Research Articles (Forestry and Agricultural Biotechnology Institute (FABI))

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Quambalaria spp. : emerging tree pathogens of concern
Jamieson, Brittney-Aiden; Paap, Trudy; Pegg, Geoff S.; Carnegie, Angus J.; Wingfield, Michael J.; Roux, Jolanda; Hardy, Giles ESt J.; Drenth, Andre; Hammerbacher, Almuth; Bose, Tanay (Springer, 2026-05-23)
PURPOSE OF REVIEW : Quambalaria spp. are fungal pathogens originating from Australian eucalypt species that are becoming increasingly important globally. For example, Quambalaria eucalypti, which was once considered a minor pathogen, now poses a significant threat to plantation productivity and forest health across continents. Their spread has been made possible through the expansion of eucalypt plantation forestry outside Australia, the movement of plant material and the increase in travel and trade, which facilitates the intercontinental movement of pathogens. This review summarises current knowledge regarding the taxonomy, distribution, life cycle and ecological and commercial impacts of Quambalaria spp. and some considerations for their control. RECENT FINDINGS : Recent studies have discovered new species of Quambalaria and there is emerging evidence of host shifts to other genera in the Myrtaceae. Outbreaks in Brazil, China, Indonesia and South Africa illustrate the rapid spread of Quambalaria spp. to new plantation environments. These pathogens threaten eucalypt plantations worldwide because clonal propagation reduces tree diversity and the trade of plant material facilitates their spread. Evidence of sexual reproduction has been identified in one species, Quambalaria pitereka, alluding to a high evolutionary potential. Although new molecular diagnostics and resistance screening tools are emerging, their use in the control of these pathogens remains limited. SUMMARY : Quambalaria spp. are important tree pathogens that are increasing their impact beyond their ancestral home in Australia. Their impact on plantation forestry and native forests underscores the broader vulnerabilities of forest ecosystems. Mitigating their impact will require integrated approaches that combine resistance breeding, enhanced surveillance, stringent quarantine measures, integrated disease management and changes to silviculture. Further research into host range, infection biology and pathogen evolution and the development of effective disease control is essential to safeguard global forests and ensure sustainable plantation forestry.
The hidden bias of missing data : multiple imputation reveals geographic disparities and nutrition-WASH synergy as drivers of childhood diarrhea in Nigeria-a cross-sectional analysis of 33,924 children
Ashaolu, Joseph Opeolu; Kaisi, Lydia Amin; Alabi, Gbenga Oluwaseyi; Esther, Omoyajowo A.; Sylvain, Y.M. (BioMed Central, 2026-06-25)
OBJECTIVE : To investigate the determinants of childhood diarrhea in Nigeria, examining socio-economic, geographic, nutritional, and WASH factors, while systematically comparing Multiple Imputation by Chained Equations (MICE) versus Complete Case Analysis (CCA) to demonstrate how missing data methods bias conclusions. METHODS : A secondary cross-sectional analysis was conducted using the latest Nigerian Demographic and Health Survey (2018 NDHS) data on 33,924 under-5 children. The primary outcome was a caregiver-reported diarrhea incidence. Independent predictors were identified using multivariable logistic regression. Robustness was tested by sensitivity analyses through comparison between MICE, CCA and testing principal results under Missing Not at Random (MNAR) assumptions. Multi-dimensional risk heatmaps and correlation networks illustrated interactive risks. RESULTS : Diarrhea prevalence was 12.0%. Profound geo-economic and geographical disparities were uncovered; residing in the North-East was the strongest risk factor (aOR = 2.61), while wealth and maternal education demonstrated protective associations. There was a very high synergistic interaction between poor nutrition and WASH, with combined high-risk categories having the greatest prevalence of diarrhea (15.4%). Intake of eggs had a strong protective association (aOR = 0.87) that persisted under MNAR models. Sensitivity analyses revealed CCA-generated biased estimates, masking protective effects of education and inducing spurious risks for vitamin A and fruit consumption. CONCLUSION : Childhood diarrhea in Nigeria is driven by a complex interplay of interacting factors. Effective control requires a mix of integrated, multi-sectoral interventions involving WASH, nutrition, and poverty concurrently, focusing on high-burden zones. Methodologically, advanced management of missing data is critical to produce valid evidence.
