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

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

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.

12S, COI, eDNA, environmental DNA, metabarcoding, reference library
0022-1112
1446-1454
Collins, Rupert A.
57855a75-6d3c-452a-8c82-50a254bda26c
Trauzzi, Giulia
975d7a9f-f947-4b9c-bd34-c6a490234400
Maltby, Katherine M.
63f71c5d-bc3d-4bca-aeb3-458669f1e3d6
Gibson, Thomas I.
25d89fdf-37ce-4c96-a667-5551a9d25540
Ratcliffe, Frances C.
c7d44606-cf88-4e51-a367-343b239926e7
Hallam, Jane
5c2f704d-645b-4893-bf3f-620c5b34bcb3
Rainbird, Sophie
9b0d0850-750b-485f-bab9-c862bc5d86ca
Maclaine, James
e5bb666d-65df-4e51-a7d3-1b2327f6f3c0
Henderson, Peter A.
93255fbf-3804-49a0-8041-6554be3c2478
Sims, David W.
7234b444-25e2-4bd5-8348-a1c142d0cf81
Mariani, Stefano
99f7ad81-4ffa-4c58-ba16-62cc1cd101a6
Genner, Martin J.
90547c65-c194-4c93-8ea4-b8523acef1a6
Collins, Rupert A.
57855a75-6d3c-452a-8c82-50a254bda26c
Trauzzi, Giulia
975d7a9f-f947-4b9c-bd34-c6a490234400
Maltby, Katherine M.
63f71c5d-bc3d-4bca-aeb3-458669f1e3d6
Gibson, Thomas I.
25d89fdf-37ce-4c96-a667-5551a9d25540
Ratcliffe, Frances C.
c7d44606-cf88-4e51-a367-343b239926e7
Hallam, Jane
5c2f704d-645b-4893-bf3f-620c5b34bcb3
Rainbird, Sophie
9b0d0850-750b-485f-bab9-c862bc5d86ca
Maclaine, James
e5bb666d-65df-4e51-a7d3-1b2327f6f3c0
Henderson, Peter A.
93255fbf-3804-49a0-8041-6554be3c2478
Sims, David W.
7234b444-25e2-4bd5-8348-a1c142d0cf81
Mariani, Stefano
99f7ad81-4ffa-4c58-ba16-62cc1cd101a6
Genner, Martin J.
90547c65-c194-4c93-8ea4-b8523acef1a6

Collins, Rupert A., Trauzzi, Giulia, Maltby, Katherine M., Gibson, Thomas I., Ratcliffe, Frances C., Hallam, Jane, Rainbird, Sophie, Maclaine, James, Henderson, Peter A., Sims, David W., Mariani, Stefano and Genner, Martin J. (2021) Meta-Fish-Lib: a generalised, dynamic DNA reference library pipeline for metabarcoding of fishes. Journal of Fish Biology, 99 (4), 1446-1454. (doi:10.1111/jfb.14852).

Record type: Article

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.

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More information

Accepted/In Press date: 12 July 2021
e-pub ahead of print date: 16 July 2021
Published date: 28 July 2021
Additional Information: 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
Keywords: 12S, COI, eDNA, environmental DNA, metabarcoding, reference library

Identifiers

Local EPrints ID: 485392
URI: http://eprints.soton.ac.uk/id/eprint/485392
ISSN: 0022-1112
PURE UUID: b92c8d49-fd36-45df-b882-465aae6be607
ORCID for David W. Sims: ORCID iD orcid.org/0000-0002-0916-7363

Catalogue record

Date deposited: 05 Dec 2023 17:51
Last modified: 19 Jun 2024 01:45

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Contributors

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

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