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

Abstract

The takin (Budorcas taxicolor) is a large bovid herbivore, belonging to the subfamily Caprinae. The number of takins was estimated to be only 7000-12,000 (Cheng et al., 2020) and it has been listed as vulnerable by the International Union for Conservation of Nature (IUCN) (Zeng & Song, 2002). It was divided into four subspecies according to physiological characteristics and geographical location (Wu, 1986). Qinling takin (Bu. t. bedfordi) and Sichuan takin (Bu. t. tibetana) are confined to China, while the Mishmi takin (Bu. t. taxicolor) has a distribution from the Gaoligong Mountains in northwestern Yunnan province, China, to India and Myanmar (Wu, 1986). In addition, Bhutan takin (Bu. t. whieti) is found in Bhutan and the Yarlung Zangbo River in Tibet, China (Li et al., 2003). Qinling takin (Bu. t. bedfordi), also known as golden takin, is mainly distributed in the Qinling Mountains of China (Figure 1a;Li, Qiu, et al., 2021).Compared to other Caprinae, the morphology, ecological traits and G-banded karyotype of takin were found to be similar to muskox (Ovibos moschatus) (Pasitschniak-Arts et al., 1994). However, analysis of mitochondrial cytochrome b (Cytb) sequences showed that

Forest fragmentation causes an isolated population of the golden takin (Budorcas taxicolor bedfordi Thomas, 1911) (Artiodactyla: Bovidae) in the Qinling Mountains (China)

“…The nucleotide diversity of B. t. bedfordi analysed by the mtDNA D-loop region was 0.0021 [ 48 ], indicating low genetic diversity [ 49 ]. The single nucleotide variants of B. t. bedfordi analysed by SNP were lower than those of the giant panda, golden monkey, goat, and cattle [ 50 – 52 ]. These results indicated that the B. t. bedfordi population suffered from poor genetic diversity, which was in accordance with the results of this study.…”

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.…”

The Development of Plant Genome Sequencing Technology and Its Conservation and Application in Endangered Gymnosperms

“…The first reference genome assembly for the high-extinction-risk Qinling serow has been made possible in large part by the use of HiFi sequencing technology in the field of animal conservation. This historic achievement has since laid the groundwork for investigating the evolutionary history of the Qin-ling serow and clarifying the fundamental causes of its elevated extinction risk [121]. Technological innovation resulting from the genetic revolution has profound consequences for the conservation of plant resources and their inherent diversity, as well as for the protection of animal resources [122].…”