The first 'in-house' fungal genome has been sequenced in the halls of FABI using Oxford NanoPore sequencing technology.  This is a step towards fungal biologists being able to sequence the genomes of the fungi they work on for approximately US$1000 while in the comfort of their own laboratory. Drs Tuan Doung, Alistair McTaggart and Prof. Brenda Wingfield have tested a MinION to sequence the genome of an important pathogen of sweet potato - with some promising results. The genomes of several plant-pathogenic fungi in South Africa will now be sequenced in collaboration with other FABIans and members of the DST-NRF Centre of Excellence in Tree Health Biotechnology (CTHB).

Photo Caption:  Dr Tuan Doung loads the first sample of genomic DNA run on the MinION at FABI.

New Publications

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Phasha MM, Wingfield BD, Coetzee MPA, Santana QC, Fourie G, Steenkamp ET. (2017) Architecture and distribution of introns in core genes of four Fusarium species. G3: Genes|Genomes|Genetics 7(11):3809-3820. 10.1534/g3.117.300344
Chen SF, Liu QL, Li GQ, Wingfield MJ. (2017) Quambalaria species associated with eucalypt diseases in southern China. Frontiers of Agricultural Science and Engineering 10.15302/J-FASE-2017173 PDF
Meyer J, Berger DK, Christensen SA, Murray SL. (2017) RNA-Seq analysis of resistant and susceptible sub-tropical maize lines reveals a role for kauralexins in resistance to grey leaf spot disease, caused by Cercospora zeina. BMC Plant Biology 17:197. 10.1186/s12870-017-1137-9
Nel WJ, Duong TA, Wingfield BD, Wingfield MJ, De Beer ZW. (2017) A new genus and species for the globally important, multi-host root pathogen Thielaviopsis basicola. Plant Pathology 10.1111/ppa.12803
Aylward J, Wingfield BD, Dreyer LL, Roets F, Wingfield MJ, Steenkamp ET. (2017) Contrasting carbon metabolism in saprotrophic and pathogenic Microascalean fungi from Protea trees. Fungal Ecology 30:88-100. 10.1016/j.funeco.2017.09.002
Wingfield BD. (2017) South Africa can’t afford to see its universities pitch over the precipice. The Conversation https://theconversation.com/south-africa-cant-afford-to-see-its-universities-pitch-over-the-precipic PDF
Li GQ, Liu FF, Li JQ, Liu QL, Chen SF. (2017) Botryosphaeriaceae from Eucalyptus plantations and adjacent plants in China. Persoonia 10.3767/persoonia.2018.40.03 PDF
Tchotet Tchoumi JM, Coetzee MPA, Vivas M, Rajchenberg M, Roux J. (2017) Wood-rotting basidiomycetes associated with declining native trees in timber-harvesting compartments of the Garden Route National Park of South Africa. Austral Ecology 10.1111/aec.12524
Theron-De Bruin N, Dreyer LL, Ueckermann EA, Wingfield MJ, Roets F. (2017) Birds mediate a fungus-mite mutualism. Microbial Ecology 10.1007/s00248-017-1093-9
Wingfield BD, Vaughan K. (2017) Money woes force South Africa to revisit how it rewards researchers. The Conversation https://theconversation.com/money-woes-force-south-africa-to-revisit-how-it-rewards-researchers-8615 PDF
De Beer ZW, Marincowitz S, Duong TA, Wingfield MJ. (2017) Bretziella, a new genus to accommodate the oak wilt fungus, Ceratocystis fagacearum (Microascales, Ascomycota). MycoKeys 27 10.3897/mycokeys.27.20657 PDF
