De Novo Genome Assembly and Annotation of the Arunachali Yak

Abstract

The Arunachali yak (Bos grunniens), a high-altitude ruminant endemic to India, is genetically and economically significant for pastoral communities. However, challenges such as population decline, inbreeding, and genetic dilution through crossbreeding threaten its conservation. We generated a high-quality reference genome using PacBio HiFi long-read sequencing, Bionano optical mapping, and Hi-C sequencing to elucidate its genomic features and adaptive mechanisms. The 2.85 Gb genome, assembled with hifiasm, achieved a contig N50 of 70.4 Mb and a scaffold N50 of 102.99 Mb, with high completeness validated by BUSCO analysis. Annotation identified 25,855 protein-coding genes, with 81.5% functionally characterized. Repeat analysis revealed 44.68% transposable elements, with LINEs (28.26%) being the most abundant. This comprehensive genomic resource can help provide crucial insights into high-altitude adaptation, disease resistance, and productivity traits, and could support genomic-assisted breeding, conservation, and sustainable management of the Arunachali yak.