The QuantStudio 12K Flex Real-Time PCR Facility

FABI News

News Archive

26 Apr 2024

Eighteen new mentorship students welcomed in the CPHB-FABI Mentorship Program for 2024

Eighteen undergraduate students have joined the 2024 CPHB-FABI Mentorship Programme.

23 Apr 2024

FABIans attend EPN conference in Spain

FABIans Prof. Brett Hurley and Innocent Rakubu attended a congress in Spain to celebrate a century of the discovery of Steinernema kraussei Steiner.

22 Apr 2024

Congratulations Firehiwot!

FABI congratulates Dr Firehiwot Eshetu on the successful completion of her PhD degree.

19 Apr 2024

FABIans celebrate Jackie Robinson Day

Some 60 FABIans gathered at the University of Pretoria’s LC de Villiers sports campus on the afternoon of 15 April to celebrate Jackie Robinson Day.

19 Apr 2024

Using art as a gateway to systems thinking, biomedical careers and health equity

Dr Jeb Owen presented an interesting and thought-provoking seminar “Using art to scaffold systems thinking and biomedical career pathways in young learners” at FABI’s Monday Morning Meeting.

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FABI Events

Monday Morning Meeting

07 May 08h00

TPCP/CPHB Symposium

FABI in a nutshell

Research Features

Archive

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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Quantitative Real-Time PCR is an extensively used analytical method in molecular biology research. With a grant from the NRF National Equipment

Platform (NEP) the QuantStudio™12K Flex Real-Time PCR Facility was established in 2014, aimed towards the provision of a user-friendly real-time PCR

platform to researchers throughout South Africa and to promote realtime PCR-based research. The QuantStudio System allows for small to large-scale

functional genomics studies, with two main functions, gene expression analysis or genotyping assays, being used in either 384 well format or high

throughput OpenArray® technology. As such the QuantStudio™12K Flex Real-Time PCR Facility has become an indispensable tool used by

staff and students in FMG, the university and surrounding universities across South Africa.

Specifically in FMG, functional genomic characterization of wood development and disease resistance projects benefit from the facility. These projects

include the expression analysis of hundreds of genes under varying conditions and treatments, as well as SNP marker genotyping of up to 256 SNP markers

across thousands of individuals. In the past, FMG as a group has used custom designed assays for SNP marker genotyping, and analysis of gene expression

of pathogen defence related genes in Eucalyptus trees. Currently FMG uses the platform to investigate genes involved in secondary cell wall development in

Populus, understanding gene expression of nuclear vs plastid genomes, and several 384 well studies looking at genes of interest. Since the establishment

of the facility the QuantStudio™12K Flex Platform has encouraged collaboration and mentorship across a wide range of research groups, universities

and institutes and has been used by researchers in many different fields whether they are studying the metabolism of humans or researching drought

tolerance in cassava.

Workshops & Symposia

Archive

The 35<sup>th</sup> Annual Meeting of the Tree Protection Co-operative Programme (TPCP) and DSI-NRF Centre of Excellence in Plant Health Biotechnology (CPHB)

The 35^th Annual Meeting of the Tree Protection Co-operative Programme

New Publications

Marais I, Buitendag C, Duong TA, Crampton BG, Theron J, Kidanemarium D, Berger DK. (2024) Double-stranded RNA uptake for the control of the maize pathogen Cercospora zeina. Plant Pathology Online first:1-11. 10.1111/ppa.13909

van Heerden A, Pham NQ, Wingfield BD, Wingfield MJ, Muro Abad JI, Durán A, Wilken PM. (2024) LAMP assay to detect Elsinoë necatrix; an important Eucalyptus shoot and leaf pathogen. Plant Disease 10.1094/PDIS-01-24-0086-RE

Silva GA, Oliveira MES, Rêgo GMS, Wingfield BD, Wingfield MJ, Ferreira MA. (2024) Chrysoporthe brasiliensis sp. nov. pathogenic to Melastomataceae in southeast Brazil. Fungal Biology 10.1016/j.funbio.2024.04.001

Fick A, Swart V, Bombarely A, van den Berg N. (2024) Comparative transcriptional analysis of Persea americana MYB, WRKY and AP2/ERF transcription factors following Phytophthora cinnamomi infection. Molecular Plant Pathology 25(4):e13453. 10.1111/mpp.13453

Van Lill M, Venter SN, Muema EK, Palmer M., Beukes CW, Chan WY, Steenkamp ET. (2024) SeqCode facilitates naming of South African rhizobia left in limbo. Systematics and Applied Microbiology 47(2-3):126504. 10.1016/j.syapm.2024.126504

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