DNA Barcoding – Southern African Experience

1. DNA Barcoding – Southern African Experience Michelle van der Bank

2. 7 & 8 April 2006 – DNA barcoding meeting hosted by SANBI SA, CBOL, BioNET-SAFRINET & BioNET • First of the regional meetings held by CBOL • Held at Kirstenbosch National Botanical Garden attended by 67 participants from 11 southern African countries, 4 other African countries, 2 from Asia, & 10 CBOL officials

3. Goals of the southern African meeting • Clarify concepts and applications of barcoding • Raise awareness of the uses of DNA barcoding for biodiversity research and species identification • Raise awareness of the pitfalls of barcoding • Explore the potential applications of DNA barcoding • Clarify funding opportunities

4. Meeting results Several barcoding projects have been identified having the following characteristics: • Address an immediate need • Focus on species of commercial value, endangered species, and endemic species • Have potential users and supporters • Are ready to be implemented by identified leaders in the region • Have an adequate supply of reference collections and taxonomic experts in the region • Are sustainable ( have users, fundings)

5. Projects identified • Pest species related to plant quarantine • Macro-invertebrates used for water quality assessments • FISH-BOL • Endangered vertebrates • Wildlife species and their related parasites and pathogens • Pests on livestock species, e.g., ticks, biting flies, parasites • Invasive alien species • Rare / endangered species (i.e. Cape Floristic Kingdom) • Plants and animals used medicinally • Groups of interest to specific sectors such as public health (mosquitoes), commercial fishermen (abalone), pet trade (birds)

6. Regional needs for capacity building and training • Biodiversity act (NEMBA No 10 of 2004) • Capacity is uneven distributed among countries • Sequencing facilities exist, establishing them in every countries would not be cost-effective • Way to go: many local labs capable of extracting DNA, PCR, and sending PCR products to central sequencing facilities in the region • Training in taxonomy, curation, barcoding is an important need

7. Next steps CBOL and BioNET to implement the following in southern Africa •Create Steering Committees for selected projects • Facilitate the formation of a Regional Barcode Network • Identify Leading Labs for information/staff exchange • Identify Participating Labs involved in regional or global projects for local training • Material Transfer Agreements • Create short courses • Respond to requests for assistance in writing proposals to funding agencies for barcoding projects •Provide copies of successful barcoding proposals on request

8. Our own experience: Barcoding the flora of the Kruger National Park

9. The four steps of barcoding • Collection • Extraction of DNA • PCR / Sequencing / Producing barcode • Databasing

10. Collection • Permit • Use of herbarium samples for DNA extraction • Housing of herbarium vouchers

11. Extraction of DNA • DNA bank at UJ (Darwin Initiative - MOU)

12. PCR / Sequencing / Barcode • Fully equipped lab at University of J’Burg • Primers from the Plant Working Group (matK, rbcL, rpoC1, rpoB, accD, YCF5, ndhJ, trnL-F, trnH psbA, trnS-G, trnK-rps16, rpl36-infA-rps8, atpB-rbcL, ycf6-psbM, trnV-atpE)

13. Databasing • BOLD website (Robert Hammer) available for plants ?

14. Acknowledgements • CBOL • Plant Working Group (Robyn Cowan) • Elida Oyieke & Dickens Odeny