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

Rupert A. Collins, Giulia Trauzzi, Katherine M. Maltby, Thomas I. Gibson, Frances Ratcliffe, Jane Hallam, Sophie Rainbird, James Maclaine, Peter A. Henderson, David W. Sims, Stefano Mariani, Martin J. Genner

Journal of Fish Biology, Volume: 99, Issue: 4, Pages: 1446 - 1454

Swansea University Author: Frances Ratcliffe

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DOI (Published version): 10.1111/jfb.14852

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 B...

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Published in: Journal of Fish Biology
ISSN: 0022-1112 1095-8649
Published: Wiley 2021
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URI: https://cronfa.swan.ac.uk/Record/cronfa58438
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first_indexed 2021-10-20T12:53:45Z
last_indexed 2021-10-21T03:26:34Z
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spelling 2021-10-20T13:56:21.3340167 v2 58438 2021-10-20 Meta-Fish-Lib: A generalised, dynamic DNA reference library pipeline for metabarcoding of fishes 613553b7a567deeb0e75d38a2702a5f0 Frances Ratcliffe Frances Ratcliffe true false 2021-10-20 SBI 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. Journal Article Journal of Fish Biology 99 4 1446 1454 Wiley 0022-1112 1095-8649 12S; COI; eDNA; environmental DNA; metabarcoding; reference library 1 10 2021 2021-10-01 10.1111/jfb.14852 Author accepted manuscript: https://research-information.bris.ac.uk/en/publications/meta-fish-lib-a-generalised-dynamic-dna-reference-library-pipelin COLLEGE NANME Biosciences COLLEGE CODE SBI Swansea University 2021-10-20T13:56:21.3340167 2021-10-20T13:50:14.8096407 Faculty of Science and Engineering School of Biosciences, Geography and Physics - Biosciences Rupert A. Collins 1 Giulia Trauzzi 2 Katherine M. Maltby 3 Thomas I. Gibson 4 Frances Ratcliffe 5 Jane Hallam 6 Sophie Rainbird 7 James Maclaine 8 Peter A. Henderson 9 David W. Sims 10 Stefano Mariani 11 Martin J. Genner 12
title Meta-Fish-Lib: A generalised, dynamic DNA reference library pipeline for metabarcoding of fishes
spellingShingle Meta-Fish-Lib: A generalised, dynamic DNA reference library pipeline for metabarcoding of fishes
Frances Ratcliffe
title_short Meta-Fish-Lib: A generalised, dynamic DNA reference library pipeline for metabarcoding of fishes
title_full Meta-Fish-Lib: A generalised, dynamic DNA reference library pipeline for metabarcoding of fishes
title_fullStr Meta-Fish-Lib: A generalised, dynamic DNA reference library pipeline for metabarcoding of fishes
title_full_unstemmed Meta-Fish-Lib: A generalised, dynamic DNA reference library pipeline for metabarcoding of fishes
title_sort Meta-Fish-Lib: A generalised, dynamic DNA reference library pipeline for metabarcoding of fishes
author_id_str_mv 613553b7a567deeb0e75d38a2702a5f0
author_id_fullname_str_mv 613553b7a567deeb0e75d38a2702a5f0_***_Frances Ratcliffe
author Frances Ratcliffe
author2 Rupert A. Collins
Giulia Trauzzi
Katherine M. Maltby
Thomas I. Gibson
Frances Ratcliffe
Jane Hallam
Sophie Rainbird
James Maclaine
Peter A. Henderson
David W. Sims
Stefano Mariani
Martin J. Genner
format Journal article
container_title Journal of Fish Biology
container_volume 99
container_issue 4
container_start_page 1446
publishDate 2021
institution Swansea University
issn 0022-1112
1095-8649
doi_str_mv 10.1111/jfb.14852
publisher Wiley
college_str Faculty of Science and Engineering
hierarchytype
hierarchy_top_id facultyofscienceandengineering
hierarchy_top_title Faculty of Science and Engineering
hierarchy_parent_id facultyofscienceandengineering
hierarchy_parent_title Faculty of Science and Engineering
department_str School of Biosciences, Geography and Physics - Biosciences{{{_:::_}}}Faculty of Science and Engineering{{{_:::_}}}School of Biosciences, Geography and Physics - Biosciences
document_store_str 0
active_str 0
description 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.
published_date 2021-10-01T04:14:58Z
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