Comparative Analysis of Mitogenomes of Chironomus (Diptera: Chironomidae)

SIMPLE SUMMARY: Mitochondrial genomes (mitogenomes) have been widely used for studying the taxonomy and phylogeny of insects. Chironomids are important bioindicators for monitoring and assessing the health of freshwater ecosystems. However, only a few complete mitogenomes of Chironomus species have been reported till now. In this study, the whole mitogenome sequences of 12 Chironomus species and one Microchironomus species are reported for the first time. Coupled with published mitogenomes, the nucleotide composition, codon usage, PCG selection pressure, and heterogeneity of the mitogenomes of 15 Chironomus species were analyzed. The phylogenetic relationships of Chironomus based on mitogenomes were reconstructed. The result showed that the mitogenomes of Chironomus species were conservative in respect of nucleotide composition and gene order. Our study enriches the library of mitogenomes of chironomids and provides a valuable resource for understanding the evolutionary history of Chironomus. ABSTRACT: (1) Background: Chironomids are biological indicators, playing an important role in monitoring and assessing the changes in water ecosystems. Mitochondrial genomes have been widely applied as a molecular marker to analyze the taxonomy and phylogeny of insects. However, knowledge of the mitogenomes of Chironomus species is scarce at present, which limits our understanding of the evolutionary relationships among Chironomus. (2) Methods: In our study, the mitogenomes and their basic structure of 12 Chironomus species and one Microchironomus species were newly sequenced. Combined with reported mitogenomes, a total of 15 mitogenomes of Chironomus were selected for a comparative mitogenomic analysis and phylogenetic reconstruction of Chironomus. (3) Results: Each mitogenome of the Chironomus species has the typical 37 genes and a control region. The basic structure of the whole mitogenomes of Chironomus species is relatively conservative, and the genetic arrangements stay the same as the ancestral mitogenome. (4) Conclusions: Our study enriches the library of mitogenomes of chironomids and provides a valuable resource for understanding the evolutionary history of Chironomus.