DNA barcoding the native flowering plants and conifers of Wales.

DNA barcoding the native flowering plants and conifers of Wales.

We 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 nati...

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Autores principales: Natasha 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
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Lenguaje:EN
Publicado: Public Library of Science (PLoS) 2012
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Science
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Acceso en línea:https://doaj.org/article/207b3391e21049a3bddb94d64c196cbd
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spelling oai:doaj.org-article:207b3391e21049a3bddb94d64c196cbd2021-11-18T07:16:14ZDNA barcoding the native flowering plants and conifers of Wales.1932-620310.1371/journal.pone.0037945https://doaj.org/article/207b3391e21049a3bddb94d64c196cbd2012-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/22701588/pdf/?tool=EBIhttps://doaj.org/toc/1932-6203We 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.Natasha de VereTim C G RichCol R FordSarah A TrinderCharlotte LongChris W MooreDanielle SatterthwaiteHelena DaviesJoel AllainguillaumeSandra RoncaTatiana TatarinovaHannah GarbettKevin WalkerMike J WilkinsonPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 7, Iss 6, p e37945 (2012)
institution DOAJ
collection DOAJ
language EN
topic Medicine
R
Science
Q
spellingShingle Medicine
R
Science
Q
Natasha 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
DNA barcoding the native flowering plants and conifers of Wales.
description We 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.
format article
author Natasha 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
author_facet Natasha 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
author_sort Natasha de Vere
title DNA barcoding the native flowering plants and conifers of Wales.
title_short DNA barcoding the native flowering plants and conifers of Wales.
title_full DNA barcoding the native flowering plants and conifers of Wales.
title_fullStr DNA barcoding the native flowering plants and conifers of Wales.
title_full_unstemmed DNA barcoding the native flowering plants and conifers of Wales.
title_sort dna barcoding the native flowering plants and conifers of wales.
publisher Public Library of Science (PLoS)
publishDate 2012
url https://doaj.org/article/207b3391e21049a3bddb94d64c196cbd
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