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DNA barcoding the native flowering plants and conifers of Wales.

de Vere N, Rich TC, Ford CR, Trinder SA, Long C, Moore CW, Satterthwaite D, Davies H, Allainguillaume J, Ronca S, Tatarinova T, Garbett H, Walker K, Wilkinson MJ - PLoS ONE (2012)

Bottom Line: We have sampled multiple individuals for each species, resulting in 3304 rbcL and 2419 matK sequences.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.

View Article: PubMed Central - PubMed

Affiliation: National Botanic Garden of Wales, Llanarthne, United Kingdom. natasha.devere@gardenofwales.org.uk

ABSTRACT
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.

Show MeSH
Species discrimination for the orders of flowering plants and conifers found within Wales.Species discrimination (%) for rbcL, matK and both combined across the 34 orders of flowering plants and conifers found within the Welsh flora. Discrimination is assessed using three methods; barcode gap using multiple alignments (Barcode gap), monophyletic groups in Neighbour-Joining trees (Tree) and BLASTn searches (BLAST). To allow for comparison across the markers and methods 808 species for which multiple individuals were sequenced for both rbcL and matK were used, but species with single sequences were included as a source of discrimination failure. The number of species per order in the Welsh flora (out of the 808) is shown in brackets next to the order name. Pearson correlation coefficients and associated p-values for the relationship between the number of species per order and % species discrimination success are shown.
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pone-0037945-g004: Species discrimination for the orders of flowering plants and conifers found within Wales.Species discrimination (%) for rbcL, matK and both combined across the 34 orders of flowering plants and conifers found within the Welsh flora. Discrimination is assessed using three methods; barcode gap using multiple alignments (Barcode gap), monophyletic groups in Neighbour-Joining trees (Tree) and BLASTn searches (BLAST). To allow for comparison across the markers and methods 808 species for which multiple individuals were sequenced for both rbcL and matK were used, but species with single sequences were included as a source of discrimination failure. The number of species per order in the Welsh flora (out of the 808) is shown in brackets next to the order name. Pearson correlation coefficients and associated p-values for the relationship between the number of species per order and % species discrimination success are shown.

Mentions: Levels of relative discrimination varied across the orders of flowering plants and conifers (Fig. 4). These were significantly negatively correlated with the number of species DNA barcoded within the order, with Pearson correlation coefficients ranging from −0.40 to −0.51 (p-values 0.018 to 0.002) using the different markers and methods of discrimination. Some orders had higher levels of discrimination than expected given the number of species they contain (Boraginales and Ericales) whilst others had lower levels than expected (Myrtales, Malvales, Malpighiales and Rosales).


DNA barcoding the native flowering plants and conifers of Wales.

de Vere N, Rich TC, Ford CR, Trinder SA, Long C, Moore CW, Satterthwaite D, Davies H, Allainguillaume J, Ronca S, Tatarinova T, Garbett H, Walker K, Wilkinson MJ - PLoS ONE (2012)

Species discrimination for the orders of flowering plants and conifers found within Wales.Species discrimination (%) for rbcL, matK and both combined across the 34 orders of flowering plants and conifers found within the Welsh flora. Discrimination is assessed using three methods; barcode gap using multiple alignments (Barcode gap), monophyletic groups in Neighbour-Joining trees (Tree) and BLASTn searches (BLAST). To allow for comparison across the markers and methods 808 species for which multiple individuals were sequenced for both rbcL and matK were used, but species with single sequences were included as a source of discrimination failure. The number of species per order in the Welsh flora (out of the 808) is shown in brackets next to the order name. Pearson correlation coefficients and associated p-values for the relationship between the number of species per order and % species discrimination success are shown.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3368937&req=5

pone-0037945-g004: Species discrimination for the orders of flowering plants and conifers found within Wales.Species discrimination (%) for rbcL, matK and both combined across the 34 orders of flowering plants and conifers found within the Welsh flora. Discrimination is assessed using three methods; barcode gap using multiple alignments (Barcode gap), monophyletic groups in Neighbour-Joining trees (Tree) and BLASTn searches (BLAST). To allow for comparison across the markers and methods 808 species for which multiple individuals were sequenced for both rbcL and matK were used, but species with single sequences were included as a source of discrimination failure. The number of species per order in the Welsh flora (out of the 808) is shown in brackets next to the order name. Pearson correlation coefficients and associated p-values for the relationship between the number of species per order and % species discrimination success are shown.
Mentions: Levels of relative discrimination varied across the orders of flowering plants and conifers (Fig. 4). These were significantly negatively correlated with the number of species DNA barcoded within the order, with Pearson correlation coefficients ranging from −0.40 to −0.51 (p-values 0.018 to 0.002) using the different markers and methods of discrimination. Some orders had higher levels of discrimination than expected given the number of species they contain (Boraginales and Ericales) whilst others had lower levels than expected (Myrtales, Malvales, Malpighiales and Rosales).

Bottom Line: We have sampled multiple individuals for each species, resulting in 3304 rbcL and 2419 matK sequences.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.

View Article: PubMed Central - PubMed

Affiliation: National Botanic Garden of Wales, Llanarthne, United Kingdom. natasha.devere@gardenofwales.org.uk

ABSTRACT
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.

Show MeSH