Comprehensive Analysis of Phylogenetic Relationship and Optimal Codons in Mitochondrial Genomes of the Genus Pseudogastromyzon

As indicator organisms for water pollution detection, Pseudogasteromyzon species play a vital role in aquatic environment monitoring. We have successfully sequenced the mitogenomes of P. fasciatus jiulongjiangensis and P. myersi and downloaded the mitogenomes of nine other Pseudogastromyzon fish on GenBank to conduct a detailed comparative analysis of their phylogenetic relationships and evolutionary history. The findings revealed a conservation in both gene composition and gene order. Except for the trnS1 gene lacking dihydrouracil arms, the other 21 tRNAs showed the typical clover-leaf secondary structure. According to the Delta RSCU method, we identified the seven most abundant optimal codons: CUA, GUA, CCA, CAA, GAA, AGC, and GGC. The construction of maximum parsimony, maximum likelihood, and Bayes trees yielded congruent topologies, and the 11 Pseudogastromyzon species were clustered into two major clusters. Among them, one of which was composed of P. fangi, P. changtingensis changtingensis, and P. changtingensis tungpeiensis, while the remaining eight species formed another cluster, further subdivided into five smaller clusters. Distinct clusters formed between P. fasciatus jiulongjiangensis and P. meihuashanensis, P. cheni and P. peristictus, and P. laticeps and P. lianjiangensis, and the remaining two species were clustered separately, thereby enhancing our understanding of them. Furthermore, our analysis results of divergence times revealed that these 11 Pseudogasteromyzon species underwent rapid differentiation in the Pleistocene epochs. Overall, our study sheds light on the phylogenetic relationship and evolutionary history of Pseudogasteromyzon species, providing a necessary knowledge foundation for further understanding the intricacies of an ecosystem health assessment.