The complete mitochondrial genome sequence and phylogenetic analysis of Sibu yak (Bos grunniens)

Abstract

Sibu yak is famous for its excellent breed in Tibet and has become a magic way for local herdsmen to get rich. The Sibu yak, however, has been identified as an endangered bovine species. In this study, the complete mitochondrial genome of Sibu yak (Bos grunniens) was sequenced. The complete mitochondrial genome is a circular molecule with 16,324 bp in length, including 2 rRNA genes, 13 protein-coding genes, 22 tRNA genes, and a non-coding control region (D-loop). The entire nucleotide composition is A(33.70%), T(27.27%), C(25,81%), G(13.21%), respectively. Except that ND6 and 7 tRNAs （tRNA-Glu,tRNA-Pro,tRNA-Cys, tRNA-Tyr, tRNA-Ala, tRNA-Asn, and tRNA-Gln) are encoded on the light strand, the remaining genes are encoded on the heavy strand. As a valuable resource, we have compared it to related Bos species to understand the evolutionary history of Sibu yak.

China is the country with the most number of yaks in the world (Wiener et al. 2011). For the Tibetan people with poor living conditions, the yak is an extremely precious treasure. As a valuable resource, however, the Sibu yak was listed as an endangered animal resource in 1999 (Ma et al. 2002). The Qinghai-Tibet Plateau is the domestication center of yaks in Asia and Tibetan ancestors have domesticated wild yak at least 4000 years ago. Sibu is a place where is full of many alpine valleys, and the grass here is dense and excellent. Therefore, Sibu yak is an ancient species resource that was acclimated by Tibetans under such superior conditions. Sibu yak is one of the four excellent yak breeds in Tibet. The Sibu yak is mainly distributed in Mozhugongka County and its surrounding areas in Lhasa, Tibet. As we know, the excellent breed left over from history is like a ‘gene treasure,’ which is a valuable asset, and its scientific and economic value is enormous. Therefore, a clear understanding of the genetic sequence and phylogenetic information of a species is needed to protect the resources of existing primordial species. So we assembled the complete mitochondrial genome of Sibu yak to compare its genetic evolution with other related Bos species, thus providing theoretical support for its molecular breeding.

In this study, the 20 blood samples of Sibu yaks were collected from Sbu Village, Mozhugongka County, Lhasa city, Tibet (N29°67′, E91°81′). The samples are preserved at −20 °C in the Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences (Lanzhou, Gansu Province, China) with an accession number: LZ2019-203. We extracted the total genomic DNA from blood samples by using Easy Pure Blood Genomic DNA Kit (Transgen Biotech, Beijing, China) according to manufacturer’s instructions. The whole mitochondrial genome was amplified with six pairs of primers by polymerase chain reaction method and conducted with the Illumina HiSeq X™ Ten Sequencing System (Illumina, CA, San Diego) by Annoroad Gene Technology (Beijing, China). We assembled the sequencing results using DNASTAR5.0 software (Madison, WI). The complete mitochondrial genome of Sibu yak was determined and deposited in GenBank with an accession number: MN398192. The complete mitochondrial genome is a circular molecule with 16,324 bp in length, including 2 rRNA genes (12s and 16s rRNA), 13 protein-coding genes, 22 tRNA genes, and a non-coding control region (D-loop). The whole nucleotide composition is A(33.70%), T(27.27%), C(25,81%), G(13.21%), respectively. The content of C + G is 39.03%. There are four overlaps in the protein-coding genes of this sequence, including ND4 overlaps with ND4L for 7 bp, ATP6 overlaps with ATP8 for 40 bp, COX3 overlaps with ATP6 for 1 bp and ND6 overlaps with ND5 for 17 bp. NADH dehydrogenase subunit 6 (ND6) and 8 tRNA genes (Gln, Ser, Ala, Asn, Pro, Cys, Glu, and Try) are encoded on the light strand (L-strand), while all the remaining genes are encoded on the heavy strand (H-strand). The alignment of these genes is conservative in comparison with other related species.

To understand the evolutionary history of Sibu yak and its relationship with other yak breeds, the complete mitochondrial genome of Sibu yak was compared with the mitochondrial genome of 16 related Bos species. We built a phylogenetic tree by MEGA version 7.0 software combined with the neighbor-joining (NJ) method of 1000 bootstrap replicates (Cummings 2004). The result was validated by 1000 bootstraps and the bootstrap values are shown next to the branches (Figure 1). The result shows clearly that Sibu yak has a closer genetic relationship with three bovine species – Huanhu yak, PALI yak, and polled yak.

Figure 1.

Phylogenetic relationships of mitochondrial genomes of 17 species based on the neighbor-joining (NJ) methods.

The lessons of history tell us that if we do not take the time to protect actively and develop rationally, it may eventually lead to the exhaustion of resources. The aims of this present study are to provide a further help in the study of the origin and evolution of yaks, and it will provide a great help for the protection of genetic resources.

Funding Statement

This study was supported by grants from the Agricultural Science and Technology Innovation Program [CAAS-ASTIP-2014-LIHPS-01], the National Beef Cattle Industry Technology & System [CARS-37], the Major Science and Technology Projects in Tibet Autonomous Region [ZDZX201900045], and the Agricultural Resources Investigation, Protection and Utilization Projects.

Disclosure statement

The authors declare that there are no financial and personal relationships with other people or organizations that can inappropriately influence our work, and no professional or other personal interest of any nature or kind in any product, service, and company that could be construed as influencing the position presented in, or the review of the manuscript.