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

Rupert A Collins, Giulia Trauzzi, Martin J Genner, et al.

Research output: Contribution to journalArticle (Academic Journal)peer-review

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.
Original languageEnglish
Number of pages9
JournalJournal of Fish Biology
Early online date16 Jul 2021
DOIs
Publication statusPublished - 28 Jul 2021

Bibliographical note

Funding Information:
This work was funded by the Natural Environment Research Council grant NE/N005937/1 (project SeaDNA). Thomas Gibson would like to acknowledge the work of Jim Drewery and the other scientists and crew of the (Marine Scotland Science) in collecting his tissue samples, although they were not sequenced in time to be included in this publication. MRV Scotia

Publisher Copyright:
© 2021 Fisheries Society of the British Isles.

Keywords

  • 12S, COI, eDNA
  • environmental DNA
  • metabarcoding
  • reference library

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