Lineage-specific diversity of pheromone response pathway genes is independent of mating strategy in Ceratocystidaceae
Lane, Frances Alice; Wingfield, Brenda D.; Wingfield, Michael J.; Wilken, P. Markus (BioMed Central, 2026-02-23)
The pheromone-receptor system plays a crucial role in mate recognition and fertilisation of ascomycete fungi and is strongly regulated by proteins coded for in the mating-type locus. This locus also determines the mating strategy, sexual identity and mate compatibility of fungal species. Genome assemblies are available for many species in the Ceratocystidaceae, a family of fungi with diverse mating strategies. This provided an opportunity to investigate the relationship between sexual strategy and the pheromone-receptor system in these species. The pheromone and pheromone-receptor genes were identified and characterised from the genome sequences of 52 isolates representing 35 species from 14 genera in the Ceratocystidaceae. Additionally, these data were used to elucidate patterns linked to differences between the pheromones and pheromone receptors, and mating strategies. To do this, the target genes were identified using homologous- and syntenic-based approaches. Putative protein sequences and genomic locations were then compared across the entire family, including species of Huntiella that had previously been characterised. With a few exceptions, putatively functional pheromones and receptors were identified in all the Ceratocystidaceae genomes. The results showed no discernible link between the presence, genomic location or structure of these proteins and mating strategy. Interspecific conservation in sequence and genomic locations revealed greater correlation to taxonomic relatedness, although intraspecific variation was also observed. Interestingly, despite reports of sexual reproduction in Ambrosiella species, all genomes of these species lacked the α-pheromone gene and encoded a non-functional α-pheromone receptor. This is the most extensive study of pheromones and their receptors in a Sordariomycetes family and complements efforts aimed at understanding the complex history of sexual reproduction in the Ceratocystidaceae.
First report of Melanterius inconspicuus (Coleoptera: Curculionidae: Cleogonini) from KwaZulu-Natal, South Africa, with observations of its development in black wattle
Nel, Wilma Janine; Barnes, Irene; Jali, Sandisiwe; Impson, Fiona; Oberprieler, Rolf G.; Hurley, Brett Phillip (Taylor and Francis, 2026)
Melanterius is a large genus of small weevils that primarily feed on the seeds of Acacia species occurring in their native range in Australia. In the latter part of the 20th century, five seed-feeding Melanterius species were released against several weedy Acacia species in South Africa as biological control agents. In early 2024, Melanterius weevils were detected damaging the vegetative plant tissues of trees in a commercial black wattle (Acacia mearnsii) compartment in the KwaZulu-Natal, South Africa. Morphological identification and DNA sequencing revealed that the weevils represent the species Melanterius inconspicuus, which is not one of the five species introduced in South Africa. This finding represents the first record of this Melanterius species outside of its native range in Australia and infesting black wattle, as well as the first record of a Melanterius species infesting vegetative tissues.
Automated waterbird detection, classification, and mapping from UAV imagery using a two-stage deep learning pipeline
Bogaert, Miel; De Cock, Andree; Liu, Xingzhen; Ho, Long; Maes, Wouter H.; Goethals, Peter L.M. (Elsevier, 2026-08)
Waterbirds function as sensitive indicators of ecological change in freshwater ecosystems. Conventional monitoring is labour-intensive, spatially limited, prone to observer bias and disturbance. Unmanned Aerial Vehicle (UAV) imagery combined with deep learning (DL) offers a promising alternative for efficient and scalable monitoring. This study evaluates a fully automated UAV-based workflow to detect, classify, and map waterbirds along a 12 km canal in Belgium. A two-stage pipeline combining YOLO-based detection and convolutional neural network (CNN) classification was developed and evaluated across varying flight altitudes and ground sampling distances (GSD). Model performance was further assessed using an independent seasonal dataset and analysed in relation to object size and habitat complexity. The detection model achieved a high precision of 0.91 and a recall of 0.81, while the classifier reached a weighted F1-score of 0.90. Detection performance was strongly dependent on ground sampling distance (GSD), with optimal results at ≤6.83 mm px−1 (≤25 m altitude) and marked declines in detection performance at higher GSD values. Additional analyses showed that smaller birds were more likely to be missed, while high-entropy environments such as reed beds may further reduce detection reliability. Comparisons between automated and manual counts revealed discrepancies, influenced by environmental conditions and survey timing. Georeferenced detections projected onto orthomosaics enabled spatially explicit mapping of waterbird distribution. Overall, UAV-based deep learning provides a promising and scalable approach for waterbird monitoring, while highlighting the importance of spatial resolution and habitat complexity in determining detection performance. HIGHLIGHTS • UAV imagery enables non-intrusive monitoring of waterbirds along freshwater canals. • A two-stage YOLO–CNN pipeline detects and classifies waterbirds. • Optimal detection performance was achieved at GSD values of 6.83 mm px−1 or below. • Mechanistic detection analyses reveal the influence of area, brightness, and entropy • Automated mapping reveals species-specific spatial patterns along the canal.
First report of pepper ringspot virus infecting sunflower (Helianthus annuus) in South Africa
Burger, Vida; Esterhuizen, Lindy; Read, David Alan (Springer, 2026-02)
No abstract available.
