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

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Hidden diversity behind the Lecanicillium-like white colony-forming mycoparasites on Hemileia vastatrix (coffee leaf rust)
Colman, A.A.; Araujo, J.P.M.; Evans, H.C.; Mansur, P.S. Correa; Salcedo-Sarmiento, S.; Silva, A.L.; Kapeua-Ndacnou, M.; Belachew-Bekele, B.K.; Pereira, C.M.; Crous, Pedro W.; Barreto, R.W. (Westerdijk Fungal Biodiversity Institute, 2025-12)
During surveys for fungal natural enemies of Hemileia vastatrix - the causal agent of coffee leaf rust (CLR) - in its African centre of origin (Cameroon, Ethiopia), as well as in its exotic South American range (Brazil, Paraguay), an eclectic and species-rich mycobiota was encountered. Here, we provide a comprehensive report on an assemblage of "white colony-forming fungi" (WCF), often treated in the earlier literature under the inadequate "label" Verticillium lecanii (=Lecanicillium lecanii). A total of 265 isolates of WCF were provisionally placed in this arbitrary group. We clarified the identity of our assemblage of Lecanicillium-like fungi using a combination of morphological characteristics and sequence data for the large subunit nuclear ribosomal DNA (LSU), translation elongation factor 1-α (TEF) and the largest subunits of RNA polymerase II (RPB1 and RPB2) regions. Fifteen WCF species belonging to eight genera across three hypocrealean families (Bionectriaceae, Clavicipitaceae and Cordycipitaceae) were found parasitizing pustules of CLR. Significantly, Lecanicillium lecanii was not found to be present amongst these taxa. Six species belonged to the known genera - Corniculantispora, Gamszarella, Lecanicillium, Ovicillium, Pleurodesmospora and Simplicillium. Two new genera are described, Bettiolomyces and Hemileiophthora, as well as seven new species, Bettiolomyces urediniophagus, Gamszarella uredinophila, Hemileiophthora denticulata, H. nodosa, Lecanicillium hemileiae, Pleurodesmospora hemileiae and Simplicillium hemileiae. The following known WCF species are recorded here for the first time on pustules of H. vastatrix: Corniculantispora dimorpha, Gamszarella buffelskloofina, Lecanicillium uredinophilum, Ovicillium attenuatum, Pleurodesmospora coccorum and Simplicillium subtropicum. Additionally, the new combination Bettiolomyces epiphytus is introduced for Verticillium epiphytum.
Inside the belly of the beast : exploring the gut bacterial diversity of Gonipterus sp. n. 2
Knoppersen, Rosa Sophie; Bose, Tanay; Coutinho, Teresa A.; Hammerbacher, Almuth (Springer, 2025-04-12)
The Eucalyptus snout beetle (Gonipterus sp. n. 2) is a destructive invasive pest of Eucalyptus plantations, responsible for significant defoliation and wood yield losses globally. Native to Australia, this beetle has adapted to thrive on diverse Eucalyptus hosts, overcoming their chemical defences. However, the mechanisms by which Gonipterus tolerates or utilises these plant defence metabolites remain poorly understood. In South Africa, Gonipterus sp. n. 2 poses a significant threat to Eucalyptus plantations by causing extensive defoliation and leading to substantial reductions in growth and wood production. This study investigates the relationship between diet, host Eucalyptus species, and the gut microbiome of Gonipterus sp. n. 2. Using controlled feeding experiments, beetles were reared on artificial, semi-artificial, and natural diets, as well as two Eucalyptus genotypes with distinct secondary metabolite profiles. High-throughput 16S rDNA sequencing and gas chromatography-mass spectrometry (GC–MS) revealed significant shifts in gut bacterial diversity and composition across diets. Natural diets supported the most diverse microbial communities, while artificial diets fostered a homogenised microbiome dominated by opportunistic taxa like Serratia. Host-specific effects were observed in frass microbiota, with substantial biotransformation of monoterpenes into less toxic derivatives. The results highlight the plasticity of Gonipterus gut microbiota, which enables metabolic adaptability and resilience in diverse environments. This microbial flexibility underpins the invasiveness of Gonipterus, emphasising the role of gut symbionts in overcoming host chemical defences. Understanding these interactions offers novel insights for microbiome-targeted pest management strategies, providing a sustainable approach to mitigate the impact of Gonipterus on global Eucalyptus forestry.
