Defining the species complex of the legume pod borer, Maruca vitrata (Lepidoptera: Crambidae), by comparative mitochondrial phylogenomics

Maruca vitrata is a pan-tropical species of Lepidoptera that is comprised of two unique strains that respectively inhabit the American continents (New World strain), and regions spanning from Africa through Southeast Asia, and Northern Australia (Old World strain). In this study, we present the complete mitochondrial genome sequence of the legume pod borer, Maruca vitrata (Lepidoptera: Crambidae) from the New World, assembled de novo from whole genome shotgun sequence data generated on an Illumina HiSeq 2000. Phylogenomic comparisons were made to other previously published mitochondrial genome sequences from crambid moths including the Old World strain of M. vitrata. The 15, 385 bp M. vitrata (New World) sequence has a 80.7% A+T content, and encodes the 13 protein-coding, 2 ribosomal RNA, and 22 transfer RNA genes in the typical orientation and arrangement of lepidopteran mitochondrial DNAs. Sequence variation between M. vitrata New World and Old World strains show an excess of synonymous substitution as a result of purifying selection, and suggest that their divergence occurred ~1.87 mya. The phylogenetic relationships constructed based on amino acid sequences of the 13 protein coding genes also supports the previously defined relationships among species of Lepidoptera. The mitochondrial genome of M. vitrata (New World strain) shares features common to those of other Crambid species, and provides quantitative estimation of divergence from the Old World strain. Furthermore, the de novo assembly of this mitochondrial genome from Next Generation Sequencing (NGS) reads represents a readily available tool for the generation of data for similar phylogenomic studies.