Perisoreus canadensis canadensis (isolate TCAG-6290) genome sequencing, assembly, and chromosomal-level scaffolding.. Perisoreus canadensis canadensis isolate:TCAG-6290

We report a chromosomal-level reference genome assembly of a female specimen of the Canada Jay (Perisoreus canadensis candensis), a corvid with long a geographic and historical association with Canada. The specimen was collected in the boreal forest near Timmins, Ontario. We annotated a comprehensive set of genes that have been associated with intelligence, an attribute for which the Corvidea is noted. In addition, we annotated genes involved in pigment and plumage development. To provide the first genome wide assessment of the phylogeography of the Canada jay, whole genome reference-assisted re-sequencing and the assembly of the mitochondrial genomes were carried out on 16 selected individuals across its range. Principle component analysis revealed three distinct clusters, corresponding to morphotypes previously identified phenotypically and through the analysis of mitochondrial DNA. Tabulation of heterozygous single nucleotide variants (SNVs) of our reference specimen revealed a heterozygosity level indicative of a relatively diverse gene pool. The present genome provides a resource for genomics-based conservation management of the Canada Jay, a cold-adapted species that is now under pressure due to habitat loss from climate change. This project is part of the CanSeq150 program provided by CGEn and its partners.