Characterization of the Complete Mitochondrial Genomes from Two Nitidulid Pests with Phylogenetic Implications

SIMPLE SUMMARY: Nitidulidae is the most diverse group of Cucujoidea. In this study, we sequence and analyze two mitochondrial genomes of the nitidulid species, Xenostrongylus variegatus and Epuraea sp. Both genomes are highly conserved in their size, base content, codon usage, and secondary structure of tRNAs. Phylogenetic analyses of Nitidulidae and related families in Cucujoidea are carried out based on three outgroups and fourteen ingroups. The results of the Bayesian inference and maximum likelihood methods support the monophyly of Nitidulidae and the sister-group relationship of Kateretidae + (Monotomidae + Nitidulidae). ABSTRACT: The complete mitochondrial genomes of Xenostrongylus variegatus and Epuraea sp. were sequenced and analyzed. The total genome lengths are 17,657 and 16,641 bp, with an A+T content of 77.2% and 76.4%, respectively. Each mitochondrial genome consists of 37 coding genes and a non-coding (AT-rich) region. All protein-coding genes (PCGs) start with the standard start codon, ATN, and end with complete stop codons, TAA and TAG, or an incomplete stop codon, T. All tRNAs can be folded into the typical clover-leaf secondary structure, with the exception of trnS1 in both species with a reduced dihydrouridine (DHU) arm. The AT-rich region has tandem repeats differing in both number and length. Genetic distance and Ka/Ks analyses show that nad6 has a higher variability and more rapid evolutionary rate than other PCGs. Both maximum likelihood and Bayesian inference phylogenetic analyses based on 13 PCGs and 2 ribosome DNAs (rDNAs) agree with the previous phylogenies in supporting the Nitidulidae monophyly and the sister-group relationship of Kateretidae + (Monotomidae + Nitidulidae).