Genome Assembly Of Wild Yak And Construction Of Yak Pan-genome

The yak is one of the rare Bovidae species that is endemic to the Qinghai-Tibet Plateau(QTP)and adjacent alpine regions,as well as a rare domestic animal that can thrive in the high-altitude environments in the world.After a long-term natural selection,the yak has adapted to the extreme environment of high altitude and hypoxia,making it an excellent model species for studying extreme environmental adaptability.However,due to long-term excessive selection and pure breeding,the quality of the existing domestic yak has been seriously degraded,which has greatly affected the stability of agricultural and animal husbandry production in the QTP and surrounding areas.Wild yak,the wild ancestor of domestic yak,is still alive today,and have more excellent production traits,such as: large body size,strong disease resistance,which makes it possible to introduce genetic resources of wild yak to improve domestic yak.Our team has published the whole genome sequence of domestic yak and the genome re-sequencing data of 13 wild yaks,but the whole genome sequence of the wild yak is still not deciphered,which hinders the application in yak breeding research.In this study,we present a high-quality draft genome sequence of wild yak using nextgeneration sequencing technology.A total of 761 Gb raw sequencing data was generated,with sequencing depth of 220×.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 analysis was carried out to assess the completeness of our assembly,which resulted in a BUSCO score of 96.8%,indicating that the wild yak assembly is of high quality?We identified 1.41 Gbp of non-redundant repetitive sequences,representing 49.65% of the wild yak genome assembly.And we predicted 22,910 protein-coding genes,with an average transcript length of 47,211 bp,coding sequence length of 1,547 bp,and a mean of nine exons per gene,all similar to those observed for domestic yak,cattle,bison and sheep.A total of 90.18% of the genes matched at least with one of the public protein databases,which proves the reliability of gene annotation is quite high.We further constructed a yak pan-genome with a size of 2.92 Gb using our assembled wild yak and domestic yak genome sequences,and identified 30 Mb wild yak specific sequences and 19 Mb domestic yak specific sequences,covering 185 and 209 genes respectively.Through functional analysis of the variable genes associated with these specific sequences,we found that the domestic yak variable genes are related to brain and nervous system development and energy metabolism,and wild yak variable genes are related to DNA damage repair and reproduction.In this study,we completed the assembly and annotation of high-quality wild yak genome,and constructed the yak pangenome,provide important insights into the genetic diversity between domestic yak and wild yak and provide a variable genetic resource for further research on genetic improvement and accelerate the applied efforts in yak breeding.