Li JQ, Wingfield MJ, Liu QL, Barnes I, Roux J, Lombard L, Crous PW, Chen SF. (2017) Calonectria species isolated from Eucalyptus plantations and nurseries in South China. IMA Fungus 8(2):259-286. 10.5598/imafungus.2017.08.02.04
Paap T, Burgess TI, Wingfield MJ. (2017) Urban trees: bridge-heads for forest pest invasions and sentinels for early detection. Biological Invasions 10.1007/s10530-017-1595-x
Pham HTL, Nguyen LTT, Duong TA, Bui DTT, Doan QT, Nguyen HTT, Mundt S. (2017) Diversity and bioactivities of nostocacean cyanobacteria isolated from paddy soil in Vietnam. Systematic and Applied Microbiology 10.1016/j.syapm.2017.08.001
Wingfield BD. (2017) The privileges and opportunities of a research sabbatical. South African Journal of Science 113(9/10):#a0234. 10.17159/sajs.2017/a0234
Bose T, Burgess TI, Roux J, Wingfield MJ. (2017) Phytophthora alticola; revised description based on new collections and a neotype. Sydowia 69:161-170. 10.12905/0380.sydowia69-2017-0161
Human ZR, Crous CJ, Roets F, Venter SN, Wingfield MJ, de Beer ZW. (2017) Biodiversity and ecology of flower-associated actinomycetes in different flowering stages of Protea repens. Antonie van Leeuwenhoek 10.1007/s10482-017-0942-3
Wingfield BD. (2017) The peer review system has flaws. But it’s still a barrier to bad science. The Conversation http://bit.ly/2holsgS
McTaggart AR, Beasley DR, Wingfield MJ, Wood AR, Pretorius ZA, Drenth A, Shivas RG, Roux J. (2017) A dynamic, web-based resource to identify rust fungi (Pucciniales) in southern Africa. MycoKeys 26:77-83. 10.3897/mycokeys.26.14602
De Maayer P, Aliyu H, Vikram S, Blom J, Duffy B, Cowan DA, Smits THM, Venter SN, Coutinho TA. (2017) Phylogenomic, pan-genomic, pathogenomic and evolutionary genomic insights into the agronomically relevant enterobacteria Pantoea ananatis and Pantoea stewartii. Frontiers in Microbiology 8(1755) 10.3389/fmicb.2017.01755
Jami F, Wingfield MJ, Gryzenhout M, Slippers B. (2017) Diversity of tree-infecting Botryosphaeriales on native and non-native trees in South Africa and Namibia. Australasian Plant Pathology 10.1007/s13313-017-0516-x
Stewart JE, Ross-Davis AL, Graҫa RN, Alfenas AC, Peever TL, Hanna JW, Uchida JY, Hauff RD, Kadooka CY, Kim MS, Cannon PG, Namba S, Simeto S, Pérez CA, Rayamajhi MB, Lodge DJ, Arguedas M, Medel-Ortiz R, López-Ramirez MA, Tennant P, Glen M, Machado PS, McTaggart AR, Carnegie AJ, Klopfenstein NB, Cleary M. (2017) Genetic diversity of the myrtle rust pathogen (Austropuccinia psidii) in the Americas and Hawaii: Global implications for invasive threat assessments. Forest Pathology 10.1111/efp.12378
Roodt D, Lohaus R, Sterck L, Swanepoel RL, Van de Peer Y, Mizrachi E. (2017) Evidence for an ancient whole genome duplication in the cycad lineage. PLOS ONE 12(9):e0184454. 10.1371/journal.pone.0184454
Liebhold AM, Brockerhoff EG, Kalisz S, Nuñez MA, Wardle DA, Wingfield MJ. (2017) Biological invasions in forest ecosystems. Biological Invasions 10.1007/s10530-017-1458-5
Amuge T, Berger DK, Katari MS, Myburg AA, Goldman SL, Ferguson ME. (2017) A time series transcriptome analysis of cassava (Manihot esculenta Crantz) varieties challenged with Ugandan cassava brown streak virus. Scientific Reports 7:9747. 10.1038/s41598-017-09617-z
