DNA Barcoding – Southern African ExperienceMichelle van der Bank

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

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

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)

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)

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

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

Our own experience:

Barcoding the flora of the

Kruger National Park

The four steps of barcoding

• Collection • Extraction of DNA• PCR / Sequencing / Producing barcode• Databasing

Collection

• Permit• Use of herbarium samples for DNA extraction• Housing of herbarium vouchers

Extraction of DNA

• DNA bank at UJ (Darwin Initiative - MOU)

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)

Databasing

• BOLD website (Robert Hammer) available for plants ?

Acknowledgements

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