Genera of phytopathogenic fungi known from culture : 1-379
Crous, Pedro W.; Groenewald, J.Z.; Bensch, K.; Gene, J.; Guarro, J. (Westerdijk Fungal Biodiversity Institute, 2025-12-03)
Approximately 200000 species of fungi have been described to date, representing nearly 8000 currently recognised genera. Many of these genera are regarded as plant pathogenic, as they include at least one species proven to cause pre- or postharvest plant disease. Following the abandonment of dual nomenclature and the advent of DNA sequencing and phylogenetic approaches, numerous para- and polyphyletic clades were resolved into distinct genera. These genera are now defined based on morphology, ecology, and DNA phylogeny. The present paper represents the first in a series that aims to provide descriptions, classification, illustrations, significant species, disease symptoms, and DNA data for the common genera of phytopathogenic fungi known from culture, including the first treatment of 379 genera. In addition, several new combinations, lecto-, epi-, or neotypes are also proposed.
Eucalyptus grandis A uxin R esponse F actor 10 (EgrARF10) is associated with the modulation of secondary xylem cell wall chemistry
Makhura, Ipeleng; Ployet, Raphael; Myburg, Alexander A.; Cassan-Wang, Hua; Hussey, Steven Grant (Springer, 2026-07-28)
Auxin Response Factors (ARFs) are of vital importance in plant growth and vascular development. Class A ARFs are the core auxin-driven drivers of embryogenesis, vascular pattern development, (pro)cambial stem cell initiation and xylem cell fate specification, while class B ARFs may attenuate or fine-tune auxin-mediated development. The potential roles of class C ARFs in vascular development and xylogenesis, however, remain largely unexplored. In this study, we identified Eucalyptus grandis ARF10 (EgrARF10) as a potential regulator of secondary cell wall (SCW) development. We show that EgrARF10 is nucleus-localised and strongly associated with SCW biosynthetic genes and transcription factors across co-expression and multi-omic networks. Mining of published spatial and single cell transcriptomic data revealed preferential expression of EgrARF10 in vessel and fusiform organizer cells of secondary xylem tissue, while EgrARF10 orthologs in other species exhibit diverse cell type-specific expression ranging from root cap vascular and metaxylem to cork cambium. Heterologous overexpression of EgrARF10 in hybrid poplar did not alter overall growth or morphology but resulted in a significant reduction in stem lignification, accompanied by relative increases in D-glucose, D-xylose and D-mannose, indicating altered SCW composition. While the molecular mechanism by which EgrARF10 acts remains unknown, these findings provide the first evidence for the role of a class C ARF in xylem SCW biology.
Identification of Botryosphaeriaceae species in the South African National Collection of Fungi, including a novel species of Oblongocollomyces
Jami, Fahimeh; Truter, Mariëtte; Pavlic, Draginja; Chen, ShuaiFei; Roux, Jolanda (South African National Biodiversity Institute, 2026-07-06)
The Botryosphaeriaceae is a diverse group of fungi that includes several important plant pathogens. This study aimed to identify the 201 Botryosphaeriaceae isolates deposited at the South African National Collection of Fungi (NCF). The isolates were revived and phylogenetic analyses, based on multiple loci (ITS, tef1-α, rpb2, tub2), revealed several distinct clades, leading to the identification of 15 known species from Botryosphaeria, Lasiodiplodia, Neofusicoccum and a new species of Oblongocollomyces. This study expands the known diversity and host ranges of the Botryosphaeriaceae in South Africa and China, significantly contributing to our understanding of this family. The results highlight the importance of national collections as valuable resources for fungal biodiversity research. Further research is needed to explore the pathogenicity and distribution of these species in local agricultural ecosystems.
Kosakonia beeri sp. nov. and Phytobacter cepae sp. nov. isolated from onion (Allium cepa)
Jordan, Sara; Pothier, Joel F.; Rezzonico, Fabio; Kvitko, Brian H.; Coutinho, Teresa A.; Smits, Theo H.M. (Microbiology Society, 2026-01)
Please read abstract in the article.
Urban green spaces as emerging hotspots for Phytophthora diversity : a global synthesis of host associations, distribution and management gaps
Vettraino, Anna Maria; Bose, Tanay (Frontiers Media, 2026-07)
Urban green spaces are increasingly recognised as interfaces for plant health, yet their role in shaping the diversity and spread of Phytophthora remains poorly synthesised globally. We compiled 166 records of Phytophthora–host associations from 16 peer-reviewed studies (2005–2025) across botanical gardens, parks, street trees, and managed urban landscapes. Only confirmed pathogenic interactions were included. The dataset comprised 28 Phytophthora taxa and 96 host taxa from 11 countries, yielding 133 unique associations. Diversity was highly uneven, with a few taxa dominating urban systems. Phytophthora multivora was the most frequently recorded taxon and had the broadest host range, followed by P. nicotianae, P. cinnamomi and P. ramorum. Associations were concentrated in angiosperms, especially Ericales, Myrtales, and Fagales, with Ericaceae, Myrtaceae, and Theaceae prominent. Nearly 60% of hosts were non-native, reflecting ornamental horticulture and global plant trade. Records were geographically biased, with Spain and South Africa accounting for over two-thirds of observations, while many regions remain underrepresented. A median 6-year lag between sampling and publication may delay recognition of emerging risks. Urban environments support structured Phytophthora communities shaped by host composition, environment, and human-mediated plant movement, functioning as reservoirs and sources of inoculum for surrounding ecosystems. To address management limitations, we propose a conceptual framework that integrates prevention, detection, response, and recovery into an adaptive cycle for urban green spaces, supporting pathway-based biosecurity, risk prioritisation, and coordinated surveillance. Our study highlights the need for more balanced global surveillance and coordinated management of Phytophthora in urban and peri-urban landscapes to improve urgently needed resilience and biosecurity outcomes globally.
