Perisoreus canadensis canadensis (isolate TCAG-6290) Genome sequencing and assembly. Perisoreus canadensis canadensis isolate:TCAG-6290 | breed:Boreal

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. The genome was assembled directly from 112-fold genome coverage of uncorrected long-reads. The final assembly comprised 1.11 Gb, which is 95% of the genome size estimated by k-mer analysis. Including a full-length mitochondrial genome, the assembly comprises 503 contigs with a contig N50 of 29.9 Mb. The longest contig is 103.6 Mb, which alone represented nearly 9% of the genome. Half of the assembled genome is represented by the longest 10 contigs (contig L50=10). A presumptive chromosomal-level assembly was generated by scaffolding the contigs against the three related chromosomal-level reference genomes available for Corvidea: the hooded crow (Corvus cornix cornix; ASM73873v5); the jackdaw (Coloeus monedula; ASM1340703v1); and the New Caledonian crow (Corvus moneduloides; bCorMon1.pri). Based on the conservation of the predicted synteny blocks, we derived a scaffold N50 of 56 Mb and a scaffold L50 of 6. The high quality of the assembly was exemplified by the near complete representation (99.8%) of the BUSCO avian gene set. 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.