The 2022 Fusarium head blight outbreak in Ethiopia : emerging pathogens, mixed mycotoxins, and interspecies interactions
DeGenring, Liza M.; Gemechu, Ashenafi; Rafiei, Vahideh; Broz, Karen; Regasa, Gizachew H.; Munsamy, Kiara; Yilmaz, Neriman; Dong, Yanhong; Rouse, Matthew N.; Drott, Milton T. (American Phytopathological Society, 2026-03)
As Ethiopia pushes toward self-sufficiency in wheat production, it has escaped large outbreaks of Fusarium head blight (FHB), a disease that threatens wheat production globally. However, in 2022, FHB incidences in Ethiopia rose to 80%, with some areas experiencing 100% disease severity. Here we provide insights into the etiology of this disease outbreak and point toward future directions to mitigate the emerging threat of FHB on a global scale. Although most wheat samples from 2022 exhibited low trichothecene levels, 26% exceeded recommended thresholds and several contained multiple trichothecene variants. We obtained 64 isolates from the outbreak and identified diverse members of the Fusarium graminearum species complex (FGSC) and many Epicoccum species. The FGSC species contributing to the outbreak are rare on a global scale. Genomic analyses reveal that Fusarium aethiopicum has persisted in Ethiopia for decades and shares ancient ancestry with a newly emerged novel species in the FGSC that we formally described as Fusarium kistleri. Single-nucleotide polymorphism–based analyses suggest high clonal fraction among FGSC isolates in Ethiopia, raising questions about a recent population expansion. Our findings reveal that although Epicoccum alone causes minimal disease on wheat, its presence can have a small but synergistic impact on disease symptoms when F. graminearum has already infected. The unique diversity and species composition of the 2022 Ethiopian outbreak underscores the importance of addressing emerging threats in a globalized agricultural economy to secure food safety, food security, and global food equity.
Evaluation of phosphite to protect a South African Proteaceae from Phytophthora root rot
Msweli, Dumsani; Geerts, Sjirk; Nndanduleni, Mashudu; Paap, Trudy (Springer, 2025-11)
Phytophthora cinnamomi is a globally recognised invasive plant pathogen, affecting approximately 5000 host species. In South Africa, previous research has linked P. cinnamomi to root rot in endemic Proteaceae, including Leucadendron argenteum. Recent observations have noted high mortality rates in L. argenteum, with P. cinnamomi readily isolated from the roots and collars of dying trees. Phosphite is commonly used to control Phytophthora diseases, but its efficacy in protecting native South African flora remains uncertain. To address this, trials were conducted to evaluate phosphite’s effectiveness against P. cinnamomi infection in L. argenteum. In the glasshouse trial, four-month-old seedlings were treated with 5 g/L phosphite and then inoculated with P. cinnamomi. Non-treated inoculated seedlings exhibited rapid wilting within three weeks, while treated seedlings showed significant disease reduction, with no difference in root weight and seedling height compared to non-inoculated controls. In the field trial, L. argenteum trees treated with 40 g/L and 50 g/L phosphite injections over 30 months showed no significant difference in survival rates compared to untreated controls. The lack of phosphite efficacy in the field trial was attributed to the presence of Armillaria spp. The study underscores the threat P. cinnamomi poses to L. argenteum populations and highlights the additional risk from Armillaria. While phosphite has demonstrated effectiveness against Phytophthora root rot, further investigation is needed to determine if P. cinnamomi and Armillaria spp. have synergistic effects on L. argenteum mortality. Additionally, exploring phosphite’s potential to protect plants from A. mellea at the seedling stage is warranted.