The Moringa value chain in Ethiopia and the socio-economic impact of pests and diseases
Fitawek, Wegayehu Bogale; Anjulo, Agena; Healey, Madaline; Lawson, Simon; Hurley, Brett Phillip (CAB International, 2026-05-20)
BACKGROUND : Moringa is a multipurpose tree, and the demand for Moringa products is growing significantly. It has gained popularity in southern Ethiopia, where the tree is cultivated for its nutritious food, medicinal properties, cultural significance, and economic value. However, there is limited research examining how pests and diseases affect the Moringa value chain. The aims of this study were to examine the socio-economic factors influencing the level of pest severity among Moringa growers and to estimate the impact of Moringa production on the income of value chain actors. METHODS : The study used primary data collected from Moringa value chain actors in the Arba Minch and Derashe districts of the southern Ethiopia Region, encompassing 507 households involved in the Moringa value chain. The study employed value chain mapping to analyse the entire chain and applied a multinomial endogenous switching regression model to address selection bias and assess the impact of Moringa production on the income of value chain actors. Results: Results show that younger individuals, women, singles, and cooperative members are more likely to participate in distribution and processing, while larger households with land and more Moringa plants tend to remain growers. Pest severity varies by location and household age, with Arba Minch growers more likely to experience medium pest severity, likely due to lower insecticide use than in Derashe. Distributors earn significantly less than growers, while processors earn similar incomes. Pest impacts on income were not statistically significant, likely because infestation periods were brief and Moringa is mainly grown for household consumption. CONCLUSIONS : The findings provide new insights into the impact of pests and diseases on the Moringa value chain and on the income of actors. The results identify key socio-economic and locational factors associated with pest severity among growers and estimate income differences across value chain actors. This highlights how participation in different stages of the value chain and pest dynamics influence economic outcomes in Moringa production systems. Given Moringa’s importance as a staple vegetable for food security, employment opportunities, and medicinal and cultural benefits, support from the government and NGOs is essential to strengthen the Moringa value chain. In addition, raising awareness of the impacts of insecticides and promoting integrated pest management is crucial for sustainable and resilient Moringa production and should inform policy and technical interventions.
Preserving the biologically coherent generic concept of Phytophthora, “plant destroyer”
Brasier, Clive M.; Grünwald, Niklaus J.; Bourret, Tyler B.; Govers, Francine; Scanu, Bruno; Cooke, David E.L.; Bose, Tanay; Hawksworth, David L.; Abad, Gloria; Albarracin, M. Victoria; Alsultan, Wael; Altamirano-Junqueira, Astrid E.; Arifin, Arild R.; Arnet, Matthew J.; Aumentado, Herbert Dustin R.; Bakonyi, József; Belisle, Wei H.; Benigno, Alessandra; Bienapfl, John C.; Bilodeau, Guillaume J.; Blair, Jaime E.; Botella, Leticia; Brandano, Andrea; Cacciola, Santa Olga; Carbone, Ignazio; Castroagudin, Vanina L.; Chaendaekattu, Narayanan; Consford, Jonathan D.; Corcobado, Tamara; Covey, Paul A.; Daniels, Hazel A.; Deidda, Antonio; Dorrance, Anne E.; Dort, Erika N.; Drenth, André; Drizou, Fryni; Evangelisti, Edouard; Fajardo, Sebastian N.; Fang, Yufeng; Ference, Christopher M.; Frankel, Susan J.; Goss, Erica M.; Guest, David I.; Hardy, Giles E.S.J.; Harris, Anna R.H.; Hawku, Mehari Desta; Heungens, Kurt; Hong, Chuanxue; Horner, Ian J.; Jung, Marília Horta; Iyanda, Olumayowa J.; Jamieson, Brittney-Aidan; Jeffers, Steven N.; Judelson, Howard S.; Junaid, Muhammad; Kalogeropoulou, Eleni; Kamoun, Sophien; Kang, Seogchan; Kasuga, Takao; Kudlácek, Tomáš; LeBoldus, Jared; Lee, Christopher A.; Li, DeWei; Llanos, Alejandro K.; Lopez-Nicora, Horacio D.; Machado, Helena; Di San Lio, Gaetano Magnano; Maia, Cristiana; Mandal, Kajal; Manosalva, Patricia; Martin, Frank N.; Matson, Michael E.H.; McDougal, Rebecca L.; McDowell, John M.; Michelmore, Richard W.; Milenkovi´c, Ivan; Moricca, Salvatore; Mostowfizadeh-Ghalamfarsa, Reza; Nagy, Zoltán Á.; Nikolaeva, Ekaterina V.; Ortega-López, Paula; Paap, Trudy; Parada-Rojas, Camilo H.; Peduto Hand, Francesca; Pérez-Sierra, Ana; Pettersson, Martin; Prasad, Pramod; Puig, Alina S.; Raco, Milica; Rajput, Nasir A.; Ristaino, Jean B.; Rooney-Latham, Suzanne; Seidl, Michael F.; Shamoun, Simon F.; Solla, Alejandro; Spies, Christoffel F. J.; Sudermann, Martha A.; Swiecki, Tedmund J.; Tian, Miaoying; Tripathy, Sucheta; Uematsu, Seiji; Van Poucke, Kris; Vichou, Aikaterini E.; Walter, Monika; Webber, Joan F.; Williams, Nari M.; Wingfield, Michael J.; Yadav, Dhananjay; Yang, Xiao; Jung, Thomas (American Phytopathological Society, 2025-06)
