Shuaifei Chen - Project

FABI News

News Archive

6 Nov 2025

Dr Andrew Hayes presents a special seminar in FABI

Dr Andrew Hayes of the University of the Sunshine Coast presented a special seminar at a recent FABI Monday Morning Meeting

4 Nov 2025

Aaron shines at the 2025 Three-Minute Thesis (3MT) competition

FABI is proud of PhD candidate Aaron Harvey's runner-up placing in the 2025 Three-Minute Thesis (3MT) competition

3 Nov 2025

FABIans at the Sixth BISMiS Meeting in China

Two FABians represented UP and FABI at the Sixth Meeting of Bergey’s International Society for Microbial Systematics (BISMiS), n Qingdao, China

31 Oct 2025

FABIans honoured at the University of Pretoria’s Academic Achievers’ Awards

FABI is proud of all the MANCOM members whose hard work and dedication was honoured at the University of Pretoria’s Academic Achievers’ Awards ceremony

22 Oct 2025

Polish collaborators visit FABI

FABI hosted a visit by two Polish collaborators

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FABI Events

10 November 08h30

Monday Morning Meeting

13 November 08h30

Student Seminars

17 November 08h30

Monday Morning Meeting

18 November 12h00

Prestige Seminar

FABI in a nutshell

Research Features

Archive

FABI researchers Prof. Cobus Visagie, Dr Neriman Yilmaz, and Nicole van Vuuren, together with international collaborators, have published a comprehensive taxonomic revision of the fungal order Eurotiales, which includes the economically important genera Aspergillus, Penicillium, and Talaromyces.

New publication explores the chemodiversity of Penicillium isolated from alpine and arctic environments, including ten new species.

Review emphasizes the importance of understanding the genetics of sex determination for effective genetic pest management in insects.

Eleven new Penicillium and Talaromyces species discovered in South African culture collections.

A new study reveals the presence of Mycotoxins in Eastern Cape maize in South Africa.

Eurotiales update: FABIans Prof. Cobus Visagie and Dr Neriman Yilmaz and their collaborators have published a review of recently described Eurotiales species, including the economically important Aspergillus, Penicillium, Paecilomyces and Talaromyces.

Da Vinci's Yeast: FABIans Prof. Cobus Visagie, Dr Neriman Yilmaz, and their collaborators have recently described and named a newly discovered yeast species of the famous Italian painter, draughtsman, engineer, scientist, theorist, sculptor, and architect Leonardo da Vinci.

The potential economic impact of the PSHB invasion in South Africa has been calculated to be a massive R275 billion over the next ten years, if nothing is done to stop the spread of this invasive beetle. Researchers from FABI collaborated with Stellenbosch University ecologists and economists to model the unmitigated economic impact of this invasion.

A recently published paper in the journal Current Forestry Reports documents a collaboration between an international team of forest pathologists and invasion scientists. Led by Dr Trudy Paap, the authors present a framework for conceptualizing and managing invasive forest pathogens.

A recently published review article by Dr Andi Wilson in a special issue of the journal 'Microbiology & Molecular Biology Reviews' provides details of the genes that are essential to the sexual cycle in filamentous Ascomycete fungi and further describes their functions in a variety of model and non-model species.

Penicillium section Canescentia re-evaluated and five new species described from the fynbos biome in South Africa.

In November 2019, the DSI-NRF Centre of Excellence for Invasion Biology hosted a workshop on ‘Frameworks used in Invasion Science’. The workshop led to a NeoBiota special issue on this theme, and includes a review by FABI researchers and international colleagues, exploring frameworks in the context of forest pathology.

A doctoral study in FABI confirms for the first time the presence of Xylosandrus crassiusculus, a polyphagous ambrosia beetle and its fungal symbiont, Ambroseilla roeperi, in three provinces in South Africa. The authors warn that this beetle species could be a threat to native and plantation trees.

A review on invasive gall-forming wasps that threaten non-native Eucalyptus plantations by researchers in the TPCP appears in Agricultural and Forest Entomology. They profile several species of likely Australian origin that have established on non-native Eucalyptus plantations globally and discuss various challenges to their management.

A study in the TPCP confirms the identity of seven novel fungal species associated with Dendroctonus valens, the red turpentine beetle. The study follows on surveys on the fungal associates of the beetle in China and North America. Results from this work appear in Persoonia.

A postdoctoral study in the TPCP describes two novel Huntiella species in the African clade, bringing the number of known species in the genus to 31. Though closely related, the two species display different mating systems. Outcomes from this study appear in the journal MycoKeys.

A review of the invasion history and global management strategies of Eucalyptus snout beetles in the Gonipterus scutellatus species complex by researchers in the TPCP appears in the Journal of Pest Science.

