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

Abstract

Background: Rangifer 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). Results: Using 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. Conclusions: This 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.

Genome-wide analysis of CNVs in three populations of Tibetan sheep using whole-genome resequencing

“…Among them, sensory perception was also significantly enriched in yaks (Qiu et al, 2012;Hui et al, 2019) and other sheep breeds (Ma et al, 2015;Yuan et al, 2021). And this was even observed in Rangifer tarandus caribou, a wild boreal ruminant (Prunier et al, 2022). The three TS populations live in alpine grasslands where the weather conditions are much harsher.…”

“…In terms of the CNVs captured by aCGH and SNP chips, the number usually ranges from dozens to hundreds, and the average length is approximately 100-300 kb (Liu et al, 2013;Ma et al, 2015;Wu et al, 2015;Jenkins et al, 2016;Zhu et al, 2016). In addition to the detection platform and algorithm, the tested breed and individual size used were other considerable factors that results in the CNVRs counts obtained (Sudmant et al, 2015;Yuan et al, 2021;Huang et al, 2021;Prunier et al, 2022). In addition, more deletion evens than duplication were detected in this research, which is similar to Huang, et al (Huang et al, 2021).…”