A draft genome of Drung cattle reveals clues to its chromosomal fusion and environmental adaptation

Abstract

Drung cattle (Bos frontalis) have 58 chromosomes, differing from the Bos taurus 2n = 60 karyotype. To date, its origin and evolution history have not been proven conclusively, and the mechanisms of chromosome fusion and environmental adaptation have not been clearly elucidated. Here, we assembled a high integrity and good contiguity genome of Drung cattle with 13.7-fold contig N50 and 4.1-fold scaffold N50 improvements over the recently published Indian mithun assembly, respectively. Speciation time estimation and phylogenetic analysis showed that Drung cattle diverged from Bos taurus into an independent evolutionary clade. Sequence evidence of centromere regions provides clues to the breakpoints in BTA2 and BTA28 centromere satellites. We furthermore integrated a circulation and contraction-related biological process involving 43 evolutionary genes that participated in pathways associated with the evolution of the cardiovascular system. These findings may have important implications for understanding the molecular mechanisms of chromosome fusion, alpine valleys adaptability and cardiovascular function.

Research Progress and Applications of Bovine Genome in the Tribe Bovini

“…Gene annotation identified 26,884 protein-coding genes. To characterize the mechanisms underlying a chromosome fusion event, a male Drung cattle genome was de novo assembled [24] and 29 scaffolds were identified, of which one scaffold sequence (Fragscaffold60) had the presence of cattle satellite I with 28 tandem repeats. Furthermore, a chromosome-level genome for gayal has been completed [32].…”

“…Functional annotation identified candidate genes, such as WNT and VSMC, for adaptation to heat tolerance traits in Pakistani indicine breeds, and VEGF and HIF1 in highland-adapted Pakistani indicine breeds. In gayal, Chen et al [24] identified expanded gene families (e.g., MYH, DHPR, ROCK), a positive selection gene (MLCK2), segmental duplication, and core drive genes (e.g., RYR2, TNNI3, and ACTC1) based on the comparative genome and transcriptome analyses, mainly related to odor sensation and cardiac function (Table 3). Li et al [36] detected several differentially expressed genes on the newly derived chromosome 2, which is functionally shown to be strongly associated with muscle traits in gayal, an adaptation to the alpine valley they inhabit.…”

“…It also provides an outlook Up to now, the genome assembly and annotation of several bovine species have been completed. The first to complete the genome sequence determination was Heifer cattle (B. taurus), followed by zebu (B. indicus) [20], yak (B. grunniens) [21,22], water buffalo (B. bubalis) [23], gayal (B. frontalis) [24], etc. (Table 1).…”

Large-Scale Chromosomal Changes Lead to Genome-Level Expression Alterations, Environmental Adaptation, and Speciation in the Gayal (Bos frontalis)

“…It is characterized by longer and thinner myofibrils and lower lipid content than other plains bovines ( Tian et al 1998 ). The karyotypic differences between and among the closely related bovine species and breeds provide an ideal model in which to assess the association between Rb and gene expression alterations, as well as the onset of speciation, although previously published gayal draft genomes failed to uncover such an association, probably due to the incompleteness of the assembled genome and the lack of information on architectural features ( Wang et al 2017 ; Chen et al 2022 ).…”