Whole Mitochondrial Genomes Analysis Revealed Genetic and Evolutionary Characterization of Chinese Donkey Breeds (Equus asinus)

Mitochondrial DNA has been widely used for species identification and tracing the evolutionary history of domesticated animals. However, the complete mitochondrial genome of Chinese indigenous donkey breeds has not been comprehensively characterized. This study aimed to investigate the genetic diversity and phylogenetic relationships of these breeds based on their complete mitochondrial genomes. Our results showed that the majority of genetic variation was derived from the Somali and Nubian lineages, with the Somali lineage exhibiting more variable sites. Comparative analysis revealed 31 fixed nucleotide differences between the two lineages, which can serve as diagnostic markers for maternal lineage assignment. In conclusion, the high mitochondrial genetic diversity in Chinese domestic donkeys is primarily attributed to the coexistence of these two distinct maternal lineages. Furthermore, the observed genetic differentiation among populations does not correspond with their geographical distribution or breed-specific characteristics, indicating a complex demographic history.