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Barcode Wales: Cod Bar Cymru

Barcode Wales / Codbar Cymru : A complete DNA Barcode Dataset of a Nation’s Native Flowering Plants: Creation, Applications and Public Engagement.

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Barcode Wales: Cod Bar Cymru

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  1. Barcode Wales / CodbarCymru: A complete DNA Barcode Dataset of a Nation’s Native Flowering Plants: Creation, Applications and Public Engagement • Natasha de Vere, Tim Rich, Col Ford, Sarah Trinder, Charlie Long, Chris Moore, Danielle Satterthwaite, Helena Davies, Joe Moughan, Addie Griffith, Laura Jones, Joel Allainguillaume, Mike Wilkinson, Tatiana Tatarinova, Hannah Garbett, Les Baillie, Jenny Hawkins

  2. Barcode Wales: Cod Bar Cymru DNA barcode the native flowering plants and conifers of Wales Develop applications that utilise this research platform

  3. Sample collection 1143 native flowering plants and conifers 455 genera, 95 families, 34 orders 4272 individuals sampled, 3637 herbarium, 635 freshly collected All specimens verified by taxonomic expert Herbarium vouchers and full collection details for all samples

  4. DNA extraction, amplification and sequencing • Qiagen kits, modified for herbarium material • rbcL: 5 primer combinations • matK 29 primer combinations • Macrogen Europe for Sanger sequencing

  5. Sequence editing and multiple alignment • Sequencher 4.9. contig assembly and manual editing • rbcL alignment: MUSCLE • matK alignment: Transalign and Geneious Pro 5.4.4 • SequencesBOLD and Genbank

  6. The workforce: research training

  7. Analysis • Interspecific and intraspecific divergence • Species discrimination: BLASTn • Barcode Gap: min. interspecific p-distance > than max. intraspecific (CBOL Plant Working Group 2009) • Test discrimination using GenBank data • Discrimination at different spatial scales, using species distribution records • Scripts written in Python

  8. Recoverability • In total 5,723 barcode sequences obtained for the 1143 species

  9. Fresh vs Herbarium matK: Fresh = 5 primer combinations Herbarium = 29 primer combinations

  10. Effect of herbarium specimen age Spearman Rank Correlation: rbcL rho = 0.993*** matK rho = 0.986***

  11. Intra and interspecific divergence Using uncorrected p-distances

  12. Relative discrimination 69 99 75 100 68 98 74 99 56 96 57 95 808 species

  13. Recoverability and discrimination 49 66 49 65 49 55 1143 species

  14. Testing discrimination • GenBank sequences queried against Barcode Wales database using BLASTn

  15. rbcL discrimination • Species lists generated for each square, discrimination assessed by presence of a barcode gap

  16. matK discrimination • Species lists generated for each square, discrimination assessed by presence of a barcode gap

  17. rbcL & matK discrimination • Species lists generated for each square, discrimination assessed by presence of a barcode gap

  18. DNA barcoding and drug discovery Collect wildflower honey from throughout UK Test antibacterial properties of honey against MRSA and Clostridium difficile DNA barcode honey Identify plant derived phytochemicals New drug discovery routes

  19. Drug discovery – prelim results • 150 honey samples • Agar diffusion assay, plates with MRSA, activity present in some samples • Successfully amplified rbcL from honey Next: • Identify cause of antimicrobial activity • Next gen sequencing of honey samples

  20. DNA barcoding and phylogenetics Good match with APGIII. 56% of species form monophyletic groups 44% with bootstrap support >70% ML tree for rbcL, RAxML (GTR+CAT) 1000 bootstraps, on the CIPRES supercomputer cluster

  21. DNA barcoding and phylogenetic ecology ML tree for rbcL, threatened species traced using Mesquite

  22. DNA barcoding and art-science

  23. DNA barcoding and community engagement

  24. DNA barcoding and community engagement

  25. Thank you! Funding from Welsh Government, National Botanic Garden of Wales, National Museum Wales, Countryside Council for Wales, Spirent Communications plc Sponsorship from the people of Wales www.gardenofwales.org.uk Science at the Garden of Wales on facebook

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