Fungal Barcoding – the South African Perspective
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Transcript of 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
Fungal Diversity inSouthern Africa
South Africa: ~10% of all plant species
200 000 species(excluding insect
associates)
Tree Protection Co-operative ProgrammeThe 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.
DST-NRF Centre of Excellence in Tree Health Biotechnology
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.
Centre for Applied Mycological StudiesThe 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.
Pathogens of exotic treesPathogens of exotic trees
Fungi of native treesFungi of native trees
Fungi of industrial Fungi of industrial importanceimportance
Some of the fungal groups studied at FABI
• Ophiostoma sensu latoOphiostoma sensu lato• Ceratocystis sensu latoCeratocystis sensu lato• BotryosphaeriaceaeBotryosphaeriaceae• CryphonectriaceaeCryphonectriaceae• MycosphaerellaMycosphaerella species species • ArmillariaArmillaria species species• Gibberella fujikuroiGibberella fujikuroi complex complex
Healthy vs diseased S. cordatum inflorescence
Fungal Diversity of Native TreesExample: Fusarium spp. on Syzygium cordatum flowers
Healthy vs diseased Mangifera indica inflorescence
F. pseudonygamai F. ramigenum 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
F. sp. 212 F. xylarioides
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 F. sp. 137 F. sp. NRRL 26152 S. hermonthica F. dlamii
F. sp. 180 F. sp. 107
F. sp. NRRL 26756 grass F. sp. NRRL 26757 reed F. sp. NRRL 25346 I. batatas
F. sterilihyphosum F. sp. NRRL 25195
F. sp. NRRL 25807 F. konzum (MP I)
F. bulbicola F. anthophilium
F. succisae F. bactridioides
F. sp. NRRL 29124 Bidens pilosa F. sp. NRRL 29123
F. circinatum (MP H) F. subglutinans (MP E)
F. sp. 25622 Z.mays F. begoniae F. sp. NRRL 25204 F. guttiforme
F. sp. 68 F. sp. 64 F. sp. 106 F. sp. 92 F. sp. 138
F. proliferatum (MP D) F. globosum
F. fujikuroi (MP C) F. sp. 188
F. sp. NRRL 26794 Cymbidium sp F. fractiflexum
F. mangiferae F.sp. NRRL 26427
F. sp. NRRL 25309 T. aestivum F. concentricum F. sp. NRRL 25303 Osativa Japan
F. sp. 21 F. sacchari (MP B)
F. oxysporum F. inflexum
F. sp. 140 F. sp. 136
F. sp. NRRL 25615 Oryza sativa F. verticillioides (MP A)
F. brevicatenulatumF. pseudoanthophilium
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maize
mango
sugar cane
coffee
Pinus species
Begonia species
sweet potato
rice
pineapple
fig
Sansevieria species
maize, sorghum, mango, asparagus
maize
sorghum
pigeon pea
TEFBeta- tubulin
F. pseudonygamai F. ramigenum 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
F. sp. 212 F. xylarioides
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 F. sp. 137 F. sp. NRRL 26152 S. hermonthica F. dlamii
F. sp. 180 F. sp. 107
F. sp. NRRL 26756 grass F. sp. NRRL 26757 reed F. sp. NRRL 25346 I. batatas
F. sterilihyphosum F. sp. NRRL 25195
F. sp. NRRL 25807 F. konzum (MP I)
F. bulbicola F. anthophilium
F. succisae F. bactridioides
F. sp. NRRL 29124 Bidens pilosa F. sp. NRRL 29123
F. circinatum (MP H) F. subglutinans (MP E)
F. sp. 25622 Z.mays F. begoniae F. sp. NRRL 25204 F. guttiforme
F. sp. 68 F. sp. 64 F. sp. 106 F. sp. 92 F. sp. 138
F. proliferatum (MP D) F. globosum
F. fujikuroi (MP C) F. sp. 188
F. sp. NRRL 26794 Cymbidium sp F. fractiflexum
F. mangiferae F.sp. NRRL 26427
F. sp. NRRL 25309 T. aestivum F. concentricum F. sp. NRRL 25303 Osativa Japan
F. sp. 21 F. sacchari (MP B)
F. oxysporum F. inflexum
F. sp. 140 F. sp. 136
F. sp. NRRL 25615 Oryza sativa F. verticillioides (MP A)
F. brevicatenulatumF. pseudoanthophilium
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TEFBeta- tubulin
Fungi of native plants studied at FABI
Acacia karoo Acacia mellifera
Proteaceae Adansonia digitata (Baobab)
Pterocarpus angolensis (Kiaat) Sclerocarya birrea (Marula)
Syzygium species Terminalia species
Widdringtonia species Podocarpus species
Aloe species Cichorium species
ArmillariaArmillaria BotryosphaeriaceaeBotryosphaeriaceae
CeratocystisCeratocystis ConiothyriumConiothyrium ChrysoportheChrysoporthe CryphonectriaCryphonectria
CylindrocladiumCylindrocladium GanodermaGanoderma FusariumFusarium
GrosmanniaGrosmannia LeptographiumLeptographium
OphiostomaOphiostoma Phoma Phoma speciesspecies
Uredinales Uredinales
Fungal GroupsFungal GroupsPlantsPlants
Native fungi cause disease on introduced hosts
African BotryosphaeriaceaeNative Syzigium species vs non-native Eucalyptus
species
African Chrysoporthe speciesNative Myrtaceae species vs non-native Eucalyptus
and Tibouchina species
African Ceratocystis speciesDiverse native plant species vs non-native Acacia
species
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
REST OF THE WORLD
>100 collaborators and co-workers world-wide.
Including North Africa
South America
North America
Europe
Australiasia
CollaboratorsSUB-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
CULTURE COLLECTIONSCAMS
(~1500 fungi)
CMW, FCC, BOT(~25000 fungi)
UP(~300 fungi)
SAPPI(+/- 400 fungi)
CSIR(~5300 fungi)
PREM (ARC)(~8000 fungi)PREM (ARC)(~8000 fungi)
US(~1000 fungi)
MRC(~8000 fungi)
“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)