New Mitogenomes of the Polypedilum Generic Complex (Diptera: Chironomidae): Characterization and Phylogenetic Implications

SIMPLE SUMMARY: Many species from the Polypedilum generic complex are renowned for their roles in aquatic ecosystems. This genus complex, as one of the most species-rich groups, has been persistently contentious. The current lack of sequence data for the Polypedilum complex limits our comprehension of their species evolution. Here, 14 mitogenomes of the Polypedilum generic complex were sequenced. Combined with three recently published mitochondrial genomes, we analyzed the features of the mitogenomes among genera. Furthermore, the phylogenetic analysis among genera within the Polypedilum complex showed that the Endochironomus + Synendotendipes is the sister group of Phaenopsectra + Sergentia. Our study provides a vital foundation for further study on the evolutionary biology of Chironomidae. ABSTRACT: Mitochondrial genomics, as a useful marker for phylogenetics and systematics of organisms, are important for molecular biology studies. The phylogenetic relationships of the Polypedilum generic complex remains controversial, due to lack taxonomy and molecular information. In this study, we newly sequenced mitogenomes of 14 species of the Polypedilum generic complex. Coupled with three recently published sequences, we analyzed the nucleotide composition, sequence length, and evolutionary rate of this generic complex. The control region showed the highest AT content. The evolution rate of protein coding genes was as follows: ATP8 > ND6 > ND5 > ND3 > ND2 > ND4L > ND4 > COX1 > ND1 > CYTB > APT6 > COX2 > COX3. We reconstructed the phylogenetic relationships among the genera within the Polypedilum generic complex based on 19 mitochondrial genomes (seventeen ingroups and two outgroups), using Bayesian Inference (BI) and Maximum Likelihood (ML) methods for all databases. Phylogenetic analysis of 19 mitochondrial genomes demonstrated that the Endochironomus + Synendotendipes was sister to Phaenopsectra + Sergentia.