The objective was to develop a spruce genome resource by integrating outcomes of genome sequence analyses and high-density genetic mapping. Our work benefited from recent advances in sequencing technologies and previously developed resources (gene catalogues, gene maps). The expected outcome produced a more complete characterization of the gene space, as well as several drafts of two white spruce genome sequences. The genetic map helped us to position thousands of gene sequences and genome scaffolds onto chromosomes (linkage groups), and generated a novel genome resource that has enhanced future marker aided selection (MAS).
Conifer genome sequencing has become possible with advances in DNA sequencing technology. We used the Illumina High Seq 2000, High Seq 2500 and the MiSeq technology of which our sequencing center (Genome Sciences Center, Vancouver) has a large number. This activity interfaced with projects in Sweden (Norway spruce), USA (loblolly pine, sugar pine, Douglas fir), and Europe (Scots and Maritime pines). The white spruce and Norway spruce have a high level of synteny (nucleotide divergence of coding regions is ~ 4%; genetic maps are largely co-linear), such that a joint assembly can be made that improves the power of assembly, and gives insights into genomic processes of adaptation among the two taxa.
- Obtain a draft genome sequence of white spruce.
- Annotate the draft sequence, identify genomic sequences of gene coding regions for association studies and breeding, and identify gene space unique to conifers.
- Contribute to the development of international conifer genome resources and promote Canada’s position on the international genome landscape.
- Assess genome-wide CNVs and PAVs for comparative genomics and association studies.
- Perform comparative genome analyses between Norway and white spruce, and between spruce and loblolly pine/sugar pine/Douglas