Complete Mitogenomes of Xinjiang Hares and Their Selective Pressure Considerations

Comparative analysis based on the mitogenomes of hares in Xinjiang, China, is limited. In this study, the complete mitochondrial genomes of seven hare samples including four hare species and their hybrids from different environments were sequenced, assembled, and annotated. Subsequently, we performed base content and bias analysis, tRNA analysis, phylogenetic analysis, and amino acid sequence analysis of the annotated genes to understand their characteristics and phylogenetic relationship. Their mitogenomes are circular molecules (from 16,691 to 17,598 bp) containing 13 protein-coding genes, two rRNA genes, 22 tRNA genes, and a control region, which are similar with other <i>Lepus</i> spp. worldwide. The relative synonymous codon usage analysis revealed that the adaptation of <i>Lepus yarkandensis</i> to its unique arid and hot environment might be associated with synthesizing amino acids like alanine, leucine, serine, arginine, and isoleucine and the terminator caused by the different usage of codons. Further, we utilized the MEME model and identified two positive selection genes (<i>ND4</i>, <i>ND5</i>) in <i>Lepus tibetanus pamirensis</i> and one (<i>ND5</i>) in <i>L. yarkandensis</i> that might be important to their adaptation to the plateau and dry and hot basin environments, respectively. Meanwhile, <i>Lepus tolai lehmanni</i> and <i>Lepus timidus</i> may have evolved different adaptive mechanisms for the same cold environment. This study explored the evolutionary dynamics of Xinjiang hares' mitochondrial genomes, providing significant support for future research into their adaptation mechanisms in extreme environments.