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DNA barcoding the native flowering plants and conifers of Wales

By 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 and Mike J Wilkinson

Abstract

RONO: 00We 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.publishersversionPeer reviewe

Year: 2012
DOI identifier: 10.1371/journal.pone.0037945
OAI identifier: oai:cadair.aber.ac.uk:2160/8110
Journal:

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Citations

  1. (2009). A DNA barcode for land plants. doi
  2. (2011). Choosing and Using a Plant DNA Barcode. PLoS one 6: doi
  3. (2003). Biological identifications through DNA barcodes. doi
  4. (2009). Plant DNA barcodes and a community phylogeny of a tropical forest dynamics plot in Panama. doi
  5. (2008). DNA barcoding the floras of biodiversity hotspots. doi
  6. (2009). Plant DNA barcodes and species resolution in sedges (Carex, doi
  7. (2010). Molecular Species Identification with Rich Floristic Sampling: DNA Barcoding the Pteridophyte Flora of Japan. PLoS one 5: doi
  8. (2010). Identification of medicinal plants in the family Fabaceae using a potential DNA barcode ITS2. doi
  9. (2010). DNA barcoding of the Lemnaceae, a family of aquatic monocots. doi
  10. (2011). Discriminating plant species in a local temperate flora using the rbcL plus matK DNA barcode. doi
  11. (2011). Use of rbcL and trnL-F as a Two-Locus DNA Barcode for Identification of NWEuropean Ferns: An Ecological Perspective. PLoS one 6: doi
  12. (2011). Applying plant DNA barcodes for Rosaceae species identification. doi
  13. (2011). Comparative analysis of a large dataset indicates that internal transcribed spacer (ITS) should be incorporated into the core barcode for seed plants. doi
  14. (2010). Identification of medicinal Dendrobium species by phylogenetic analyses using matK and rbcL sequences. doi
  15. (2010). Validation of the ITS2 Region as a Novel DNA Barcode for Identifying Medicinal Plant Species. PLoS one 5: doi
  16. (2011). Use of DNA barcode sensu lato to identify traditional Tibetan medicinal plant Gentianopsis paludosa (Gentianaceae). doi
  17. (2011). A comparative study of different DNA barcoding markers for the identification of some members of Lamiaceae. doi
  18. (2010). Novel approaches based on DNA barcoding and high-resolution melting of amplicons for authenticity analyses of berry species. doi
  19. (2011). A rapid screening for adulterants in olive oil using DNA barcodes. doi
  20. (2010). Characterisation of insect and plant origins using DNA extracted from small volumes of bee honey. doi
  21. (2008). DNA sequences identify invasive alien Cardamine at Lake Constance. doi
  22. (2009). Routine DNA barcoding of Canadian Gracilariales (Rhodophyta) reveals the invasive species Gracilaria vermiculophylla in British Columbia. doi
  23. (2009). DNA barcoding discriminates the noxious invasive plant species, floating pennywort (Hydrocotyle ranunculoides L.f.), from non-invasive relatives. doi
  24. (2011). Spatial patterns of plant diversity below-ground as revealed by DNA barcoding. doi
  25. (2010). Using next-generation sequencing for molecular reconstruction of past Arctic vegetation and climate. doi
  26. (2010). Advances in the Use of DNA Barcodes to Build a Community Phylogeny for Tropical Trees in a Puerto Rican Forest Dynamics Plot. PLoS one 5: doi
  27. (2006). 300,000 species to identify: problems, progress, and prospects in DNA barcoding of land plants. doi
  28. (2004). A doi
  29. (2010). New Flora of the British Isles. Cambridge: doi
  30. (2008). A Vascular Plant Red Data List for Wales: Plantlife Wales.
  31. (2010). Habitats of Wales: A comprehensive field survey, 1979–1997: University of Wales Press.
  32. (2010). Grasslands of Wales: A survey of lowland species-rich grasslands 1987–2004. Cardiff: University of Wales Press.
  33. (2007). BOLD: The Barcode of Life Data System (www.barcodinglife.org). doi
  34. (1990). Basic local alignment search tool. doi
  35. (2011). DNA barcoding of lichenized fungi demonstrates high identification success in a floristic context. doi
  36. (1985). Extraction of DNA from milligram amounts of fresh, herbarium and mummified plant-tissues. doi
  37. (2002). Comparison of seven DNA extraction and amplification protocols in historical herbarium specimens of Juncaceae. doi
  38. (2008). Assessment of age and greenness of herbarium specimens as predictors for successful extraction and amplification of DNA. doi
  39. (2011). Refining the DNA barcode for land plants. doi
  40. (2011). DNA barcode sequence identification incorporating taxonomic hierarchy and within taxon variability. PLoS one 6: doi
  41. (2004). MUSCLE: multiple sequence alignment with high accuracy and high throughput. doi
  42. (2005). transAlign: using amino acids to facilitate the multiple alignment of protein-coding DNA sequences.
  43. (2005). DNA barcoding: Error rates based on comprehensive sampling. doi
  44. (2012). Chater A (2010) Flora of Cardiganshire.

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