A chromosome-scale reference genome and genome-wide genetic variations elucidate adaptation in yak.

Yak is an important livestock animal for the people indigenous to the harsh, oxygen-limited Qinghai-Tibetan Plateau and Hindu Kush ranges of the Himalayas. The yak genome was sequenced in 2012, but its assembly was fragmented because of the inherent limitations of the Illumina sequencing technology used to analyse it. An accurate and complete reference genome is essential for the study of genetic variations in this species. Long-read sequences are more complete than their short-read counterparts and have been successfully applied towards high-quality genome assembly for various species. In this study, we present a high-quality chromosome-scale yak genome assembly (BosGru_PB_v1.0) constructed with long-read sequencing and chromatin interaction technologies. Compared to an existing yak genome assembly (BosGru_v2.0), BosGru_PB_v1.0 shows substantially improved chromosome sequence continuity, reduced repetitive structure ambiguity, and gene model completeness. To characterize genetic variation in yak, we generated de novo genome assemblies based on Illumina short reads for seven recognized domestic yak breeds in Tibet and Sichuan and one wild yak from Hoh Xil. We compared these eight assemblies to the BosGru_PB_v1.0 genome, obtained a comprehensive map of yak genetic diversity at the whole-genome level, and identified several protein-coding genes absent from the BosGru_PB_v1.0 assembly. Despite the genetic bottleneck experienced by wild yak, their diversity was nonetheless higher than that of domestic yak. Here, we identified breed-specific sequences and genes by whole-genome alignment, which may facilitate yak breed identification.

Evaluation of the economic impact of brucellosis in domestic yaks of Tibet.

Brucellosis is considered as an endemic disease in yaks (Bos grunniens) in China, but few economic analyses describing the cost of the disease and potential benefits of control have been reported. The aim of the study was to estimate the economic cost of brucellosis in yaks and the economic value of three control strategies: (a) vaccination; (b) test-and-slaughter; and (c) a combination of vaccination and test-and-slaughter programs in Damxung and Maizhokunggar counties and Pali township of Yadong county in Tibet. Using data from a cross-sectional seroprevalence survey conducted in 2015, combined with financial data, the predicted costs and benefits of the different control strategies were simulated over a 6-year period. The annual estimated cost of brucellosis in yaks within the study area was US$ 521,043 (95% CI: US$ 334,441; US$ 759,862), with an annual average cost per yak estimated at US$ 1.42 (95% CI: US$ 0.91, US$ 2.07). The benefit-cost analysis predicted that vaccination was the most effective control method with a benefit-cost ratio (BCR) of 3.19 (95% CI: 2.17, 4.66) and a net present value (NPV) of US$ 313,355 (95% CI: US$ 157,679, US$ 541,062) over a 6-year period. A sensitivity analysis found the NPV was most sensitive to the loss from a female yak aborting in the vaccination control program. In contrast, the price of yaks that were slaughtered had the largest influence on the NPV for both the test-and-slaughter control program and the combination control program. These estimates provide valuable information and establish a foundation for formulating and implementing cost-effective measures for controlling the disease in yaks on the Tibetan plateau, and more broadly in China.

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

In the present study, we report the complete mitochondrial genome of Niangya yak (Bos grunniens) and its phylogenetic inferences. The complete mitochondrial DNA is a circular molecule with 16,322 bp length consisting of 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, and a non-coding control region(D-loop). Both ND6 and 7 tRNAs (tRNA-Pro, tRNA-Glu, tRNA-Tyr, tRNA-Cys, tRNA-Asn, tRNA-Ala and tRNA-Gln) are encoded on the light strand, and the remaining genes are encoded on the heavy strand. The overall nucleotide composition is A(33.73%), T(27.28%), C(25.80%), G(13.19%) respectively. The content of C + G is 38.99%. Given that yak is indispensable for the Tibetan people, it is important to understand the genetic status of the population for further systematic genetics, evolutionary significance and protection of genetic resources. Therefore, to understand the evolutionary history of Niangya yak, the complete mitochondrial genome of Niangya yak was sequenced and compared with the mitochondrial genome of closely related Bos species.