Phytophthora is a long-established, well-known, and globally important genus of plant pathogens. Phylogenetic evidence has shown that the biologically distinct, obligate biotrophic downy mildews evolved from Phytophthora at least twice. Because, cladistically, this renders Phytophthora “paraphyletic,” it has been proposed that Phytophthora evolutionary clades be split into multiple genera (Crous et al. 2021; Runge et al. 2011; Thines 2023, 2024). In this letter, we review arguments for the retention of the generic name Phytophthora with a broad circumscription made by Brasier et al. (2022) and by many delegates at an open workshop organized by The American Phytopathological Society. We present our well-considered responses to the genus splitting proposals, both in general terms and in terms of the specific proposals for new genera, alongside new information regarding the biological properties and mode of origin of the Phytophthora clades. We consider that the proposals are mostly non-rigorous and not supported by the scientific evidence. Further, given (i) the apparent lack of any distinguishing biological characteristics (synapomorphies) between the Phytophthora clades; (ii) the fundamental monophyly of Phytophthora in the original Haeckelian sense (Haeckel 1877); (iii) the fact that paraphyly is not a justification for taxonomic splitting; and (iv) the considerable likely damage to effective scientific communication and disease management from an unnecessary breakup of the genus, we report that workshop delegates voted unanimously in favor of preserving the current generic concept and for seeking endorsement of this view by a working group of the International Commission on the Taxonomy of Fungi.
Comparative analysis of mitochondrial genomes in the Ceratocystidaceae reveals highly conserved gene organization despite substantial genome size variation
Viljoen, Anien; Duong, Tuan A.; Kanzi , Aquillah M.; Wingfield, Brenda D. (BMC, 2026-03-19)
BACKGROUND : Comparative studies of mitochondrial genomes can assist in determining evolutionary and phylogenetic relationships. In the Ceratocystidaceae fungal family, mitochondrial genomes from only two genera are publicly available. In this study, mitochondrial genomes from 10 genera in Ceratocystidaceae were characterised and comparatively analysed. RESULTS : Mitochondrial (mt) genomes were fully assembled and characterized for 18 species and 10 genera of the Ceratocystidaceae. These mt genomes displayed a remarkable level of diversity owing to the variation in the intergenic regions and intron, both in size and number. Despite large variation in size, these mt genomes displayed high levels of synteny and sequence conservation in the oxidative phosphorylation (OXPHOS) genes and the ribosomal RNA and tRNA genes. The genes are found in identical order and orientation in all mt genomes characterized and the coding sequence of all the OXPHOS genes are highly conserved. Phylogenetic analysis of mitochondrial and nuclear DNA sequences reveals significant differences in evolutionary relationships among species and genera of Ceratocystidaceae. CONCLUSION : The remarkable variation in mt genome sizes in species of the Ceratocystidaceae is due to the variation observed in the intergenic regions and intron size and number in the conserved protein-coding genes. The gene order and content are identical across all species investigated.
The critically endangered geophyte Gladiolus aureus threatened by a wilt disease associated with Fusarium libertatis
Balocchi, Felipe; Duncan, Graham; Yilmaz, Neriman; Wingfield, Michael J.; Paap, Trudy (Springer, 2026-05)
Gladiolus aureus is a geophyte species endemic to the South African Cape Peninsula. Pressures including land-use change and invasion by alien plants have caused severe population declines, leading to its classification as Critically Endangered (CR). Kirstenbosch National Botanical Garden (NBG) maintains the largest ex situ collection of this species. During plant health surveys conducted as part of a sentinel plant research project, a recurring wilt disease was observed in the ex situ collection. Symptomatic plants were sampled and fungal isolations consistently yielded a Fusarium species, identified as F. libertatis, as confirmed through DNA sequencing and phylogenetic analyses. Dormant corms donated by Kirstenbosch NBG for pathogenicity tests were asymptomatically colonised by the same fungus, suggesting that F. libertatis may be widespread in the collection and may be moved through contaminated planting material as well as growing media. This study highlights the challenges posed by plant pathogens to the conservation of threatened plant taxa and underscores the limited disease management tools available in ex situ collections.
