Background: Gut microbiota plays a significant role in host survival, health, and diseases; however, compared to other livestock, research on the gut microbiome of donkeys is limited. Results: In this study, a total of 30 donkey samples of rectal contents from six regions, including Shigatse, Changdu, Yunnan, Xinjiang, Qinghai, and Dezhou, were collected for metagenomic sequencing. The results of the species annotation revealed that the dominant phyla were Firmicutes and Bacteroidetes, and the dominant genera were Bacteroides, unclassified_o_Clostridiales (short for Clostridiales) and unclassified_f_Lachnospiraceae (short for Lachnospiraceae). The dominant phyla, genera and key discriminators were Bacteroidetes, Clostridiales and Bacteroidetes in Tibet donkeys (Shigatse); Firmicutes, Clostridiales and Clostridiales in Tibet donkeys (Changdu); Firmicutes, Fibrobacter and Tenericutes in Qinghai donkeys; Firmicutes, Clostridiales and Negativicutes in Yunnan donkeys; Firmicutes, Fibrobacter and Fibrobacteres in Xinjiang donkeys; Firmicutes, Clostridiales and Firmicutes in Dezhou donkeys. In the functional annotation, it was mainly enriched in the glycolysis and gluconeogenesis of carbohydrate metabolism, and the abundance was the highest in Dezhou donkeys. These results combined with altitude correlation analysis demonstrated that donkeys in the Dezhou region exhibited strong glucose-conversion ability, those in the Shigatse region exhibited strong glucose metabolism and utilization ability, those in the Changdu region exhibited a strong microbial metabolic function, and those in the Xinjiang region exhibited the strongest ability to decompose cellulose and hemicellulose. Conclusion: According to published literature, this is the first study to construct a dataset with multi-regional donkey breeds. Our study revealed the differences in the composition and function of gut microbes in donkeys from different geographic regions and environmental settings and is valuable for donkey gut microbiome research.

Domestic cattle represent one of the most significant evolutionary successes in the history of human–animal mutualism. This review synthesizes evidence from paleogenomics and modern population genetics, particularly recent pangenome analyses, to reconstruct a comprehensive evolutionary trajectory of cattle. We outline the two domestication events: the emergence of taurine cattle (Bos taurus) in the Fertile Crescent (~10,500 years ago) and zebu cattle (Bos indicus) in the Indus Valley (~8000 years ago). Following domestication, cattle dispersed globally alongside human migration, resulting in a complex genetic mosaic shaped by introgression with wild relatives and extensive admixture between lineages. By integrating data from mitochondrial DNA, Y-chromosome haplotypes, and whole-genome sequencing of modern, ancient, and wild samples, we reconstruct the detailed global dispersal of cattle. Furthermore, we dissect the molecular mechanisms underlying phenotypic diversity, emphasizing how natural selection has driven environmental adaptation, how artificial selection has optimized production traits, and how the emerging bovine pangenome is unveiling “hidden” genetic variations critical for climate resilience and disease resistance. Ultimately, this review summarizes the origin, dispersal, and genomic diversity of cattle, offering vital insights for the conservation of indigenous genetic resources and the advancement of molecular breeding strategies in the face of a changing global climate.

This study investigates the genetic diversity, population structure, and adaptive differentiation of Yunnan native cattle (YNC) using whole-genome SNP data from 457 individuals, representing eight cattle populations and two closely related bovine species (Zhongdian yak and Dulong gayal). Genetic diversity analyses revealed a distinct latitudinal gradient from north to south, with the highest diversity observed in the northern Diqing (DQC) and Zhaotong (ZTC) populations. The observed population structure was largely consistent with geographic distribution, identifying distinct ancestral components and complex admixture patterns. Genome-wide selective sweep scans revealed several key candidate genes underlying local adaptation. Notably, GRIA4 and DUOXA2 were associated with cold tolerance in northern populations, and ST3GAL3 and MST1 were implicated in heat stress adaptation in southern populations. Genome-wide balancing selection analyses further detected significant loci, such as MGST1 and SLC36A1, where divergent haplotype frequencies reflected differential selective pressures on milk-related traits between northern and southern populations. Additionally, we detected signals of historical introgression from Zhongdian yak into DQC cattle, highlighting the introgressed gene SLIT3 as a potential candidate associated with high-altitude thermogenesis. Collectively, these results provide a comprehensive genomic framework for the management and conservation of indigenous bovine genetic resources in Southwest China.