In a collaborative venture with Dr Jos Houbraken (Westerdijk Fungal Biodiversity Institute, the Netherlands), Prof. Cobus M Visagie, Dr Neriman Yilmaz (both from FABI) and others have recently completed and published a major study updating the taxonomy of the Eurotiales.

A study in the Forest Molecular Genetics (FMG) Programme at FABI interrogates the benefits of implementing genomic selection for growth and wood quality traits in an established Eucalyptus grandis breeding programme in South Africa. Outcomes from this study appear in an article.

The first study on alternative weed and cultivated hosts of Spongospora subterraneaf. sp. subterranea (Sss), in southern Africa identifies two species as ideal trap crops for rotation with potatoes. The study also introduces three new families to the known hosts of Sss in the region.

A consortium of microbiologists from around the globe, FABI included, is pushing for an overhaul in how scientific names are assigned to uncultivated bacteria and archaea. Despite their ecological, agricultural and medical importance, these organisms traditionally have not been recognized by the international body governing the nomenclature of prokaryotes.

Professor Cobus Visagie is a researcher in the Applied Mycology group at FABI. One of the group’s research goals is to discover fungal diversity in South Africa, and Cobus’ research is strongly focussed on the economically important genera Aspergillus, Penicillium and Talaromyces.

Postdoctoral research by Dr Norman Muzhinji in the Potato Pathology Programme at the Forestry and Agricultural Biotechnology Institute (FABI) sheds light on the genetic structure and diversity of Spongospora subterranea f. sp. subterranea in four potato-growing regions in South Africa, providing valuable insights on its management.

An MSc study by Kira Lynn in the RGE-FABI Tree Health Programme at the University of Pretoria has described a new Fusarium species, Fusarium rekanum sp. nov., associated with Euwallacea perbrevis, an ambrosia beetle species infesting Acacia crassicarpa plantations in Riau, Indonesia.

FABI postdoctoral Fellow Dr Andi Wilson has established a CRISPR-Cas9-based genome editing protocol for use in Huntiella omanensis, a tree-inhabiting fungus belonging to the Ceratocystidaceae family.

Research undertaken as part of a PhD study by Molly Malefo at the University of Pretoria’s Department of Plant and Soil Sciences and Forestry and Agricultural Biotechnology Institute sheds more light on the role of protease inhibitors in plants under drought stress.

The South African National Biodiversity Institute (SANBI) has funded a postdoctoral research project dedicated to monitoring plant health in botanical gardens and arboreta across South Africa. Two postdoctoral Fellows at the University of Pretoria’s Forestry and Agricultural Biotechnology Institute have held these fellowships.

The first comprehensive study mapping the distribution and genetic diversity of invasive Eucalyptus insect pests in sub-Saharan Africa confirms the presence of five major foliage-feeding species in 14 countries. The results of this study have implications on the quarantine, future research and management of these pests on the continent and beyond.

Dr Joey Hulbert broke new ground when he became the first candidate at the Forestry and Agricultural Biotechnology Institute to complete a PhD study incorporating citizen science. Citizen science is an approach that involves members of the public as active participants in scientific research.

FABI technology unravels the genetics behind fungal genome evolution The RIPper is a bioinformatics tool for the for quantifying genome-wide RIP mutations in fungal genomes. The strength of this software lies in the automation of laborious techniques to study the mutation process called Repeat-Induced Point mutations (RIP). The RIPper applies these technique

With the increased availability in genome data, inferences regarding evolutionary relationships among taxa can now be performed on a genome-wide scale. But it is widely accepted that not all parts of such massive datasets support the same evolutionary hypothesis. Because of this, a group of researchers at FABI recently investigated the effect of this.

The use of genome data to characterize species and elucidate relationships, particularly between problematic taxa, has become routine practice in bacteria. Recently, researchers from FABI joined in an international effort to describe two novel genera and characterize these within the larger context of the important bacterial group Burkholderia.

A PhD student in FABI, Runlei Chang, has discovered and described 19 new fungal species from China as part of the research for his thesis. These fungi are all associated with conifer-infesting bark beetles and their mites and belong to well-known genera such as Ophiostoma and Leptographium.

Two research papers from FABI were selected as cover stories in two consecutive issues of the international journal, Plant Pathology. The journal is published by Wiley for the British Society of Plant Pathology.

Plastids play an integral role in wood formation, and yet they are routinely ignored in the study of xylogenesis in forest trees. Desre Pinard and Dr Eshchar Mizrachi have published a review highlighting the unique biology of plastids in wood, suggesting that a new type of plastid, the xylopast, exists.

Approaches for characterizing metabolic potential from genomic sequences have previously been predicted to be useful in the description of bacterial taxa. Dr Marike Palmer, has recently employed these approaches for identifying biological processes contributing to the divergence of bacteria with a variety of lifestyles.

Comparative genomics is shaping our notion of what fungal species are. Based on current data, these unique evolutionary units are separated from one another by boundaries that are porous under certain conditions. This affects our expectations regarding their population biology and evolution, and our strategies for recognizing and controlling them.

