What are the best practices for curating eDNA custom barcode reference libraries? A case study using Australian subterranean fauna

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dc.contributor.authorGuzik, M.T.
dc.contributor.authorStringer, D.N.
dc.contributor.authorThornhill, J.
dc.contributor.authorCoates, P.J.
dc.contributor.authorvan der Heyde, M.
dc.contributor.authorHillyer, M.J.
dc.contributor.authorWhite, N.E.
dc.contributor.authorSaccò, M.
dc.contributor.authorBeasley-Hall, P.G.
dc.contributor.authorHumphreys, W.F.
dc.contributor.authorHarvey, M.S.
dc.contributor.authorHuey, J.A.
dc.contributor.authorWilson, N.G.
dc.contributor.authorAlexander, J.
dc.contributor.authorHumphreys, G.
dc.contributor.authorKing, R.A.
dc.contributor.authorCooper, S.J.B.
dc.contributor.authorPinder, A.
dc.contributor.authorPerina, G.
dc.contributor.authorHosie, A.M.
dc.contributor.authoret al.
dc.date.issued2025
dc.description.abstractIdentification of species for environmental assessment and monitoring is essential for understanding anthropogenic impacts on biodiversity, but for subterranean fauna this task is frequently difficult and time consuming. The implementation of environmental DNA (eDNA) metabarcoding for biodiversity discovery and assessment offers considerable promise for improving the speed, accuracy, and efficiency of species detection in ecosystems both above and below the ground. Importantly, for a better understanding of the biodiversity and ecology of organisms detected using eDNA, a custom library of known reference sequences with associated correct taxonomic metadata—i.e. a barcode reference library (BRL)—is required. Yet, minimal guidance is currently available on how an effective (i.e. shareable, multisequence, that permits metadata, and has a unified nomenclature) and accurate (i.e. verified) custom BRL can be achieved. Here, we present a detailed roadmap for curation of a BRL for subterranean fauna. To do this, we curated a custom sequence database of subterranean fauna at an environmentally sensitive location, for four gene loci useful for eDNA metabarcoding, worked toward addressing the disparate nomenclature of subterranean fauna, and summarized a best practice workflow for curation of a custom BRL that is broadly applicable.
dc.description.statementofresponsibilityMichelle T. Guzik, Danielle N. Stringer, Jake Thornhill, Peterson J. Coates, Mieke van der Heyde, Mia J. Hillyer, Nicole E. White, Mattia Saccò, Perry G. Beasley-Hall, William F. Humphreys, Mark S. Harvey, Joel A. Huey, Nerida G. Wilson, Jason Alexander, Garth Humphreys, Rachael A. King, Steven J.B. Cooper, Adrian Pinder, Giulia Perina, Andrew M. Hosie, Lisa Kirkendale, Paul Nevill, Andrew D. Austin
dc.identifier.citationBiological Journal of the Linnean Society, 2025; 146(1):blaf053-1-blaf053-12
dc.identifier.doi10.1093/biolinnean/blaf053
dc.identifier.issn0024-4066
dc.identifier.issn1095-8312
dc.identifier.orcidGuzik, M.T. [0000-0002-4947-9353]
dc.identifier.orcidStringer, D.N. [0000-0002-6562-5031]
dc.identifier.orcidBeasley-Hall, P.G. [0000-0002-7360-7933]
dc.identifier.orcidCooper, S.J.B. [0000-0002-7843-8438]
dc.identifier.orcidAustin, A.D. [0000-0002-9602-2276]
dc.identifier.urihttps://hdl.handle.net/2440/148069
dc.language.isoen
dc.publisherOxford University Press
dc.relation.granthttp://purl.org/au-research/grants/arc/LP140100555
dc.rights© The Author(s) 2025. Published by Oxford University Press on behalf of The Linnean Society of London. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
dc.source.urihttps://doi.org/10.1093/biolinnean/blaf053
dc.subjectBiodiversity; taxonomic impediment; biomonitoring; databases
dc.titleWhat are the best practices for curating eDNA custom barcode reference libraries? A case study using Australian subterranean fauna
dc.typeJournal article
pubs.publication-statusPublished

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