Baseline sensitivity of South African Fusarium circinatum to tebuconazole
Masuku, Sicelo K.; De Vos, Lieschen; Motaung, Thabiso Eric; Steenkamp, Emma Theodora; Wingfield, Brenda D. (Springer, 2026-05)
Pine pitch canker, caused by Fusarium circinatum, is among the most destructive forest diseases worldwide, leading to growth suppression, wilting, and root disease in pine seedlings. Infections result in canker formation, contributing to significant losses in wood quality and yield in pine plantations. In South Africa, the sensitivity of F. circinatum to fungicides has not been investigated, representing a critical knowledge gap, particularly because fungicides are widely used to control other Fusarium species. This study aimed to establish the baseline sensitivity of a South African F. circinatum population to tebuconazole (TBZ), a sterol biosynthesis inhibitor. A total of 86 isolates, collected from various pine species across different geographic regions and years, were tested in vitro for their response to increasing concentrations of TBZ. Sensitivity was assessed by measuring mycelial growth inhibition and calculating the mean effective concentration (EC50). The population-wide EC50 was 0.039 ± 0.012 µg mL− 1, establishing a baseline sensitivity to TBZ. No significant differences in EC50 values were observed across years of isolation, provinces, host species, or mating types. These results provide an important reference for future resistance monitoring and inform the strategic use of TBZ in South African forestry. Interestingly, less sensitive isolates observed in a subset of older isolates may reflect historical exposure to fungicides in nursery environments or the introduction of less sensitive strains later on through trade, infected planting material, or other propagative sources.
Unveiling the hidden virome of Sclerotinia sclerotiorum : new tools and discoveries in mycovirus detection
Bornman, Simoné; Read, David Alan; Wingfield, Brenda D.; Wilken, Pieter Markus (Elsevier, 2026-10)
Mycoviruses are widespread in fungi and can influence fungal physiology, pathogenicity, and ecological interactions. In the plant pathogenic fungus Sclerotinia sclerotiorum, increasing attention has been directed toward understanding the diversity and functional roles of its associated viruses. This review synthesizes current knowledge on mycovirus detection methods and summarizes the diversity of viruses reported in S. sclerotiorum. Early detection strategies based on double-stranded RNA profiling, virion purification, and RT-PCR laid the foundation for mycovirus discovery but were limited in their ability to detect low-abundance or highly divergent viruses. The emergence of next-generation sequencing (NGS) and metatranscriptomic approaches has transformed the field, enabling large-scale in silico mining of fungal transcriptomes and facilitating the discovery of numerous novel viruses. To date, more than 270 mycoviruses have been reported from S. sclerotiorum, spanning over 30 viral families and representing diverse genome types. Many of these viruses occur in mixed infections and some are associated with hypovirulence, a phenotype characterized by reduced fungal growth and pathogenicity that holds potential for biological control. Despite rapid advances in virus discovery, significant gaps remain in understanding the functional consequences of infection, transmission dynamics, and ecological interactions within fungal populations. Integrating classical molecular techniques with high-throughput sequencing and functional studies will be essential for translating mycoviral diversity into mechanistic insights and applied strategies for disease management. HIGHLIGHTS • Advances in sequencing reveal extensive mycovirus diversity in fungi • Over 270 mycoviruses reported in Sclerotinia sclerotiorum • NGS enables detection of low-abundance and novel viral sequences • Many mycoviruses linked to hypovirulence in fungal pathogens • Mycoviruses show promise for biological control of plant diseases
Constitutive foliar metabolite variation in conifers shapes their susceptibility to the invasive herbivore Lymantria dispar asiatica
Cui, Mingming; Iyiola, Ebenezer A.; Chen, Chen; Hammerbacher, Almuth; Audet, Pierre; Blackburn, Gwylim S.; Keeling, Christopher I.; Stoehr, Michael; Bird, Keith; Degner, Jonathan; El-Kassaby, Yousry A.; Bernier, Louis; Keena, Melody; Porth, Ilga M. (Canadian Science Publishing, 2026-05-28)
Forest ecosystems are increasingly threatened by invasive pests due to global trade and changing environmental conditions. Improving tree resilience through selective breeding represents an effective management strategy. We used a combination of Lymantria dispar asiatica insect rearing, host metabolomic profiling, and full-sib family effect parameter evaluation of metabolites to identify defenses with greatest genetic potential. Among conifers studied for larval development, coastal Douglas-fir was the most and Norway spruce the least favorable host. Phenolics in foliage grouped conifer species phylogenetically, whereas terpenes reflected feeding behavior of the larvae better. Analysis of Douglas-fir full-sib families revealed moderate to high family effects of phytochemicals, suggesting potential for direct improvement of resistance. However, terpene profiles of nursery versus field grown Douglas-fir and Norway spruce were highly dissimilar, illustrating environmental and ontogenetic variability of biochemical traits. Insect bioassays thus need to be directly linked to terpene profiles of tested trees and data cannot be extrapolated to the species level. This integrated framework proposes a way for identifying targeted defenses and assessing their genetic potential, supporting evidence-based strategies for developing pest-resistant forest trees under increasing biological invasions. Follow-up work is needed to enhance phenotyping capacities of targeted resistance traits and obtain breeding values for these.
