Intraspecific variations on mitochondrial genomes of Aphis glycines (Hemiptera: Aphididae) using mitogenomes from the publicly available next-generation sequencing data

Abstract

Aphis glycines Matsumura, 1917 is a significant agricultural pest worldwide, responsible for the damages to soybeans. In this study, we have assembled three mitogenomes of A. glycines based on the public next-generation sequencing raw reads generated for the whole genome project. Phylogenetic analysis revealed that one of the A. glycines mitogenomes (partial genome; KT889380) was misidentified. Intraspecific variations identified from four aphid species, Aphis glycine, Aphis gossypii, Aphis craccivora, and Myzus pericae mitogenomes exhibited that A. glycines mitogenomes contained a small number of single nucleotide polymorphisms (SNPs) but a large coverage of insertions and deletions (INDELs). In addition, nad2 and nad3 of the A. glycines mitogenomes presented the largest number of SNPs among genes. Various structural variations of transfer RNAs in the three species were investigated. Nucleotide diversity analysis of each gene displayed the same trend between Aphis and Aphididae mitogenomes. Identification and comparison of simple sequence repeats (SSRs) from A. glycines mitogenomes showed that meaningful variations of SSRs were found in the repeat region between nad3 and nad5. Consequently, the observed intraspecific variation within Aphididae species, including A. glycine, can be leveraged to develop molecular markers that facilitate the distinction of populations within species.