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Fungal Barcoding – the South African Perspective

Fungal Barcoding – the South African Perspective. Emma Steenkamp Forestry and Agricultural Biotechnology Institute (FABI) Department of Microbiology and Plant Pathology, University of Pretoria, South Africa. South Africa: ~10% of all plant species. Fungal Diversity in Southern Africa.

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Fungal Barcoding – the South African Perspective

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  1. Fungal Barcoding – the South African Perspective Emma Steenkamp Forestry and Agricultural Biotechnology Institute (FABI) Department of Microbiology and Plant Pathology, University of Pretoria, South Africa

  2. South Africa: ~10% of all plant species Fungal Diversity in Southern Africa

  3. 200 000 species (excluding insect associates)

  4. Tree Protection Co-operative Programme The Tree Protection Cooperative Programme (TPCP), a programme of the Forestry and Agricultural Biotechnology Institute (FABI), represents a cooperative venture between the major players in the South African Forestry Industry and the University of Pretoria, to deal with tree disease problems. The programme is based on a membership concept where forestry organisations are members and contribute to a collaborative effort through the payment of annual fees. The University of Pretoria in turn provides the infrastructure necessary to conduct research into tree pests and diseases, which is technologically complicated and thus expensive. Centre for Applied Mycological Studies DST-NRF Centre of Excellence in Tree Health Biotechnology The Centre for Applied Mycological Studies (CAMS) was established in 2003 through the collaboration between Council for Scientific and Industrial Research (CSIR) Biosciences and the University of Pretoria at the Forestry and Agricultural Biotechnology Institute (FABI). Both these institutions have joined forces in the protection and utilization of South Africa's fungal biodiversity. CAMS functions as a vehicle to utilize and develop value added products and technologies from the indigenous mycoflora in South Africa and the rest of the continent. The joint collaboration between FABI and CSIR Biosciences makes CAMS the ideal means to bring research and development in mycology close to the technological applications in the industry. CAMS also strives to address the need for developing human resources and popularizing mycology population in South Africa. The Centre of Excellence in Tree Health Biotechnology (CTHB) at FABI represents one of six designated Science Centres supported by the Government Department of Science and Technology (DST) and the National Research Foundation (NRF). CTHB research concentrates on the health of native trees, particularly those in forests and it has both a national and and international perspective. A core focus is to provide the highest possible quality of post graduate education in fields such as plant pathology, entomology, biochemistry, genetics, molecular biology, biotechnology and ecology. The CTHB functions alongside the Tree Protection Co-operative Programme (TPCP) with the two programmes providing synergy for each other. Pathogens of exotic trees Fungi of native trees Fungi of industrial importance

  5. Some of the fungal groups studied at FABI • Ophiostoma sensu lato • Ceratocystis sensu lato • Botryosphaeriaceae • Cryphonectriaceae • Mycosphaerella species  • Armillaria species • Gibberella fujikuroi complex

  6. Fungal Diversity of Native Trees Healthy vs diseased S. cordatum inflorescence Healthy vs diseased Mangifera indica inflorescence Example: Fusarium spp. on Syzygium cordatum flowers

