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  Improved white spruce (Picea glauca) genome assemblies and annotation of large gene families of conifer terpenoid and phenolic defense metabolism

Warren, R., Keeling, C., Man Saint Yuen, M., Raymond, A., Taylor, G., Vandervalk, B., et al. (2015). Improved white spruce (Picea glauca) genome assemblies and annotation of large gene families of conifer terpenoid and phenolic defense metabolism. The Plant Journal, 83(2), 189-212. doi:10.1111/tpj.12886.

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 Creators:
Warren, RL, Author
Keeling, CI, Author
Man Saint Yuen, M, Author
Raymond, A, Author
Taylor, GA, Author
Vandervalk, BP, Author
Mohamadi, H, Author
Paulino, D, Author
Chiu, R, Author
Jackman, SD, Author
Robertson, G, Author
Yang, C, Author
Boyle, B, Author
Hoffmann, M1, Author           
Weigel, D1, Author           
Nelson, DR, Author
Ritland, C, Author
Isabel, N, Author
Jaquish, B, Author
Yanchuk, A, Author
Bousquet, J, AuthorJones, SJM, AuthorMacKay, J, AuthorBirol, I, AuthorBohlmann, J, Author more..
Affiliations:
1Department Molecular Biology, Max Planck Institute for Developmental Biology, Max Planck Society, ou_3375790              

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 Abstract: 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.

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 Dates: 2015-07
 Publication Status: Issued
 Pages: -
 Publishing info: -
 Table of Contents: -
 Rev. Type: -
 Identifiers: DOI: 10.1111/tpj.12886
PMID: 26017574
 Degree: -

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Title: The Plant Journal
  Other : Plant J.
Source Genre: Journal
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Publ. Info: Oxford : Blackwell Science
Pages: - Volume / Issue: 83 (2) Sequence Number: - Start / End Page: 189 - 212 Identifier: ISSN: 0960-7412
CoNE: https://pure.mpg.de/cone/journals/resource/954925579095_1