MitoFinder: Efficient automated large‐scale extraction of mitogenomic data in target enrichment phylogenomics

Thanks to the development of high-throughput sequencing technologies, target enrichment sequencing of nuclear ultraconserved DNA elements (UCEs) now allows routine inference of phylogenetic relationships from thousands of genomic markers. Recently, it has been shown that mitochondrial DNA (mtDNA) is frequently sequenced alongside the targeted loci in such capture experiments. Despite its broad evolutionary interest, mtDNA is rarely assembled and used in conjunction with nuclear markers in capture-based studies. Here, we developed MitoFinder, a user-friendly bioinformatic pipeline, to efficiently assemble and annotate mitogenomic data from hundreds of UCE libraries. As a case study, we used ants (Formicidae)…

• AN
  Agence Nationale de la Recherche

  Awards: ANR‐10‐LABX‐0004, 10-LABX-25-01, ANR‐10‐LABX‐25‐01, ANR-10-LABX-0004, ANR-10-LABX-25-01, ANR-10
• H2
  Horizon 2020 Framework Programme

  Award: 683257
• HE
  H2020 European Research Council

  Awards: ERC‐2015‐CoG‐683257, ERC-2015-CoG-683257, 683257, ERC-2015-CoG, H2020