Ophiostoma ipsi-confusi sp. nov. six, Marinc. & Duong, a consistent symbiotic fungus of the pinyon ips bark beetle, ips confusus LeConte
Six, Diana L.; Marincowitz, Seonju; Duong, Tuan A. (Springer, 2026)
Several tree-killing bark beetle species have nutritional mutualisms with specific fungi. However, few secondary bark beetles (those that colonize weak or dying trees) have been investigated for symbiotic fungi and most are thought to have only incidental fungal associates and no dependence on fungi for nutritional or other benefits. In contrast to this supposition, we consistently isolated (> 97%) a fungus from adult Ips confusus (pinyon ips) collected from Pinus edulis (two-needle pinyon pine) from Arizona and New Mexico, USA. Using morphology and DNA sequences for three gene regions, we found the fungus is most closely related to an obligate mutualist fungus of Dendroctonus ponderosae (mountain pine beetle), Ophiostoma montium (Ascomycota: Ophiostomatales), but is morphologically and genetically distinct from it and other known species in Ophiostoma. It is also capable of growth at relatively high temperatures compared with other Ophiostoma, reflective of its southwestern USA distribution. The high frequency of its association with the beetle indicates it is symbiotic and suggests it may be a mutualist.
Global dominance of Haloquadratum walsbyi by a single genomovar with distinct gene content and viral cohorts from close relatives
Bustos-Caparros , Esteban; Viver , Tomeu; Gago, Juan F.; Avontuur, Juanita R.; Amiour, Souad; Baxter, Bonnie K .; Llames, María E.; Mutlu, Mehmet B.; Oren, Aharon; Ramírez, Ana S.; Stott, Matthew B.; Venter, S.N. (Stephanus Nicolaas); Santos , Fernando; Antón, Josefa; Rodriguez-R, Luis M.; Bosch, Rafael; Hedlund, Brian P.; Konstantinidis, Konstantinos T.; Rossello-Mora, Ramon (Oxford University Press, 2025-01)
Haloquadratum walsbyi is generally the dominant species in hypersaline ecosystems at salt saturation conditions. Here, we followed the dynamics of its genomovars and associated viruses during recurrent evaporation-dilution disturbances of varying intensities at the mesocosm scale over 813 days. The diversity observed within a single mesocosm was also compared with that in a global-scale inventory of hypersaline environments of thalassohaline origin. The 140 binned metagenome assembled genomes (MAGs) together with the genomes of the (only) two available of H. walsbyi isolates grouped into four highly related (98.25% > Average Nucleotide Identity [ANI] > 99.5%) dominant genomovars (intra-genomovar ANI > 99.5%). In mesocosm experiments, moderate disturbances (i.e. recurrent dilution from saturation to 20% salts) enhanced the abundance of the already-dominant genomovar Hqrw1, resulting in reduced intraspecific diversity. This genomovar also dominated in almost all sites sampled around the globe. In contrast, more intense disturbance (i.e. recurrent dilution from saturation to 13% salts) decreased the abundance of Hqrw1 to lower levels than genomovar Hqrw2 by the end of the incubation, which seems to resist better osmotic changes. Further, our results showed that genomovars were followed by their viral cohorts, who play a significant role in the global dominance of the four H. walsbyi genomovars and their replacement under unfavorable conditions. We propose that the global dominance of H. walsbyi in thalassohaline hypersaline sites is enabled by both the success of Hqrw1 in high but stable salinities and the larger resistance of Hqrw2 to extreme osmotic stress, safeguarding the presence of the species in the system.
