DNA barcoding the native flowering plants and conifers of Wales

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dc.contributor.authorde Vere, N.
dc.contributor.authorRich, T.
dc.contributor.authorFord, C.
dc.contributor.authorTrinder, S.
dc.contributor.authorLong, C.
dc.contributor.authorMoore, C.
dc.contributor.authorSatterthwaite, D.
dc.contributor.authorDavies, H.
dc.contributor.authorAllainguillaume, J.
dc.contributor.authorRonca, S.
dc.contributor.authorTatarinova, T.
dc.contributor.authorGarbett, H.
dc.contributor.authorWalker, K.
dc.contributor.authorWilkinson, M.
dc.contributor.editorSteinke, D.
dc.date.issued2012
dc.description.abstractWe present the first national DNA barcode resource that covers the native flowering plants and conifers for the nation of Wales (1143 species). Using the plant DNA barcode markers rbcL and matK, we have assembled 97.7% coverage for rbcL, 90.2% for matK, and a dual-locus barcode for 89.7% of the native Welsh flora. We have sampled multiple individuals for each species, resulting in 3304 rbcL and 2419 matK sequences. The majority of our samples (85%) are from DNA extracted from herbarium specimens. Recoverability of DNA barcodes is lower using herbarium specimens, compared to freshly collected material, mostly due to lower amplification success, but this is balanced by the increased efficiency of sampling species that have already been collected, identified, and verified by taxonomic experts. The effectiveness of the DNA barcodes for identification (level of discrimination) is assessed using four approaches: the presence of a barcode gap (using pairwise and multiple alignments), formation of monophyletic groups using Neighbour-Joining trees, and sequence similarity in BLASTn searches. These approaches yield similar results, providing relative discrimination levels of 69.4 to 74.9% of all species and 98.6 to 99.8% of genera using both markers. Species discrimination can be further improved using spatially explicit sampling. Mean species discrimination using barcode gap analysis (with a multiple alignment) is 81.6% within 10×10 km squares and 93.3% for 2×2 km squares. Our database of DNA barcodes for Welsh native flowering plants and conifers represents the most complete coverage of any national flora, and offers a valuable platform for a wide range of applications that require accurate species identification.
dc.description.statementofresponsibilityNatasha de Vere, Tim C. G. Rich, Col R. Ford, Sarah A. Trinder, Charlotte Long, Chris W. Moore, Danielle Satterthwaite, Helena Davies, Joel Allainguillaume, Sandra Ronca, Tatiana Tatarinova, Hannah Garbett, Kevin Walker, Mike J. Wilkinson
dc.identifier.citationPLoS ONE, 2012; 7(6):1-12
dc.identifier.doi10.1371/journal.pone.0037945
dc.identifier.issn1932-6203
dc.identifier.issn1932-6203
dc.identifier.urihttp://hdl.handle.net/2440/84872
dc.language.isoen
dc.publisherPUBLIC LIBRARY SCIENCE
dc.rights© 2012 de Vere et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
dc.source.urihttps://doi.org/10.1371/journal.pone.0037945
dc.subjectRibulose-Bisphosphate Carboxylase
dc.subjectCluster Analysis
dc.subjectSequence Alignment
dc.subjectSequence Analysis, DNA
dc.subjectComputational Biology
dc.subjectDemography
dc.subjectPhylogeny
dc.subjectSpecies Specificity
dc.subjectBase Sequence
dc.subjectMolecular Sequence Data
dc.subjectDatabases, Genetic
dc.subjectWales
dc.subjectDNA Barcoding, Taxonomic
dc.subjectMagnoliopsida
dc.subjectTracheophyta
dc.titleDNA barcoding the native flowering plants and conifers of Wales
dc.typeJournal article
pubs.publication-statusPublished

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