Limited Variation in Codon Usage across Mitochondrial Genomes of Non-Biting Midges (Diptera: Chironomidae)

Simple Summary There are thousands of species of non-biting midges. They face various living pressures which may influence their codon usage in mitochondrial genomes. Codon usage analysis has been conducted on only a few species, and the codon usage across Chironomidae is still unclear. In this study, we sequenced a new mitochondrial genome and compared codon usage across as many genera as possible. Limited variation was observed in most genera, except one which presented a weaker codon usage bias. We speculated that most of its mitochondrial genes experienced natural selection. Additionally, three genes, ND1, ND2 and ND3, were found to have experienced natural selection across most genera. To some extent, this work adds to our understanding of the evolution and phylogeny of non-biting midges.Abstract The codon usage patterns of mitochondrial genomes offer insights into the evolutionary and phylogenetic studies of species. Codon usage analysis has been conducted in a few Chironomidae species, and the codon usage patterns in other species remain ambiguous. We aim to reveal the codon usage differences in the mitochondrial genomes across this family. We sequenced the first mitochondrial genome of the genus Conchapelopia and the third mitochondrial genome of the subfamily Tanypodinae. Then, we analyzed its relative synonymous codon usage and effective number of codons with registered mitochondrial genomes from 28 other genera. The results indicated that there was limited variation in codon usage across five subfamilies, Chironominae, Orthocladiinae, Diamesinae, Prodiamesinae and Tanypodinae. While Parochlus steinenii from Podonominae presented a weaker codon bias, P. steinenii possessed the most genes experiencing natural selection. Additionally, ND1, ND2 and ND3 were found to be the most frequently selected genes across all species. Our findings contribute to further understanding the evolutionary and phylogenetic relationships of Chironomidae.