Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2021 Oct;99(4):1446-1454.
doi: 10.1111/jfb.14852. Epub 2021 Jul 28.

Meta-Fish-Lib: A generalised, dynamic DNA reference library pipeline for metabarcoding of fishes

Rupert A Collins  1 , Giulia Trauzzi  1   2 , Katherine M Maltby  3 , Thomas I Gibson  4 , Frances C Ratcliffe  5 , Jane Hallam  6 , Sophie Rainbird  7 , James Maclaine  8 , Peter A Henderson  9 , David W Sims  7   10 , Stefano Mariani  11   12 , Martin J Genner  1
Affiliations

Meta-Fish-Lib: A generalised, dynamic DNA reference library pipeline for metabarcoding of fishes

Rupert A Collins et al. J Fish Biol. 2021 Oct.

Abstract

The accuracy and reliability of DNA metabarcoding analyses depend on the breadth and quality of the reference libraries that underpin them. However, there are limited options available to obtain and curate the huge volumes of sequence data that are available on public repositories such as NCBI and BOLD. Here, we provide a pipeline to download, clean and annotate mitochondrial DNA sequence data for a given list of fish species. Features of this pipeline include (a) support for multiple metabarcode markers; (b) searches on species synonyms and taxonomic name validation; (c) phylogeny assisted quality control for identification and removal of misannotated sequences; (d) automatically generated coverage reports for each new GenBank release update; and (e) citable, versioned DOIs. As an example we provide a ready-to-use curated reference library for the marine and freshwater fishes of the U.K. To augment this reference library for environmental DNA metabarcoding specifically, we generated 241 new MiFish-12S sequences for 88 U.K. marine species, and make available new primer sets useful for sequencing these. This brings the coverage of common U.K. species for the MiFish-12S fragment to 93%, opening new avenues for scaling up fish metabarcoding across wide spatial gradients. The Meta-Fish-Lib reference library and pipeline is hosted at https://github.com/genner-lab/meta-fish-lib.

Keywords: 12S; COI; eDNA; environmental DNA; metabarcoding; reference library.

PubMed Disclaimer

References

REFERENCES

    1. Arranz, V., Pearman, W. S., Aguirre, J. D., & Liggins, L. (2020). MARES, a replicable pipeline and curated reference database for marine eukaryote metabarcoding. Scientific Data, 7, 209. https://doi.org/10.1038/s41597-020-0549-9.
    1. Axtner, J., Crampton-Platt, A., Hörig, L. A., Mohamed, A., Xu, C. C. Y., Yu, D. W., & Wilting, A. (2019). An efficient and robust laboratory workflow and tetrapod database for larger scale environmental DNA studies. GigaScience, 8, giz029. https://doi.org/10.1093/gigascience/giz029.
    1. Bengtsson-Palme, J., Richardson, R. T., Meola, M., Wurzbacher, C., Tremblay, É. D., Thorell, K., … Nilsson, R. H. (2018). Metaxa2 database builder: enabling taxonomic identification from metagenomic or metabarcoding data using any genetic marker. Bioinformatics, 34, 4027-4033. https://doi.org/10.1093/bioinformatics/bty482.
    1. Bergsten, J., Bilton, D. T., Fujisawa, T., Elliott, M., Monaghan, M. T., Balke, M., … Vogler, A. P. (2012). The effect of geographical scale of sampling on DNA barcoding. Systematic Biology, 61, 851-869. https://doi.org/10.1093/sysbio/sys037.
    1. Berry, T. E., Osterrieder, S. K., Murray, D. C., Coghlan, M. L., Richardson, A. J., Grealy, A. K., … Bunce, M. (2017). Metabarcoding for diet analysis and biodiversity: a case study using the endangered Australian sea lion (Neophoca cinerea). Ecology and Evolution, 7, 5435-5453. https://doi.org/10.1002/ece3.3123.

Substances

LinkOut - more resources