Copy number variations with adaptive potential in caribou (Rangifer tarandus): genome architecture and new annotated genome assembly

Abstract

BackgroundRangifer tarandus (caribou and reindeer) has experienced recent drastic population size reductions throughout its circumpolar distribution. In efforts aimed at preserving caribou in North America and reindeer in Eurasia, genetic diversity conservation is of utmost importance, particularly the adaptive genetic diversity. To facilitate genomic studies of the caribou population, we improved genome assembly and annotation by combining long-read, linked-read and RNA sequencing technologies. As copy number variations (CNVs) are known to impact phenotype and are therefore likely to play a key role in adaptation, we investigated CNVs among the genomes of individuals representing three ecotypes of caribou (migratory, boreal and mountain). ResultsUsing de novo transcriptome assembly and similarity with annotated human gene sequences, we identified 17,394 robust gene models embedded in a new highly contiguous genome assembly made of 13,994 scaffolds and presenting the highest N50 reported to date. A BUSCO analysis supported the high accuracy of this assembly, 90% of which being represented by only 131 scaffolds. Genome level comparisons with domestic ruminant species showed high synteny within this clade. A total of 1,698 large CNVs (length > 1kb) were identified, including 332 overlapping coding sequences annotated for functions related to immunity, musculoskeletal development or metabolism regulation and others. While the CNV distribution over the genome revealed 31 CNV hotspots, 43 large CNVs were particularly distinctive of the migratory and sedentary ecotypes and included genes annotated for functions related to cardiac development, fatty acid regulation, cold responses, locomotory behavior or environmental perception (hearing and sight), that can be related to the expected adaptations. ConclusionsThis work includes the first publicly available annotation of the Rangifer tarandus genome and the first genome assembly allowing genome architecture analyses. This robust annotation based on truly expressed sequences showed a distribution overlapping many CNVs that are promising candidates given the annotations supporting their involvement in adaptation. This new highly contiguous assembly will allow relative localization of genetic variations and features and will be a valuable resource for molecular tool development and genomic studies aimed at describing and preserving this species.