  7. TEF + Beta- tubulin F. sp. 140 90/8100/1.00 100/100/1.00 F. sp. 136 85/84/1.00 F. sp. NRRL 25615 Oryza sativa maize F. verticillioides (MP A) F. brevicatenulatum 100/100/1.00 95/96/1.00 F. pseudoanthophilium F. pseudonygamai 99/100/1.00 F. ramigenum 99/96/1.00 F. napiforme F. sp. NRRL 26793 Striga hermonthica F. sp. 32 fig F. lactis F. pseudocircinatum F. nygamai (MP G) sorghum F. thapsinum (MP F) sweet potato F. denticulatum 85/87/0.96 93/98/1.00 F. sp. 212 coffee F. xylarioides Sansevieria species 99/100/1.00 77/86/1.00 F. phyllophium pigeon pea F. udum F. sp. NRRL 26064 Sorghum bicolor F. sp. 44 F. acutatum F. sp. NRRL 25221 Zea mays F. sp. NRRL 26061 S. hermonthica 93/100/1.00 F. sp. 137 100/100/1.00 F. sp. NRRL 26152 S. hermonthica F. dlamii 97/930.95 F. sp. 180 95/95/1.00 F. sp. 107 F. sp. NRRL 26756 grass 74/88/0.99 F. sp. NRRL 26757 reed F. sp. NRRL 25346 I. batatas 97/97/1.00 F. sterilihyphosum 65/76/0.95 F. sp. NRRL 25195 F. sp. NRRL 25807 F. konzum (MP I) F. bulbicola F. anthophilium 100/100/1.00 F. succisae F. bactridioides 100/100/1.00 100/100/1.00 F. sp. NRRL 29124 Bidens pilosa F. sp. NRRL 29123 Pinus species F. circinatum (MP H) 96/96/1.00 maize F. subglutinans (MP E) F. sp. 25622 Z.mays Begonia species F. begoniae 78/75/0.97 F. sp. NRRL 25204 pineapple F. guttiforme 85/89/1.00 F. sp. 68 99/100/1.00 F. sp. 64 F. sp. 106 F. sp. 92 73/99/1.00 F. sp. 138 maize, sorghum, mango, asparagus 100/100/1.00 F. proliferatum (MP D) F. globosum 97/98/1.00 rice F. fujikuroi (MP C) F. sp. 188 98/100/1.00 F. sp. NRRL 26794 Cymbidium sp 91/96/1.00 F. fractiflexum mango 100/99/1.00 F. mangiferae 88/92/1.00 F.sp. NRRL 26427 F. sp. NRRL 25309 T. aestivum 100/100/1.00 95/99/1.00 F. concentricum F. sp. NRRL 25303 Osativa Japan sugar cane 100/100/1.00 F. sp. 21 F. sacchari (MP B) 100/100/1.00 F. oxysporum F. inflexum Gibberella fujikuroi complex

  8. TEF + Beta- tubulin F. sp. 140 90/8100/1.00 100/100/1.00 F. sp. 136 85/84/1.00 F. sp. NRRL 25615 Oryza sativa F. verticillioides (MP A) F. brevicatenulatum 100/100/1.00 95/96/1.00 F. pseudoanthophilium F. pseudonygamai 99/100/1.00 F. ramigenum 99/96/1.00 F. napiforme F. sp. NRRL 26793 Striga hermonthica F. sp. 32 F. lactis F. pseudocircinatum F. nygamai (MP G) F. thapsinum (MP F) F. denticulatum 85/87/0.96 93/98/1.00 F. sp. 212 F. xylarioides 99/100/1.00 77/86/1.00 F. phyllophium F. udum F. sp. NRRL 26064 Sorghum bicolor F. sp. 44 F. acutatum F. sp. NRRL 25221 Zea mays F. sp. NRRL 26061 S. hermonthica 93/100/1.00 F. sp. 137 100/100/1.00 F. sp. NRRL 26152 S. hermonthica F. dlamii 97/930.95 F. sp. 180 95/95/1.00 F. sp. 107 F. sp. NRRL 26756 grass 74/88/0.99 F. sp. NRRL 26757 reed F. sp. NRRL 25346 I. batatas 97/97/1.00 F. sterilihyphosum 65/76/0.95 F. sp. NRRL 25195 F. sp. NRRL 25807 F. konzum (MP I) F. bulbicola F. anthophilium 100/100/1.00 F. succisae F. bactridioides 100/100/1.00 100/100/1.00 F. sp. NRRL 29124 Bidens pilosa F. sp. NRRL 29123 F. circinatum (MP H) 96/96/1.00 F. subglutinans (MP E) F. sp. 25622 Z.mays F. begoniae 78/75/0.97 F. sp. NRRL 25204 F. guttiforme 85/89/1.00 F. sp. 68 99/100/1.00 F. sp. 64 F. sp. 106 F. sp. 92 73/99/1.00 F. sp. 138 100/100/1.00 F. proliferatum (MP D) F. globosum 97/98/1.00 F. fujikuroi (MP C) F. sp. 188 98/100/1.00 F. sp. NRRL 26794 Cymbidium sp 91/96/1.00 F. fractiflexum 100/99/1.00 F. mangiferae 88/92/1.00 F.sp. NRRL 26427 F. sp. NRRL 25309 T. aestivum 100/100/1.00 95/99/1.00 F. concentricum F. sp. NRRL 25303 Osativa Japan 100/100/1.00 F. sp. 21 F. sacchari (MP B) 100/100/1.00 F. oxysporum F. inflexum Gibberella fujikuroi complex

