Mitogenome metadata: current trends and proposed standards

Abstract

Mitogenome metadata are descriptive terms about the sequence, and its specimen description that allow both to be digitally discoverable and interoperable. Here, we review a sampling of mitogenome metadata published in the journal Mitochondrial DNA between 2005 and 2014. Specifically, we have focused on a subset of metadata fields that are available for GenBank records, and specified by the Genomics Standards Consortium (GSC) and other biodiversity metadata standards; and we assessed their presence across three main categories: collection, biological and taxonomic information. To do this we reviewed 146 mitogenome manuscripts, and their associated GenBank records, and scored them for 13 metadata fields. We also explored the potential for mitogenome misidentification using their sequence diversity, and taxonomic metadata on the Barcode of Life Datasystems (BOLD). For this, we focused on all Lepidoptera and Perciformes mitogenomes included in the review, along with additional mitogenome sequence data mined from Genbank. Overall, we found that none of 146 mitogenome projects provided all the metadata we looked for; and only 17 projects provided at least one category of metadata across the three main categories. Comparisons using mtDNA sequences from BOLD, suggest that some mitogenomes may be misidentified. Lastly, we appreciate the research potential of mitogenomes announced through this journal; and we conclude with a suggestion of 13 metadata fields, available on GenBank, that if provided in a mitogenomes’s GenBank record, would increase their research value.

• Reference sequence
• reproducibility
• reproducible research
• specimen metadata
• voucher

Acknowledgements

We wish to thank James Robertson from the centre for Biodiversity Genomics for suggesting that Lepidoptera would make an interesting specimen identification case study. We would also like to thank Scott Federhen, head of the NCBI taxonomy group, for clarifying the changes made to the Perciformes taxonomy. We would like to thank Greg Singer for querying mitogenome sequence data in BOLD for an earlier version of this manuscript. Finally, we wish to thank the Hanner Lab graduate students for their valuable comments, on this work as it progressed.

Declaration of interest

The authors declare no conflict of interest and are entirely responsible for the writing of this paper. The authors received no specific funding for writing this manuscript.

Supplementary material available online.

Supplementary Tables 1 and 2 & Figures 1 and 2.