Phylogenetic and population genetic analyses reveal patterns of divergence among isolates of Ceratocystis manginecans
Lynn, Kira Mary Theresa; Wingfield, Michael J.; Oliveira, Leonardo S.S.; Alfenas, Acelino C.; Alfenas, Rafael Ferreira; Marincowitz, Seonju; Barnes, Irene (Wiley, 2026-05)
The taxonomic boundaries of Ceratocystis species related to C. manginecans have remained contentious due to limited morphological variation, interfertility in laboratory mating studies, and the application of different species concepts. However, recent studies have highlighted significant differences among species recently reduced to synonymy with C. manginecans, including host associations and biological traits, all with important implications for disease management. We examined the phylogenetic relationships, genetic diversity and population structure of isolates considered broadly as Ceratocystis manginecans, specifically those treated as C. eucalypticola and C. manginecans in various previous studies. The study included a comprehensive dataset of isolates from multiple hosts and regions, including both historical and recent outbreaks of Ceratocystis canker and wilt disease. Multi-locus phylogenetic analyses, supported by genotyping at 16 SSR loci, resolved two genetically distinct lineages: Lineage 1 (previously treated as C. eucalypticola) and Lineage 2 (previously treated as C. manginecans). These lineages showed structured genetic differentiation across geographic regions and host associations, consistent with previously reported differences in aggressiveness and infection biology. Detailed morphological comparisons also provided support for the two groupings. Although the results revealed the existence of two lineages among isolates currently treated as C. manginecans, discordance among loci and signals of admixture in a subset of isolates were consistent with evidence for mixed ancestry and/or incomplete lineage sorting. This suggests incomplete reproductive isolation that is contributing to current taxonomic ambiguity and confusion. The results support treating the isolates in the two groups as distinct lineages (Lineage 1 and 2) within C. manginecans, recognising their differences while maintaining a conservative taxonomic approach and thus facilitating important quarantine considerations and future studies focused on disease management.
Orders of ascomycota
Thiyagaraja, V.; Hyde, K.D.; Piepenbring, M.; Davydov, E.A.; Dai, D.Q.; Abdollahzadeh, J.; Bundhun, D.; Chethana, K.W.T.; Crous, Pedro W.; Gajanayake, A.J.; Gomdola, D.; Haelewaters, D.; Johnston, P.R.; Mardones, M.; Perera, R.H.; Senanayake, I.C.; Tibpromma, S.; Yasanthika, W.A.E.; Abbasi, M.W.; Abdel-Wahab, M.A.; Absalan, S.; Acharya, Krishna Prasad; Afshari, N.; Aouali, S.; Aptroot, A.; Apurillo, C.C.S.; Armand, A.; Avasthi, S.; Bao, D.F.; Bhat, D.J.; Blondelle, A.; Boonmee, S.; Boonyuen, N.; Braun, U.; Čadež, N.; Calabon, M.S.; Cazabonne, J.; Chakraborty, N.; Cheewangkoon, R.; Chen, K.-H.; Coleine, C.; Darmostuk, V.; Daroodi, Z.; Dasgupta, D.; De Groot, M.D.; De Hoog, S.; Deng, W.; Dissanayake, A.J.; Dissanayake, L.S.; Doilom, M.; Dong, W.; Ertz, D.; Fortuna, J.L.; Gautam, A.K.; Gorczak, M.; Groenewald, M.; Groenewald, J.Z.; Gunarathne, A.; Han, Y.; Hongsanan, S.; Hou, C.L.; Htet, Y.M.; Htet, Z.H.; Huang, Q.; Huang, S.K.; Huanraluek, N.; Jayalal, R.G.U.; Jayasiri, S.C.; Jayawardena, R.S.; Jiang, S.H.; Jones, E.B.G.; Karimi, O.; Karunarathna, S.C.; Khuna, S.; Kossmann, T.; Kularathnage, N.D.; Lestari, A.S.; Li, C.J.Y.; Li, J.F.; Lin, C.G.; Liu, J.K.; Liu, X.; Liu, Y.; Lu, L.; Lu, Y.; Luo, Z.L.; Ma, J.; Madagammana, A.S.; Maharachchikumbura, S.S.N.; Marasinghe, D.S.; Martzoukou, E.; Marin-Felix, Y.; Miller, A.N.; Monkai, J.; Noorabadi, M.T.; Norphanphoun, C.; Olariaga, I.; Opiña, L.A.D.; Pang, K.L.; Peng, X.; Péter, G.; Phillips, A.J.L.; Pineda, M.M.; Prieto, M.; Quan, Y.; Quandt, A.; Rajeshkumar, K.C.; Rambold, G.; Raymundo, T.; Raza, M.; Réblová, M.; Samaradiwakara, N.P.; Sarma, V.V.; Schultz, M.; Seifollahi, E.; Selbmann, L.; Su, H.; Sun, Y.R.; Tehler, A.; Tennakoon, D.S.; Thambugala, K.M.; Tian, W.H.; Tsurykau, A.; Valenzuela, R.; Verma, R.K.; Wang, J.; Wang, W.P.; Wang, X.Y.; Wang, Y.; Wang, Z.; Wei , D.P.; Wen, T.; Wijayawardene, N.N.; Wimalasena, M.K.; Worthy, F.R.; Wu, H.X.; Xu, L.; Yakovchenko, L.S.; Yu, F.M.; Zeng, X.Y.; Zhang, S.N.; Zhang, Z.Y.; Zhao, Q.; Wanasinghe, D.N. (Maximum Academic Press, 2025-05-18)
