Meta‐Fish‐Lib : a generalised, dynamic DNA reference library pipeline for metabarcoding of fishes

Collins, RA ORCID: https://orcid.org/0000-0002-9135-1169, Trauzzi, G, Maltby, KM, Gibson, TI, Ratcliffe, FC, Hallam, J, Rainbird, S, Maclaine, J, Henderson, PA, Sims, DW, Mariani, S ORCID: https://orcid.org/0000-0002-5329-0553 and Genner, MJ 2021, 'Meta‐Fish‐Lib : a generalised, dynamic DNA reference library pipeline for metabarcoding of fishes' , Journal of Fish Biology, 99 (4) , pp. 1446-1454.

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Access Information: This is the peer reviewed version of the following article: Collins, R.A., Trauzzi, G., Maltby, K.M., Gibson, T.I., Ratcliffe, F.C., Hallam, J., Rainbird, S., Maclaine, J., Henderson, P.A., Sims, D.W., Mariani, S. and Genner, M.J. (2021), Meta-Fish-Lib: A generalised, dynamic DNA reference library pipeline for metabarcoding of fishes. J Fish Biol., which has been published in final form at https://doi.org/10.1111/jfb.14852. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Use of Self-Archived Versions.

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 includes: (i) support for multiple metabarcode markers; (ii) searches on species synonyms and taxonomic name validation; (iii) phylogeny assisted quality control for identification and removal of misannotated sequences; (iv) automatically generated coverage reports for each new GenBank release update; and (v) citable, versioned DOIs. As an example we provide a ready-to-use curated reference library for the marine and freshwater fishes of the United Kingdom. To augment this reference library for environmental DNA metabarcoding specifically, we generated 241 new MiFish-12S sequences for 88 UK marine species, and make available new primer sets useful for sequencing these. This brings the coverage of common UK 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.

Item Type: Article
Additional Information: ** Article version: VoR ** From Crossref journal articles via Jisc Publications Router **Journal IDs: pissn 0022-1112; eissn 1095-8649 **History: issued 16-07-2021; published_online 16-07-2021 **License for this article: starting on 16-07-2021, , http://onlinelibrary.wiley.com/termsAndConditions#vor
Schools: Schools > School of Environment and Life Sciences
Journal or Publication Title: Journal of Fish Biology
Publisher: Wiley
ISSN: 0022-1112
Related URLs:
Funders: Natural Environment Research Council (NERC)
SWORD Depositor: Publications Router
Depositing User: Publications Router
Date Deposited: 26 Jul 2021 11:12
Last Modified: 19 Oct 2021 08:00
URI: http://usir.salford.ac.uk/id/eprint/61292

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