Wild yak (Bos mutus) and domestic yak (Bos grunniens) are adapted to high altitude environment and have ecological, economic, and cultural significances on the Qinghai-Tibetan Plateau (QTP). Currently, the genetic and cellular bases underlying adaptations of yak to extreme conditions remains elusive. In the present study, we assembled two chromosome-level genomes, one each for wild yak and domestic yak, and screened structural variants (SVs) through the long-read data of yak and taurine cattle. The results revealed that 6733 genes contained high-FST SVs. 127 genes carrying special type of SVs were differentially expressed in lungs of the taurine cattle and yak. We then constructed the first single-cell gene expression atlas of yak and taurine cattle lung tissues and identified a yak-specific endothelial cell subtype. By integrating SVs and single-cell transcriptome data, we revealed that the endothelial cells expressed the highest proportion of marker genes carrying high-FST SVs in taurine cattle lungs. Furthermore, we identified pathways which were related to the medial thickness and formation of elastic fibers in yak lungs. These findings provide new insights into the high-altitude adaptation of yak and have important implications for understanding the physiological and pathological responses of large mammals and humans to hypoxia.

Summary: The previous studies have reported that the mammalian gut microbiota is a physiological consequence; nonetheless, the factors influencing its composition and function remain unclear. In this study, to evaluate the contributions of the host and environment to the gut microbiota, we conducted a sequencing analysis of 16S rDNA and shotgun metagenomic DNA from plateau pikas and yaks, two sympatric herbivorous mammals, and further compared the sequences in summer and winter. The results revealed that both pikas and yaks harboured considerably more distinct communities between summer and winter. We detected the over‐representation of Verrucomicrobia and Proteobacteria in pikas, and Archaea and Bacteroidetes in yaks. Firmicutes and Actinobacteria, associated with energy‐efficient acquisition, significantly enriched in winter. The diversity of the microbial community was determined by the interactive effects between the host and season. Metagenomic analysis revealed that methane‐metabolism‐related pathway of yaks was significantly enriched in summer, while some pathogenic pathways were more abundant in pikas. Both pikas and yaks had a higher capacity for lipid degradation in winter. Pika and yak shared more OTUs when food shortage occurred in winter, and this caused a convergence in gut microbial composition and function. From winter to summer, the network module number increased from one to five in pikas, which was different in yaks. Our study demonstrates that the host is a dominant factor in shaping the microbial communities and that seasonality promotes divergence or convergence based on dietary quality across host species identity.

Pastoralists on the Tibetan alpine rangeland suffered great economic loss in cold season, due to serious live-weight loss of domestic livestock under traditional grazing management. This study aimed to evaluate the effect of dietary types (crude protein levels) on feed intakes, growth performance and economic returns of local Tibetan sheep and yaks during cold season. Twenty-four yearling Tibetan sheep (25.29±3.95 kg LW) and twenty two-year-old yaks (100.62±4.55 kg LW) with familiar body conditions were randomly assigned to four groups, fed oats hay (OH), oats silage (OS), total mixed ration (TMR) and traditionally grazed on the local cool-season pasture (TG), respectively, over a 135-day experiment. Daily dry matter intake was determined; all animals were weighed at the beginning and every 15 days of the 135-day experiment. Then, the total live-weight gain, average daily live-weight gain, gain rate, feed efficiency and net economic benefit were calculated. Results indicated that feed and nutrient intakes (DMI, DMI/kg LW, DMI/kg LW^0.75 and CPI) of TMR, OH and OS were higher than TG (P < 0.05). Grazing animals suffered serious live-weight loss, while TMR, OS and OH significantly (P < 0.05) improved total live-weight gain and gain rate in both Tibetan sheep and yaks during the entire experiment. TMR worked better in animal performance and feed efficiency, obtained the highest breeding profit in both Tibetan sheep and yaks among four treatments (P < 0.05). When expressed on net economic benefit, TMR shared the highest net economic benefit in Tibetan sheep, OH shared the highest net economic benefit in yaks, but, no significant difference of net economic benefit in yaks fed TMR and OH diets was determined (P > 0.05). Results indicated that TMR was a reasonable diet in promoting feed intakes, animal performance, feed efficiency and economic returns in domestic livestock, which should be considered by local herdsmen to increase their breeding profit during cold season.

The rumen microbiota is strongly associated with host health, nutrient absorption, and adaptability. However, the composition, functioning and adaptability of rumen microbiota in Tibetan sheep (TS) across different phenological periods are unclear. In this study we used sequencing of the V4-V5 region of 16S rRNA, qPCR technology and metagenomics to investigate the adaption of rumen microbiota to forage in different stages of phenology. In a grassy period, due to the high nutritional quality of the forage, TS can produce high concentrations of NH₃-N and short fatty acids by increasing the content of key bacteria in the rumen, such as Bacteroidetes, Prevotella, Succiniclasticum, Treponema, Butyrivibrio fibrisolvens, Fibrobacter succinogenes, Prevotella ruminicola, Ruminococcus albus, and Ruminococcus flavefaciens to aid in growth. In the withering period, there was a positive correlation between microorganisms which indicated the closely cooperation between microorganisms, and metagenomic analysis showed that the high genes (GHs and CBMs) and subtribe (GH8, GH12, GH45, GH6, GH9, GH5, GH10, GH3, GH52, GH11, GH57, CBM1, CBM4, CBM6, CBM16, CBM37, CBM13, CBM35, CBM42, CBM32, and CBM62) that encode cellulolytic enzymes were significantly increased when the host faced low quantity and quality of forage. Genes involved in metabolic pathways, fatty acid biosynthesis and biosynthesis of antibiotics were significantly enriched, which indicated that rumen microbiota could improve plant biomass deconstruction and energy maintenance in the face of nutritional deficiencies. In the regreen period, both the composition and function of rumen microbiota had obvious disadvantages, therefore, to improve the competitiveness of microorganisms, we suggest TS should be supplemented with high-protein feed. This study is of great significance for exploring the high altitude adaptability of TS.