Uneven sequencing (coverage) depth can bias microbial intraspecies diversity estimates and how to account for it
Bustos-Caparros, Esteban; Viver, Tomeu; Gago, Juan F.; Venter, S.N. (Stephanus Nicolaas); Bosch, Rafael; Konstantinidis, Konstantinos T.; Rodriguez-R, Luis M.; Rossello-Mora, Ramon (Oxford University Press, 2025-01)
An unbiased and accurate estimation of intraspecies diversity, i.e. the extent of genetic diversity within species (or microdiversity), is crucial for clinical and environmental microbiome studies. Although it is well appreciated that sequencing depth (or coverage depth) below 10X can provide biased estimates of microdiversity, typically underestimating diversity due to the random sampling of alleles, there is a widely accepted convention that microdiversity estimates tend to be relatively stable at sequencing depth exceeding 10X. Therefore, discarding species with <10X or rarefying to 10-20X sequencing depth are generally used to compare microdiversity among taxa and samples. Our findings showed that these biases may persist even at depth levels above 50-200X for all popular sequencing platforms, including Illumina, PacBio, and Oxford Nanopore. The biases mostly, but not always, represent an underestimation of diversity and were attributable to the incomplete recovery of Single Nucleotide Variants (SNVs) at lower sequencing depth levels. To address this issue, we recommend using rarefaction-based approaches to standardize data at least 50X, and ideally at 200X sequencing depth, which reduces differences between observed and expected microdiversity values to <0.5%. Furthermore, the Average Nucleotide Identity of reads (ANIr) metric is significantly less sensitive to sequencing depth variability than nucleotide diversity (π), making it a robust alternative for estimating microdiversity at sequencing depth close or exceeding 10X, without a need to rarefying data. Therefore, the sequencing depth thresholds proposed herein provide a more standardized framework for direct comparisons of microdiversity across samples and studies.
Microscale assessment of brush packing mulch as a method for enhancing soil moisture content and promoting delayed grass seedling mortality of subtropical grasses
Mangani, Tshepiso; Monegi, Piet; Mangani, Robert (Wiley, 2026-04)
Recurring droughts in South Africa's dryland rangelands have profound effects on ecosystem health. Consequently, identifying sustainable soil moisture content techniques is critical for enhancing plant growth to support ecosystem function. Soil moisture content was measured daily for five weeks using the field capacity as a reference and compared within the two mulching densities, high and low versus bare soil. The effect thereof was evaluated on growth parameters: emergence, relative growth, and survival rate of three subtropical grasses (Cenchrus ciliaris, Chloris gayan, and Panicum maximum) in seedling trays under a greenhouse. Soil moisture content significantly differed in all the treatments (p < 0.05); the mulching treatments retained half their moisture compared to the no cover treatment, which lost more than 77% moisture. The evapotranspiration was cumulatively lowest in the high-density mulching. Overall, Chloris gayana and Panicum maximum had the highest emergence (> 40%) and relative growth in the mulching treatments, while Cenchrus ciliaris emerged better (56%) and had relative growth in the no cover. By Week 6, many seedlings did not survive; however, Panicum maximum persisted in the high-density mulching with almost 17% seedlings survival. The mulching effect improved soil moisture content, thus providing more conducive conditions for germination and survival, especially of understorey grasses. While this approach is effective for certain grass species, it has demonstrated ecologically significant enhancement for soil moisture content and reducing evaporation, potentially promoting good soil structure and health.
Pseudoteratosphaeria supramediana sp. nov. (Teratosphaeriaceae, Mycosphaerellales), a new foliar pathogen on Eucalyptus in Indonesia
Pham, Nam Q.; Marincowitz, Seonju; Wingfield, Brenda D.; Crous, Pedro W.; Santos, Samuel A.; Duran, Alvaro; Tarigan, Marthin; Wingfield, Michael J. (Springer, 2026-02)
The Eucalyptus plantation industry in Indonesia has expanded rapidly during the last few decades. This growth is primarily attributed to the replacement of Acacia mangium, that was severely damaged by diseases. The rapid shift to large-scale monoculture plantations of Eucalyptus has introduced new challenges, particularly the emergence of new disease and pest problems. During routine Eucalyptus disease surveys in Indonesia, symptoms of a new leaf and shoot disease were observed on a single hybrid Eucalyptus grandis × pellita clone in Riau and Kalimantan. Leaf samples were collected, and isolations were made from the disease symptoms. Isolates were identified based on their morphological characteristics and DNA sequence data for seven loci. Phylogenetic analyses of the isolates revealed a novel species of Pseudoteratosphaeria, described here as Pseudoteratosphaeria supramediana sp. nov. A greenhouse pathogenicity test resulted in symptoms similar to those found under field conditions, and the inoculated fungus was consistently reisolated from the resulting lesions. Its appearance in two geographically distinct locations of Indonesia raises the possibility of multiple independent introductions of the pathogen.
