Higher DNA insert fragment sizes improve mitogenomic assemblies from metagenomic pyrosequencing datasets: an example using Limenitidinae butterflies (Lepidoptera, Nymphalidae)

Abstract

A large number of diverse mitogenomic sequences can be obtained more easily and affordably via mitochondrial metagenomics, which generates high-throughput sequences directly from sheared DNA extractions and assembles mitogenomic sequences using a few bioinformatic processing steps. However, following de novo assembly analysis, the optimal DNA fragment insert size is unclear. In this study, four extracted Limenitidinae butterfly DNA samples were sonically fragmented, and two fragment size ranges (200–400 and 400–600 bp) of each sample were tagged with different barcodes, producing pyrosequencing datasets. The results show that the datasets generated from longer DNA insert fragments result in better coverage and more complete mitogenomic sequences, and the phylogenetic analysis shows high support at nodes, revealing that Athyma butterflies do not represent a monophyletic group. Therefore, we recommend using longer insert DNA fragment sizes to generate high-throughput datasets for obtaining complete mitogenomic sequences which can improve phylogenetic studies.