  9. Fungi of native plants studied at FABI Plants Fungal Groups Acacia karoo Acacia mellifera Proteaceae Adansonia digitata (Baobab) Pterocarpus angolensis (Kiaat) Sclerocarya birrea (Marula) Syzygium species Terminalia species Widdringtoniaspecies Podocarpus species Aloe species Cichorium species Armillaria Botryosphaeriaceae Ceratocystis Coniothyrium Chrysoporthe Cryphonectria Cylindrocladium Ganoderma Fusarium Grosmannia Leptographium Ophiostoma Phoma species Uredinales

  10. Native fungi cause disease on introduced hosts African Chrysoporthe species Native Myrtaceae species vs non-native Eucalyptus and Tibouchina species African Botryosphaeriaceae Native Syzigium species vs non-native Eucalyptus species African Ceratocystis species Diverse native plant species vs non-native Acacia species

  11. Research Team

  12. Collaborators SOUTH AFRICA Dr. Hugh Glen, SANBI, KZN Herbarium, Durban Dr. Andre Cilliers, 14 Field Road, Lilianton, Boksburg, Gauteng Dr. Marieka Schoeman, Institute for Tropical and Subtropical Crops, Nelspruit Prof. Steven Chown, University of Stellenbosh Prof. Coert Geldenhuys, University of Stellenbosch Dr. Karin Jacobs, University of Stellenbosch Ms. Thembi Khoza, Science Liaison Officer, Kruger National Park Prof. Braam van Wyk, University of Pretoria Prof. Paulette Bloomer, University of Pretoria Counsellor Lee, Chinese Consulate in South Africa Dr. Oliver Preisig, Inqaba biotech, Pretoria Mr. Leon Visser, Trees Unlimited, Stellenbosch Prof. Egmont Rohwer, University of Pretoria Dr. Ben Eisenberg, Dept Statistics, University of Pretoria Dr. Hester Vismer, PROMEC, Medical Research Council, Tygerberg Dr Leanne Dreyer, University of Stellenbosch Ms Riana Jacobs, Mycology Unit, Biosystematics Division, PPRI-ARC, Pretoria SUB-SAHARA AFRICA Dr. Percy Chimwamurumbe, Namibian University, Windhoek Dr. Muimba A Kangolongo, School for Natural Resources, Copperbelt University, Kitwe, Zambia Mr. Gerald Meke, Zomba, Malawi Mr. Fabian Mlambo, Copperbelt University, Kitwe, Zambia, Dr. Eddie Mwenje, Dept. Applied Biology and Biochemistry, NUST, Bulawayo Zimbabwe Mr. H Nemato, Dept. Applied Biology and Biochemistry, NUST, Bulawayo, Zimbabwe Dr. Grace Nakabonge, Makerere University, Uganda Ms Jane Njuguna, Kenai Forestry Research, Nairobi, Kenai SA Forestry Industries located in SADC countries REST OF THE WORLD >100 collaborators and co-workers world-wide. Including North Africa South America North America Europe Australiasia

  13. CAMS (~1500 fungi) CSIR (~5300 fungi) CMW, FCC, BOT (~25000 fungi) SAPPI (+/- 400 fungi) UP (~300 fungi) MRC (~8000 fungi) PREM (ARC) (~8000 fungi) US (~1000 fungi) CULTURE COLLECTIONS

  14. “Given the current importance placed on ecotourism and the preservation of unique southern African flora and fauna, it is clearly timely that some thought, financial resources and research be focused on preserving the basal links of the ecosystem, which are the fungi. Clearly, South Africa’s undescribed fungi represent a vast biological resource which has yet to be collected, cultured and studied. Undoubtedly the fungi of southern Africa contain numerous beneficial biological properties and other attributes that could be used to greatly improve the quality of life for all future generations of humanity.” (Crous et al. 2006)

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