Chromosome-level Genome Assembly for Takin (Budorcas taxicolor) Provides Insights into Its Taxonomic Status and Genetic Diversity

Abstract

The takin (Budorcas taxicolor) is one of the largest bovid herbivores across caprinae subfamily. The takin is at high risk of extinction, however, its taxonomic status is still unclear. In this study, we constructed the first reference genome of B. taxicolor using PacBio long High-Fidelity reads and Hi-C technology. The assembled genome is ~2.95 Gb with a contig N50 of 68.05 Mb and a scaffold N50 of 101.27 Mb, which were anchored onto 25+XY chromosomes. Compared to the common ancestral karyotype of bovidae (2n=60), we found the takin (2n=52) experienced four chromosome fusions and one large translocation. We also found that the takin was most closely related to muskox, not other caprinae species. Further, we re-sequenced nine golden takins from the main distribution area, Qinling Mountains, and identified 3.3 million SNPs. The genetic diversity of takin was very low (θπ=0.00028 and heterozygosity=0.00038), which was among the lowest detected in the domestic and wild mammals. We also found takin genomes showed high inbreeding coefficient (FROH=0.217) suggesting severe inbreeding depression. The genome analysis show that the effective population size of takins declined significantly from ~100,000 years ago. Our results provide valuable information for protection of takins and insights into its evolution.

Long‐read sequencing in ecology and evolution: Understanding how complex genetic and epigenetic variants shape biodiversity

“…This Special Issue includes examples of long‐read genome‐scale analyses in vulnerable or threatened species. For instance, Li, Yang, et al (2023) rely on PacBio data and Hi‐C technology to assemble the genome of the takin, a large bovid herbivore currently listed as vulnerable by the International Union for Conservation of Nature (IUCN; Li, Yang, et al, 2023). This high‐quality chromosome‐level assembly was used, along with resequencing data, to demonstrate important declines in effective population size during the past million years, and to uncover evidence of runs of homozygosity caused by recent inbreeding.…”