Chromosome-level genome assembly for takin (Budorcas taxicolor) provides insights into its taxonomic status and genetic diversity

The takin (Budorcas taxicolor) is one of the largest bovid herbivores in the subfamily Caprinae. The takin is at high risk of extinction, but its taxonomic status and genetic diversity remain unclear. In this study, we constructed the first reference genome of Bu. taxicolor using PacBio long High-Fidelity reads and Hi-C technology. The assembled genome is similar to 2.95 Gb with a contig N50 of 68.05 Mb, which were anchored onto 25+XY chromosomes. We found that the takin was more closely related to muskox than to other Caprinae species. Compared to the common ancestral karyotype of bovidae (2n = 60), we found the takin (2n = 52) experienced four chromosome fusions and one large translocation. Furthermore, we resequenced nine golden takins from the main distribution area, the Qinling Mountains, and identified 3.3 million single nucleotide polymorphisms. The genetic diversity of takin was very low (theta pi = 0.00028 and heterozygosity =0.00038), among the lowest detected in domestic and wild mammals. Takin genomes showed a high inbreeding coefficient (FROH =0.217), suggesting severe inbreeding depression. The demographic history showed that the effective population size of takins declined significantly from similar to 100,000 years ago. Our results provide valuable information for protection of takins and insights into their evolution.

Automated summary

This study constructed the first reference genome of the takin and provided valuable information on its taxonomic status, genetic diversity, and evolution. The takin was found to be more closely related to muskox, showed low genetic diversity, and displayed severe inbreeding depression. The effective population size of takins has significantly declined over the past 100,000 years.