First report of mitochondrial genomes in Hydryphantoidea: novel genomes, evolution rate, and gene rearrangement patterns in two water mites (Acari: Hydrachnidia).

Water mites are very diverse and species-rich group of invertebrates and also are excellent bioindicators. However, relatively little attention has been paid to their molecular data, limiting our understanding of their evolutionary and phylogenetic relationships. In this study, the complete mitochondrial genomes of Hydrodroma diploflagellis Jin, 1997 and Thyas weichangensis Zhong, 2026 were determined for the first time and analyzed in detail. The mitochondrial genomes of H. diploflagellis and T. weichangensis both contained 37 genes, including 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs), and two ribosomal RNAs (rRNAs). Both species exhibited a pronounced AT bias in their genetic composition. Meanwhile, ENC-plot, PR2-bias, and neutrality plot analysis indicated that the codon usage of PCGs is mainly affected by natural selection. Most tRNAs lacked canonical cloverleaf structures due to the loss of D- or T-arm. Furthermore, a comprehensive analysis of 15 existing mitochondrial genomes of water mites revealed that the cox1 gene showed the lowest nucleotide diversity and Ka/Ks values, indicating strong purifying selection and sequence conservation. This conservation makes cox1 a reliable marker for species identification and resolving deep phylogenetic relationships, although markers with higher variability may be more suitable for population-level studies. Gene rearrangements occurred in all examined water mite mitochondrial genomes. Phylogenetic analyses based on mitochondrial genomes provided support for the classification of superfamily-level taxa. Our findings establish a foundation for future research on the phylogeny and evolutionary history of water mites.