Next-Generation Sequencing of the Complete Huaibei Grey Donkey Mitogenome and Mitogenomic Phylogeny of the Equidae Family

SIMPLE SUMMARY: The phylogenetic status of the Huaibei grey donkey based on its complete mitochondrial genome, phylogeny, and maternal origin has not been fully established. This study reports the mitochondrial DNA diversity of the Huaibei grey donkey breed and presents its origin and genetic characterization. The Huaibei grey donkey’s complete mitogenome was 16,680 bp in length, containing 22 tRNAs, 2 rRNAs, 13 PCGs, and 1 D-loop region. The median-joining network and phylogenetic tree indicated two possible maternal lineages, with the Somali lineage as the most probable domestication center of Huaibei grey donkey. These results provide novel information on the origin and phylogeny of the Huaibei grey donkey and can be used as a reference for breeding and conservation management. ABSTRACT: The Huaibei grey donkey (HGD) is an endangered species and a vital native breed in Anhui Province, China. However, its complete mitogenome, phylogeny, and maternal origin remain unclear. The objectives of this study were to detect the genetic diversity of the HGD and investigate its phylogenetic relationship with other breeds to inform conservation management. The complete mitogenome of the HGD was sequenced through next-generation sequencing, and the most variable region in the mitochondrial DNA displacement-loop (D-loop) was amplified via a polymerase chain reaction (PCR). Next, we used the median-joining network (MJN) to calculate the genetic relationships among populations and the neighbor-jointing method to build a phylogenetic tree and speculate as to its origin. The results showed that the mitogenome contains 22 tRNAs, 2 rRNAs, 13 PCGs, and 1 D-loop region. Analyzing the D-loop region of the HGDs, we identified 23 polymorphic sites and 11 haplotypes. The haplotype and nucleotide diversity were 0.87000 (Hd) and 0.02115 (Pi), respectively. The MJN analysis indicated that the HGD potentially has two maternal lineages, and phylogenetic analysis indicated that the Somali lineage could be the most probable domestication center for this breed. Therefore, our mitogenome analysis highlights the high genetic diversity of the HGD, which may have originated from the Somali wild ass, as opposed to the Asian wild ass. This study will provide a useful resource for HGD conservation and breeding.