Avocado Genome Consortium

FABI News

News Archive

28 May 2026

FABI mycologist lands major Oppenheimer Memorial Trust award to unlock South Africa's fungal secrets

Professor. Cobus Visagie has received one of South Africa's most prestigious research grants

27 May 2026

FABI researchers participate in the IUFRO Tree Wilt Disease Congress in Athens

A group of FABI researchers met in Athens to attend and participate in a joint meeting of two IUFRO Division 7 Working Parties

26 May 2026

FABI researchers study and compare Croatian and South African bark beetle fungi

Prof. Mike Wingfield recently visited Croatia to inspect various field sites and to plan further details of a research project

25 May 2026

TPCP field extension and diagnostic clinic trip visits the Eastern Cape

Teams from the Tree Protection Co-operative Programme (TPCP) field extension and diagnostic clinic embark on a joint field trip to the Eastern Cape.

20 May 2026

CPHB-FABI interns at Nampo Harvest Day 2026

On 12 May, interns in the Phytosanitation and Biosecurity Internship Program at FABI had the exciting opportunity to attend NAMPO Harvest Day 2026

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Research Features

Archive

Tracing the past, building the future: FABI research unlocks the genetics and genomics of the Sirex woodwasp complex

FABI researcher co-authors global perspective on mycotoxins and food safety.

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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The advent of next-generation sequencing (NGS) technologies has revolutionised research capacity and its broad applicability over the past decade. These technologies have directly impacted researchers’ ability to understand host-pathogen interactions, holistically, and on a molecular scale. Recently, the avocado industry has begun to unravel some of the underlying mysteries that pertain to prevalent avocado pests and diseases; the Avocado Research Programme (ARP) has been highly influential in this space.

As a founding member of the Avocado Genome Consortium - an international collaborative effort which was established in 2016 - the ARP has directly contributed to the development of a high quality, chromosome-level reference genome assembly for Persea americana (avocado). The Avocado Genome Consortium has used this new reference genome to re-sequence more than 10 additional cultivars and rootstocks as part of an ongoing project, with plans to increase this number soon. Provided with this data, researchers will be able to accelerate the arduous process of selecting rootstocks and cultivars with desirable traits.

As part of the broader objectives of the Avocado Genome Consortium, transcriptomic data has also been generated. This data will be utilized to answer fundamental questions pertaining to the evolutionary biology, gene expression, physiological processes, and molecular pathways in avocado. Transcriptomic data from a dual RNA-sequencing experiment - involving both susceptible and partially resistant avocado rootstocks challenged with Phytophthora cinnamomi - was also used to identify avocado defence targets and discovery of pathogen effectors involved in disease development. The data from this work has been published across several research articles and will be used to further our understanding of the avocado-P. cinnamomi interaction.

The researchers involved are:

David Kuhn, USDA, Florida
Patricia Manosalva, UCR, California
Noëlani van den Berg, UP, South Africa
Antonio Javier Matas Arroyo, Departamento de Biología Vegetal, University of Malaga, Spain
Aureliano Bombarley Gomez, Virginia Tech Horticulture, USA
Randy Ploetz, University of Florida, USA
Alan Chambers, University of Florida, USA

Workshops & Symposia

Archive

The TPCP / FMG-EPPI Symposium 2026

New Publications

Townsend G, Hill M, Hurley BP, Roets F. (2026) Native Scolytinae and Platypodinae beetle assemblages in indigenous South African forests and their co-occurrence with the invasive PSHB beetle. Journal of Insect Conservation 30 10.1007/s10841-026-00779-8

Botha I, Maduna SN, Hagen SB, Lall N, Berger DK. (2026) 3RAD-guided SNP discovery for species identification and conservation of the medicinal southern African tree Genus Greyia Hook. & Harv.. Ecology and Evolution 16(5):e73412, 1-29. 10.1002/ece3.73412

Balocchi F, Duncan G, Yilmaz N, Wingfield MJ, Paap T. (2026) The critically endangered geophyte Gladiolus aureus threatened by a wilt disease associated with Fusarium libertatis. Journal of Plant Pathology 10.1007/s42161-026-02227-7

Bose T, Wingfield MJ. (2026) Plantations are invasive pathogen bridgeheads—response to Li et al.. Trends in Ecology & Evolution 10.1016/j.tree.2026.05.006

Jamieson B-A, Paap T, Pegg GS, Carnegie AJ, Wingfield MJ, Roux J, Hardy GEStJ, Drenth A, Hammerbacher A, Bose T. (2026) Quambalaria spp.: Emerging Tree Pathogens of Concern. Current Forestry Reports 12:13. 10.1007/s40725-026-00274-y

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