The Polyphagous Shot Hole Borer is an ambrosia beetle native to Southeast Asia. In 2017 this pest was detected in South Africa. Its presence has since been confirmed in all provinces except Limpopo. The beetle has a symbiotic relationship with the fungus Fusarium euwallaceae, which causes branch die-back and death of susceptible trees.

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Shuaifei Chen is the first Ph. D student under CFEPP. His research focuses on fungal disease of eucalypts from South China both in nurseries and plantations.

Fig. 1. One World-One Dream, Keeping Trees Healthy.	Fig. 2. Eucalypt diseases survey (Dec., 2006). Left to right: ShuaiFei Chen, XuDong Zhou, Michael J. Wingfield, JiaGuang Cao.
Fig. 3. Cryphonectriaceae survey (Jan., 2007). Left to right: XuDong Zhou and ShuaiFei Chen.	Fig. 4. Eucalypt diseases survey (Sept., 2008). Left to right: Jolanda Roux, ShuaiFei Chen, XinTao Mu, GuiXiang Zhao.
Fig. 5. TPCP disease clinic team (2008). Left to right: ShuaiFei Chen, Donald Chungu, Guillermo Perez, Didier Begoude.	Fig. 6. TPCP disease clinic team (2009). Left to right: Michael Mbenoun, Darryl Herron, Johan Van der Linde, ShuaiFei Chen, Bernice Porter.
Fig. 7. Field inoculation trials (Sep, 2008). Left to right: ChunYan Xie, XinTao Mu, ShuaiFei Chen, GuiXiang Zhao.	Fig. 8. Eucalypt diseases survey (Oct, 2008).
Fig. 9. Young researchers in CERC (Sep, 2008). Left to right: XiuHua Shang, ShiChao Zhang, Ying Jiang, Qiu Liu, HuaLin Zhang, ChunYan Xie, WanHong Lu, GuiXiang Zhao, FeiYang Han,ShiQi Ren, XinTao Mu, ShuaiFei Chen.	Fig. 10. My supervisors and mentors. Left to right: (back row): XuDong Zhou (primary supervisor), Marieka Gryzenhout, Jolanda Roux (co-supervisor), Marelize Van Wyk, DraginjaPavlic, Lorenzo Lombard, Irene Barnes and Donald Chungu; (front row): YaoJian Xie (co-supervisor), ShuaiFei Chen, and Michael J. Wingfield (co-supervisor).

Workshops & Symposia

Archive

Joint IUFRO meeting of IUFRO WP 7.03.13 and 7.03.16: Intersection of Behavioural / Chemical Ecology and Biological Control in Forest Ecosystems

Joint IUFRO meeting: Intersection of Behavioural / Chemical Ecology and Biological Control in Forest Ecosystems

New Publications

Nadasen T, Buitendag C, Visser R, Welgemoed T, Hein I, Berger DK. (2025) A latent invader: transcriptomics reveals Cercospora zeina’s stealth infection strategy of maize and immune-activating effectors. Frontiers in Plant Science 16:1-23. 10.3389/fpls.2025.1703682

Shaw PL, Slippers B, Wingfield BD, Laurent B, Penaud B, Wingfield MJ, Crous PW, Bihon W, Duong TA. (2025) Chromosome-level genome assemblies for the latent pine pathogen, Diplodia sapinea, reveal two accessory chromosomes with distinct genomic features and evolutionary dynamics. G3 Genes|Genomes|Genetics :jkaf239. 10.1093/g3journal/jkaf239

Coelho MA, David-Palma M, Marincowitz S, Aylward J, Pham NQ, Yurkov AM, Wingfield BD, Wingfield MJ, Sheng S, Heitman J. (2025) The complex evolution and genomic dynamics of mating-type loci in Cryptococcus and Kwoniella. PLoS Biology 23:e3003417. 10.1371/journal.pbio.3003417

Visagie CM, Houbraken J, Overy DP, Sklenář F, Bensch K, Frisvad JC, Mack J, Perrone G, Samson RA, van Vuuren NI, Yilmaz N, Hubka V. (2025) From chaos to tranquillity: a modern approach to the identification, nomenclature and phylogeny of Aspergillus, Penicillium and other Eurotiales, including an updated accepted species list. Studies in Mycology 112:117–260. 10.3114/sim.2025.112.04

Vincent C, Singh A, Michalczyk GZ, Lane SL, Kaur R, Gill AR, Dziedzic N, De Silva K, Cho A, Cardoso AA, Alade DO, Tejera-Nieves M, Sharkey TD, Schmiege SC, Pelech E, Locke AM, Leisner CP, Teshome DT. (2025) Importance of measuring and reporting environmental conditions across plant science subdisciplines. Plant Physiology 199(2) 10.1093/plphys/kiaf405

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