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

René L. Warren, Christopher I. Keeling, Macaire Man Saint Yuen, Anthony Raymond, Greg A. Taylor, Benjamin P. Vandervalk, Hamid Mohamadi, Daniel Paulino, Readman Chiu, Shaun D. Jackman, Gordon Robertson, Chen Yang, Brian Boyle, Margarete Hoffmann, Detlef Weigel, David Nelson, Carol Ritland, Nathalie Isabel, Barry Jaquish, Alvin Yanchuk & 5 others Jean Bousquet, Steven J.M. Jones, John Mackay, Inanc Birol, Joerg Bohlmann

Research output: Contribution to journalArticle

69 Citations (Scopus)

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.

Original languageEnglish (US)
Pages (from-to)189-212
Number of pages24
JournalPlant Journal
Volume83
Issue number2
DOIs
StatePublished - Jul 1 2015

Fingerprint

Coniferophyta
Picea
genome assembly
Molecular Sequence Annotation
Picea glauca
Terpenes
terpenoids
conifers
Genome
metabolism
Genomics
genes
Genotype
genome
genomics
Gymnosperms
Synteny
Genome Size
genotype
Mevalonic Acid

All Science Journal Classification (ASJC) codes

  • Genetics
  • Plant Science
  • Cell Biology

Cite this

Warren, R. L., Keeling, C. I., Yuen, M. M. S., Raymond, A., Taylor, G. A., Vandervalk, B. P., ... 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. https://doi.org/10.1111/tpj.12886

Improved white spruce (Picea glauca) genome assemblies and annotation of large gene families of conifer terpenoid and phenolic defense metabolism. / Warren, René L.; Keeling, Christopher I.; Yuen, Macaire Man Saint; Raymond, Anthony; Taylor, Greg A.; Vandervalk, Benjamin P.; Mohamadi, Hamid; Paulino, Daniel; Chiu, Readman; Jackman, Shaun D.; Robertson, Gordon; Yang, Chen; Boyle, Brian; Hoffmann, Margarete; Weigel, Detlef; Nelson, David; Ritland, Carol; Isabel, Nathalie; Jaquish, Barry; Yanchuk, Alvin; Bousquet, Jean; Jones, Steven J.M.; Mackay, John; Birol, Inanc; Bohlmann, Joerg.

In: Plant Journal, Vol. 83, No. 2, 01.07.2015, p. 189-212.

Research output: Contribution to journalArticle

Warren, RL, Keeling, CI, Yuen, MMS, Raymond, A, Taylor, GA, Vandervalk, BP, Mohamadi, H, Paulino, D, Chiu, R, Jackman, SD, Robertson, G, Yang, C, Boyle, B, Hoffmann, M, Weigel, D, Nelson, D, Ritland, C, Isabel, N, Jaquish, B, Yanchuk, A, Bousquet, J, Jones, SJM, Mackay, J, Birol, I & 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, vol. 83, no. 2, pp. 189-212. https://doi.org/10.1111/tpj.12886
Warren, René L. ; Keeling, Christopher I. ; Yuen, Macaire Man Saint ; Raymond, Anthony ; Taylor, Greg A. ; Vandervalk, Benjamin P. ; Mohamadi, Hamid ; Paulino, Daniel ; Chiu, Readman ; Jackman, Shaun D. ; Robertson, Gordon ; Yang, Chen ; Boyle, Brian ; Hoffmann, Margarete ; Weigel, Detlef ; Nelson, David ; Ritland, Carol ; Isabel, Nathalie ; Jaquish, Barry ; Yanchuk, Alvin ; Bousquet, Jean ; Jones, Steven J.M. ; Mackay, John ; Birol, Inanc ; Bohlmann, Joerg. / Improved white spruce (Picea glauca) genome assemblies and annotation of large gene families of conifer terpenoid and phenolic defense metabolism. In: Plant Journal. 2015 ; Vol. 83, No. 2. pp. 189-212.
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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.",
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