Phylogeny and Selection Pressure of Genus Chimarrogale in China Based on Mitochondrial Genomes

The genus Chimarrogale is an ideal group to study the evolutionary mechanisms of semi-aquatic adaptation, but there is a lack of data on its genomic data and molecular mechanisms. Using Illumina sequencing, this study assembled mitogenomes of C. himalayica and C. styani (newly characterized), alongside C. leander, covering all Chimarrogale species in China. Results showed that three complete circular mitochondrial genomes were successfully assembled, with full lengths of 17,202–17,218 bp, including the 37 typical genes: 13 protein-coding genes (PCGs), 22 tRNAs, two rRNAs, and a D-loop region. There were nine overlapping regions and 14 intergenic spacer regions identified, showing significant AT bias. Relative synonymous codon usage (RSCU) analysis showed that Serine (Ser) was used most frequently. Selection pressure analysis showed that the Ka/Ks ratios of PCGs in 44 Soricidae mitogenomes were less than 1, indicated strong purification selection and functional conservation. Among them, the evolution rate of the ATP8 gene was the fastest. The phylogenetic analysis using Maximum Likelihood (ML) and Bayesian Inference (BI) methods showed that the three Chimarrogale species clustered into a monophyletic clade, which formed a sister group with Nectogale elegans within the tribe Nectogalini. This study fills the gap in mitochondrial genome data of semi-aquatic shrews and offers fundamental references for the conservation of shrews.