Canadian Forest Service Publications

Improved white spruce (Picea glauca) genome assemblies and annotation of large gene families of conifer terpenoid and phenolic defense metabolism. 2015. 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.; Bohlmann, J. Plant J. 83:189-212.

Year: 2015

Available from: Laurentian Forestry Centre

Catalog ID: 36352

Language: English

CFS Availability: PDF (request by e-mail)

Available from the Journal's Web site.
DOI: 10.1111/tpj.12886

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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.

Plain Language Summary

This study describes the genome of two white spruces (one from British Columbia, the other from Quebec) used in Canadian genetic improvement programs.

The DNA sequences for each genome were assembled using innovative bioinformatics tools developed specifically for sequencing very large genomes. With these new tools, researchers were able to update existing descriptions of white spruce genomes more rapidly and with greater precision.

The results of this study revealed the presence of a wide variety of genes that contribute to chemical defense mechanisms in these two trees.

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