Mitochondrial metagenomics and the phylogeny of Ochthebiini: A new batch mitogenomes example

Abstract

Phylogenetic trees are not always recovered with enough support to test particular hypothesis. An increase in the number of gene fragments usually improves support, but traditional PRCs and Sanger sequencing is time consuming, the selection of markers is always problematic, and the costs increase linearly with the number of sequences. An easy, fast, cheap and trustworthy way to increase the amount of sequence, recognised by researchers who started using mitochondrial metagenomics (MMG), is the recovery of batch mitogenomes from a single Next-Generation Sequencing run. We present here a pipeline to perform MMG from a pool of DNA extractions using the Illumina MiSeq Sequencing platform. We recovered ca. 40 multiple complete or partial mitogenomes from a single Illumina run, and combined them with a dataset of Sanger sequences of two mitochondrial and two nuclear markers for 245 species to try to improve the support of a phylogeny of the water beetle tribe Ochthebiini (Coleoptera: Hydraenidae).