The sequence and de novo assembly of the wild yak genome

Abstract

Vulnerable populations of wild yak (Bos mutus), the wild ancestral species of domestic yak, survive in extremely cold, harsh and oxygen-poor regions of the Qinghai-tibetan Plateau (QtP) and adjacent high-altitude regions. In this study, we sequenced and assembled its genome de novo. In total, six different insert-size libraries were sequenced, and 662 Gb of clean data were generated. The assembled wild yak genome is 2.83 Gb in length, with an N50 contig size of 63.2 kb and a scaffold size of 16.3 Mb. BUSCO assessment indicated that 93.8% of the highly conserved mammal genes were completely present in the genome assembly. Annotation of the wild yak genome assembly identified 1.41 Gb (49.65%) of repetitive sequences and a total of 22,910 protein-coding genes, including 20,660 (90.18%) annotated with functional terms. This first construction of the wild yak genome provides a variable genetic resource that will facilitate further study of the genetic diversity of bovine species and accelerate yak breeding efforts.

The Landscape of Accessible Chromatin during Yak Adipocyte Differentiation

“…The yak is a unique and rare ruminant living in the Qinghai–Tibet Plateau and adjacent regions. As an important livestock species for animal husbandry in this area, yaks provide local residents with agricultural products such as meat, milk, and hair while adapting to environmental conditions including cold, low oxygen, and high altitude and ultraviolet rays [ 16 , 17 ]. Because yaks graze year-round, their growth and development is restricted by the yield and quality of forage [ 18 ].…”

The Gut Microbiota Determines the High-Altitude Adaptability of Tibetan Wild Asses (Equus kiang) in Qinghai-Tibet Plateau

“…Advances in sequencing technology over the past decade have provided novel insights into microbiome co-evolution and adaptability. Furthermore, herbivore adaptation mediated via the gut microbiota has attracted a great deal of research attention (Liu et al, 2020d ; Song et al, 2020 ; Fu et al, 2021 ).…”

Long read genome assemblies complemented by single cell RNA-sequencing reveal genetic and cellular mechanisms underlying the adaptive evolution of yak

“…The domestic yak normally lives between 3000 and 5000 m above sea level while the wild yak, the ancestor of domestic yak, inhabits at elevations from 4000 to 6000 m on the QTP [1][2][3][4][5] . Archaeological and molecular evidences revealed that wild yak was domesticated at least 7300 years ago [6][7][8][9] . Although significant morphologic differences exist between wild and domestic yak 1 , both species share genetic features of high-altitude adaptation and are considered excellent models for studying hypoxia tolerance in large mammals.…”

“…In 2012, the genome of a female domestic yak was sequenced using the Illumina-based whole-genome shotgun method 6 . In 2020, the genome of a female wild yak was assembled with the Illumina data 7 , and chromosome-scale genomes of female domestic yak were constructed using long-read sequencing and chromatin interaction technologies 10,11 . However, previous studies on yak have primarily focused on single nucleotide variants to reveal the genomic diversity and historical population dynamics 6,[12][13][14][15][16][17][18] .…”