A chromosome-scale genome assembly for Clark's Nutcracker (Nucifraga columbiana)

Focal and intelligent passerine songbirds, corvids (Aves: Corvidae) have served as models for research on the genomics of hybridization and cognition. Clarks Nutcracker (Nucifraga columbiana), the sole North American member of its genus, is distributed in mountain forests from northern Mexico to northern British Columbia. A seed predator, N. columbiana is highly reliant on pine nuts from Pinus spp. conifers, which it both consumes directly from cones and caches for future use. Because cached seeds are often forgotten or abandoned, it is a major seed disperser for high elevation pines--in particular Whitebark Pine P. albicaulis. Previous studies of genetic variation in Clarks Nutcracker found range-wide panmixia and generally high levels of heterozygosity at a handful of nuclear and mitochondrial loci, potentially due to seasonal elevational movements and long term dispersal. An earlier genome assembly from low-coverage short read data was highly fragmented and has not to date been used as the basis for population-level resequencing. Here we report on the first chromosome-scale genome assembly for N. colombiana. We generated long-read sequencing and genome conformation mapping data from tissues sampled from a male N. columbiana individual in Wyoming, USA. These data were assembled into a highly contiguous and complete assembly, which showed strong chromosomal synteny with New Caledonian crow (Corvus moneduloides). This genome has relatively low heterozygosity compared to other Corvid genomes and to previous population-level heterozygosity estimates for the species. We also found evidence of a long-term decline in effective population size dating back to the Pleistocene, after accounting for a technical artifact common to demographic inference using the pairwise sequential Markovian coalescent. These findings raise concerns about the future viability of the species and its mutualist P. albicaulis; we hope the assembly will motivate further comparative and conservation genomics research.