Liu QL, Chen SF. (2017) Two novel species of Calonectria isolated from soil in a natural forest in China. MycoKeys 26:25-60. 10.3897/mycokeys.26.14688 PDF
McTaggart AR, Shuey LS, Granados GM, du Plessis E, Fraser S, Barnes I, Naidoo S, Wingfield MJ, Roux J. (2017) Evidence that Austropuccinia psidii may complete its sexual life cycle on Myrtaceae. Plant Pathology 10.1111/ppa.12763
Wondafrash M, Slippers B, Garnas J, Hurley BP. (2017) Parasitoid assemblage associated with a North American pine weevil in South Africa. Agricultural and Forest Entomology 10.1111/afe.12246
Nzuki I, Katari MS, Bredeson JV, Masumba E, Kapinga F, Salum K, Mkamilo GS, Shah T, Lyons JB, Rokhsar DS, Rounsley S, Myburg AA, Ferguson ME. (2017) QTL Mapping for Pest and Disease Resistance in Cassava and Coincidence of Some QTL with Introgression Regions Derived from Manihot glaziovii. Frontiers in Plant Science 8(1168) 10.3389/fpls.2017.01168
Mostert D, Molina AB, Daniells J, Fourie G, Hermanto C, Chao C-P, Fabregar E, Sinohin VG, Hossain MDS, Masdek N, Visarto P, Rajapakse C, Thanh DT, Thangavelu R, Li C, Yi G, Wei Y, Mostert L, Viljoen A. (2017) The distribution and host range of the banana Fusarium wilt fungus, Fusarium oxysporum f. sp. cubense, in Asia. PLoS ONE 12(7):24. 10.1371/journal.pone.0181630
Masumba EA, Kapinga F, Mkamilo G, Salum K, Kulembeka H, Rounsley S, Bredeson JV, Lyons JB, Rokhsar DS, Kanju E, Katari MS, Myburg AA, van der Merwe NA, Ferguson ME. (2017) QTL associated with resistance to cassava brown streak and cassava mosaic diseases in a bi-parental cross of two Tanzanian farmer varieties, Namikonga and Albert. Theoretical and Applied Genetics 10.1007/s00122-017-2943-z
Fraser S, McTaggart AR, Wingfield MJ, Roux J. (2017) Effect of temperature, leaf wetness and the developmental stage of host tissue on infection of Acacia mearnsii by Uromycladium acaciae (Pucciniales). Australasian Plant Pathology 10.1007/s13313-017-0503-2
Jankowiak R, Strzałka B, Bilański P, Linnakoski R, Aas T, Solheim H, Groszek M, De Beer ZW. (2017) Two new Leptographium spp. reveal an emerging complex of hardwood-infecting species in the Ophiostomatales. Antonie van Leeuwenhoek 110(12):1537-1553. 10.1007/s10482-017-0905-8
Ozturk KI, Chettri P, Dupont P-Y, Barnes I, McDougal RL, Moore GG, Sim A, Bradshaw RE. (2017) Evolution of polyketide synthesis in a Dothideomycete forest pathogen. Fungal Genetics and Biology 10.1016/j.fgb.2017.07.001
Wilken PM, Steenkamp ET, Wingfield MJ, De Beer ZW, Wingfield BD. (2017) Which MAT gene? Pezizomycotina (Ascomycota) mating-type gene nomenclature reconsidered. Fungal Biology Reviews 31:199-211. 10.1016/j.fbr.2017.05.003
Bush SJ, Dittrich-Schröder D, Neser S, Gevers C, Baffoe KO, Slippers B, Hurley BP. (2017) First record of Quadristichus mendeli, a parasitoid of Leptocybe invasa, in South Africa. Southern Forests 10.2989/20702620.2017.1318347
Chen SF, Liu QL, Li GQ, Wingfield MJ, Roux J. (2017) A new genus of Cryphonectriaceae isolated from Lagerstroemia speciosa in southern China. Plant Pathology 10.1111/ppa.12723
