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Rice leaffolders are important pests on rice in Asia, Oceania, and Africa, causing serious loss to rice production. There are two main rice leaffolders in China, namely Cnaphalocrocis medinalis (Guenée) and C. exigua (Butler) with the former having the ability of long-distance migration. To reveal the differences in the mitochondrial genomes (mitogenome) between them, we compared the completed mitogenome of C. exigua with three C. medinalis individuals. Although phylogenetic analysis based on the mitogenomic data strongly supported the close relationship between these two species, many differences were still being revealed. The results showed that the mitogenome of C. exigua was shorter in length (15,262 bp) and slight lower in AT content than that of C. medinalis. Except for the different start codons of nad3 and nad6 gene, we also found the cox1 gene had a typical start codon ‘ATG’ which suggested that the starting position of this gene must be reconsidered in the entire superfamily Pyraloidea. All tRNAs have a typical clover-leaf structure, except for the dihydrouridine (DHU) stem losing of trnS1, which has the atypical anticondon ‘TCT’ instead of ‘GCT’ in C. medinalis and most Pyraloidea species. Two intergenic regions (between trnY and cox1, nad3 and trnA) featured by AT repeats were only found in C. medinalis and even rarely appeared in reported Pyraloidea species. Furthermore, regardless of interspecific comparison or intraspecific comparison of these two species, protein coding genes, especially the atp8 genes, had quite different evolutionary rates.

Comparative Mitochondrial Analysis of Cnaphalocrocis exigua (Lepidoptera: Crambidae) and Its Close Relative C. medinalis