Ascomycota, the most speciose phylum of fungi, is a complex entity, comprising three diverse subphyla: Pezizomycotina, Saccharomycotina, and Taphrinomycotina. The largest and most diverse subphylum, Pezizomycotina, is a rich tapestry of 16 classes and 171 orders. Saccharomycotina, the second largest subphylum, is a diverse collection of seven classes and 12 orders, while Taphrinomycotina, the smallest, is a unique assembly of six classes and six orders. Over the past decade, numerous taxonomic studies have focused on the generic, family, and class classifications of Ascomycota. These efforts, well-documented across various databases, are crucial for a comprehensive understanding of the classification. However, the study of taxonomy at the ordinal level, a crucial tier in the taxonomic hierarchy, has been largely overlooked. In a global collaboration with mycologists and lichenologists, this study presents the first comprehensive information on the orders within Pezizomycotina and Taphrinomycotina. The recent taxonomic classification of Saccharomycotina has led to the exclusion of this subphylum from the present study, as an immediate revision is not necessary. Each order is thoroughly discussed, highlighting its historical significance, current status, key identification characteristics, evolutionary relationships, ecological and economic roles, future recommendations, and updated family-level classification. Teaching diagrams for the life cycles of several orders, viz. Asterinales, Helotiales, Hypocreales, Laboulbeniales, Meliolales, Mycosphaerellales, Ophiostomatales, Pezizales, Pleosporales, Phyllachorales, Rhytismatales, Sordariales, Venturiales, Xylariales (Pezizomycotina) and Pneumocystidales, Schizosaccharomycetales and Taphrinales (Taphrinomycotina) are provided. Each diagram is explained with a representative genus/genera of their sexual and asexual cycles of each order. Within Pezizomycotina, Dothideomycetes contains the highest number of orders, with 57, followed by Sordariomycetes (52 orders), Lecanoromycetes (21 orders), Eurotiomycetes and Leotiomycetes (12 orders each), Laboulbeniomycetes (3 orders), and Arthoniomycetes and Xylonomycetes (2 orders each). Candelariomycetes, Coniocybomycetes, Geoglossomycetes, Lichinomycetes, Orbiliomycetes, Pezizomycetes, Sareomycetes, and Xylobotryomycetes each contain a single order, while Thelocarpales and Vezdaeales are treated as incertae sedis within Pezizomycotina. Notably, the classes Candelariomycetes, Coniocybomycetes, Geoglossomycetes, Sareomycetes, and Xylonomycetes, all recently grouped under Lichinomycetes, are treated as separate classes based on phylogenetic analysis and current literature. Within Lecanoromycetes, the synonymization of Sporastatiales with Rhizocarpales and Sarrameanales with Schaereriales is not supported in the phylogenetic analysis. These orders are retained separately, and the justifications are provided under each section as well as in the discussion. Within Leotiomycetes, the order Medeolariales, which was once considered part of Helotiales, is treated as a distinct order based on phylogenetic evidence. The classification of Medeolariales may change as more data becomes available from different gene regions. Lahmiales (Leotiomycetes) is not included in the phylogenetic analysis due to a lack of molecular data. Sareomycetes and Xylonomycetes are treated as separate classes. Spathulospora mixed with Lulworthiales and the inclusion of Spathulosporales within Lulworthiomycetidae is supported and extant molecular sampling is important to resolve the phylogenetic boundaries of members of this subclass. The majority of the classes of Pezizomycotina and Taphrinomycotina formed monophyletic clades in the phylogenetic analysis conducted based on SSU, LSU, 5.8S, TEF and RPB2 sequence data. However, Arthoniomycetes nested with the basal lineage of Dothideomycetes and formed a monophyletic clade also known as the superclass, Dothideomyceta. In Taphrinomycotina, a single order is accepted within each class.

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