TY - JOUR T1 - CNVs with adaptive potential in <em>Rangifer tarandus</em>: genome architecture and new annotated assembly JF - Life Science Alliance JO - Life Sci. Alliance DO - 10.26508/lsa.202101207 VL - 5 IS - 3 SP - e202101207 AU - Julien Prunier AU - Alexandra Carrier AU - Isabelle Gilbert AU - William Poisson AU - Vicky Albert AU - Joëlle Taillon AU - Vincent Bourret AU - Steeve D Côté AU - Arnaud Droit AU - Claude Robert Y1 - 2022/03/01 UR - https://www.life-science-alliance.org/content/5/3/e202101207.abstract N2 - Rangifer tarandus has experienced recent drastic population size reductions throughout its circumpolar distribution and preserving the species implies genetic diversity conservation. To facilitate genomic studies of the species populations, we improved the genome assembly by combining long read and linked read and obtained a new highly accurate and contiguous genome assembly made of 13,994 scaffolds (L90 = 131 scaffolds). Using de novo transcriptome assembly of RNA-sequencing reads and similarity with annotated human gene sequences, 17,394 robust gene models were identified. As copy number variations (CNVs) likely play a role in adaptation, we additionally investigated these variations among 20 genomes representing three caribou ecotypes (migratory, boreal and mountain). A total of 1,698 large CNVs (length &gt; 1 kb) showing a genome distribution including hotspots were identified. 43 large CNVs were particularly distinctive of the migratory and sedentary ecotypes and included genes annotated for functions likely related to the expected adaptations. This work includes the first publicly available annotation of the caribou genome and the first assembly allowing genome architecture analyses, including the likely adaptive CNVs reported here. ER -