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MitoGeneExtractor: Efficient extraction of mitochondrial genes from next generation sequencing libraries
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  • Marie Brasseur,
  • Jonas Astrin,
  • Matthias Geiger,
  • Christoph Mayer
Marie Brasseur
Leibniz Institute for the Analysis of Biodiversity Change

Corresponding Author:[email protected]

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Jonas Astrin
Zoological Research Museum Alexander Koenig
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Matthias Geiger
Zoologisches Forschungsinstitut und Museum Alexander Koenig
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Christoph Mayer
Zoological Research Museum Alexander Koenig
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Abstract

Mitochondrial DNA sequences (mtDNA) are often found as byproduct in hybrid enrichment data sets originally created to capture anchored hybrid enrichment (AHE) or ultra-conserved element (UCE) nuclear loci. The mtDNA sequences in these data sets are currently rarely used, even though mitochondrial genes such as COI, ND5, CytB, and 16S are of general interest and often not yet known and deposited in public databases. We developed MitoGeneExtractor to extract mitochondrial genes of interest from genomic libraries. Gene sequences are reconstructed through multiple sequence alignments of sequencing reads to an amino acid reference. We applied MitoGeneExtractor to recently published data created for UCE enrichment and were able to extract complete or nearly complete COI and ND5 sequences for a large proportion of the sequencing libraries. MitoGeneExtractor can be used to extract mitochondrial protein coding genes from a wide range of next generation sequencing data sets.
23 Mar 2022Submitted to Molecular Ecology Resources
04 Apr 2022Submission Checks Completed
04 Apr 2022Assigned to Editor
04 Apr 2022Reviewer(s) Assigned
26 May 2022Review(s) Completed, Editorial Evaluation Pending
09 Jun 2022Editorial Decision: Revise Minor
30 Jul 2022Review(s) Completed, Editorial Evaluation Pending
30 Jul 20221st Revision Received