { Scopus },
    URL = { http://www.scopus.com/inward/record.url?eid=2-s2.0-84936845853&partnerID=40&md5=2c8cc50c4685ccd2c1fcca7b22dd8893 },
}

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