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In this study, we presented the complete mitochondrial genome of a tropical midge Chironomus kiiensis Tokunaga by Illumina sequencing technology. The complete mitogenome of C. kiiensis is 15,710 bp in length, including 13 protein-coding genes (PCGs), two ribosomal RNAs and 22 tRNAs. The overall nucleotide composition is A: 39.3%, T: 37.6%, C: 13.6%, and G: 9.5%. Most PCGs use ATN as the start codon excluding COX1 (TTG), and most PCGs use TAA as the stop codon excluding ND4 (TAG). Gene order of the C. kiiensis mitogenome is identical to those of other Chironomidae mitogenomes. Phylogenetic analysis based on the mitogenomic PCGs indicate that Chironomus is a sister clade to Polypedilum .

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