Beukes CW, Palmer M, Manyaka P, Chan W-Y, Avontuur JR, Van Zyl E, Huntemann M, Clum A, Pillay M, Palaniappan K, Varghese N, Mikhailova N, Stamatis D, Reddy TBK, Daum C, Shapiro N, Markowitz V, Ivanova N, Kyrpides N, Woyke T, Blom J, Whitman WB, Venter SN, Steenkamp ET. (2017) Genome data provides high support for generic boundaries in Burkholderia sensu lato. Frontiers in Microbiology 8 10.3389/fmicb.2017.01154
Hurley BP, Slippers B, Sathyapala S, Wingfield MJ. (2017) Challenges to planted forest health in developing economies. Biological Invasions 10.1007/s10530-017-1488-z
Bouwer MC, Slippers B, Wingfield MJ, Allison JD, Rohwer ER. (2017) Optimization of Pheromone Traps for Coryphodema tristis (Lepidoptera: Cossidae) . Journal of Economic Entomology 10.1093/jee/tox171
du Plessis E, McTaggart AR, Granados GM, Wingfield MJ, Roux J, Pegg GS, Makinson J, Purcell M, Ali M. (2017) First report of myrtle rust caused by Austropuccinia psidi on Rhodomyrtus tomentosa (Myrtaceae) from Singapore. Plant Disease 10.1094/PDIS-04-17-0530-PDN
Hussey SG, Loots MT, van der Merwe K, Mizrachi E, Myburg AA. (2017) Integrated analysis and transcript abundance modelling of H3K4me3 and H3K27me3 in developing secondary xylem. Scientific Reports 7:3370. 10.1038/s41598-017-03665-1
Wingfield MJ, Barnes I, De Beer ZW, Roux J, Wingfield BD, Taerum SJ. (2017) Novel associations between ophiostomatoid fungi, insects and tree hosts: current status—future prospects. Biological Invasions 19:3215-3228. 10.1007/s10530-017-1468-3
Vivas M, Kemler M, Mphahlele MM, Wingfield MJ, Slippers B. (2017) Maternal effects on phenotype, resistance and the structuring of fungal communities in Eucalyptus grandis. Environmental and Experimental Botany 140:120-127. 10.1016/j.envexpbot.2017.06.002
Miller A, Cai L, Crous PW, De Beer ZW, Hawksworth DL, Hyde KD, Kirk PM, Lücking R, Lumbsch HT, May TW, Rossman AY, Schoch CL, Seifert KA. (2017) Mycologists' committees strongly support changes to the governance of fungal nomenclature. IMA Fungus 8(1):(9)-(11). PDF
Linnakoski R, Forbes KM, Wingfield MJ, Pulkkinen P, Asiegbu FO. (2017) Testing projected climate change conditions on the Endoconidiophora polonica / Norway spruce pathosystem shows fungal strain specific effects. Frontiers in Plant Science 8:883. 10.3389/fpls.2017.00883 PDF
Crous CJ, Burgess TI, Le Roux JJ, Richardson DM, Slippers B, Wingfield MJ. (2017) Ecological disequilibrium drives insect pest and pathogen accumulation in non-native trees. AoB Plants 9:plw081. 10.1093/aobpla/plw081
Mbenoun M, Garnas JR, Wingfield MJ, Begoude Boyogueno AD, Roux J. (2017) Metacommunity analyses of Ceratocystidaceae fungi across heterogeneous African savanna landscapes. Fungal Ecology 28:76-85. 10.1016/j.funeco.2016.09.007
Swart V, Crampton BG, Ridenour JB, Bluhm BH, Olivier NA, Meyer JJM, Berger DK. (2017) Complementation of CTB7 in the maize pathogen Cercospora zeina overcomes the lack of in vitro cercosporin production. Molecular Plant-Microbe Interactions 30(9):710-724. 10.1094/MPMI-03-17-0054-R
Wingfield MJ, Slippers B, Wingfield BD, Barnes I. (2017) The unified framework for biological invasions: a forest fungal pathogen perspective. Biological Invasions 10.1007/s10530-017-1450-0