Comparative Mitogenomes and Phylogenetic Analyses of Coccinellidae (Coleoptera: Coccinelloidea)

Coccinellidae (ladybird beetles) comprises around 6900 described species with a worldwide distribution and exhibits a broad trophic diversity. Complete mitochondrial genomes (mitogenomes) are valuable resources in many research fields, such as genomics, population genetics, molecular evolution, and phylogenetics. Here we sequenced and report the complete mitogenome of Calvia chinensis, Micraspis discolor, Harmonia eucharis, and Oenopia kirbyi. By comparing with the 36 complete mitogenomes published in GenBank, we found that the long noncoding region (LNCR) between trnI and trnQ is present in the mitogenome of Chilocorini and Coccinellini, and the size of LNCR is positively correlated with their mitogenome size. The variable number tandem repeat (VNTR) was detected in the LNCR of Calvia chinensis and Oenopia kirbyi, indicating that the LNCR may be associated with the transcriptional regulation of the mitogenome. Heterogeneity in the base composition was encountered among the mitogenomes in Coccinellidae, especially in Noviini and some species of Epilachnini and Coccinellini, which may lead to unstable phylogenetic topologies. Phylogenetic relationships have been reconstructed by maximum likelihood and Bayesian inferences based on two mitogenomic datasets, PCG_rRNA (all 13 PCGs and two rRNAs) and PCG12_rRNA (all 13 PCGs with the third codon position excluded and two rRNAs). Our results are close to the subfamily and tribe classification system reported in previous studies and suggest the maximum likelihood analysis based on the PCG12_rRNA dataset is more sensitive in avoiding the false grouping of unrelated taxa with similar base composition in the reconstruction of the phylogeny.