Cold storage of Gonipterus platensis (Coleoptera: Curculionidae) eggs for Anaphes nitens (Hymenoptera: Mymaridae) rearing
Ribeiro, Murilo Fonseca; Cavallini, Gabriela; Solce, Gabriel Negri; Favoreto, Ana Laura; Passos, Jose Raimundo De Souza; Barbosa, Leonardo Rodrigues; Hurley, Brett Phillip; Wilcken, Carlos Frederico (PeerJ, Inc., 2026-03-13)
BACKGROUND : Anaphes nitens (Girault, 1928) (Hymenoptera: Mymaridae) is an egg parasitoid used for the biological control of Gonipterus spp. in regions where this pest is present. Cold storage of host eggs is a crucial strategy in biological control programs. This study aimed to evaluate the effects of cold storage on G. platensis eggs for laboratory rearing of both the host and its parasitoid, A. nitens. METHODS : Gonipterus platensis eggs, aged 1 and 3 days, were stored in a refrigerator at 7 ± 1 °C for 5, 10, 20, 30, 40, and 50 days in complete darkness. After each storage period, the eggs were transferred to a biochemical oxygen demand (BOD) chamber at 25 °C and hatching rates and larval survival were assessed. To evaluate parasitoid reproduction, fresh host eggs were stored at 7 ± 1 °C for 5, 10, 15, 20, and 25 days under dark conditions and subsequently exposed to A. nitens. Parasitism rate, sex ratio, and offspring longevity were recorded. RESULTS : Results showed that 1- and 3-day-old G. platensis eggs maintained the highest viability within the first 10 days of storage, with hatching rates exceeding 50% up to 20 days post-storage. A 20-day storage period was the longest duration that did not differ significantly from the non-stored eggs (control) considering A. nitens parasitism and progeny longevity when stored host eggs were offered. CONCLUSION : Therefore, storing host eggs for this period effectively supports colony maintenance while simultaneously facilitating parasitoid propagation.
Comparative population genetics of Exserohilum turcicum in smallholder farms of Kenya and Uganda
Mahlangu, Jabulile N.N.; Berger, David Kenneth; Nsibo, David Livingstone (Wiley, 2026-01)
Exserohilum turcicum, the causal agent of northern leaf blight (NLB), poses a major threat to maize production in sub-Saharan Africa. Effective disease management depends on understanding the biology and population genetic structure of the pathogen, yet studies from Africa remain limited. Here, we investigated the genetic diversity and evolutionary forces shaping E. turcicum populations in Kenya and Uganda. A total of 494 strains were genotyped using 12 microsatellite markers. Gene diversity was relatively low in Kenya (He = 0.45) and Uganda (He = 0.42) compared with previous reports. Analysis of molecular variance revealed weak but significant differentiation between countries (ΦPT = 0.178, p = 0.001), with more variation occurring within countries (82%) than among them (18%). Cluster analyses showed high levels of gene flow within each country but limited admixture between countries, suggesting geographical barriers to dispersal. Grouping populations according to shared agroecological zones did not result in distinct genetic clustering, indicating that population structure was not driven by agroecological similarity. This interpretation was supported by a weak isolation-by-distance correlation (R2 = 0.077), consistent with restricted long-distance gene flow. Most populations deviated from the expected 1:1 mating-type ratio, highlighting the importance of clonal reproduction in shaping population structure. Collectively, these findings suggest that E. turcicum populations are largely panmictic within countries but exhibit restricted cross-country movement. These results provide a valuable foundation for developing sustainable, regionally targeted strategies to manage NLB in East Africa.
Bodyguard interactions : a beneficial endophyte triggers emission of methyl salicylate in infested tomato plant mediating attraction of a parasitoid wasp
Akutse, Komivi S.; Agbessenou, Ayaovi; Yusuf, Abdullahi Ahmed; Khamis, Fathiya Mbarak (Springer, 2026-03-13)
The endoparasitoid Dolichogenidea gelechiidivoris is a potential candidate biocontrol agent of Phthorimaea absoluta. We previously reported that the endophyte Trichoderma asperellum M2RT4 triggers the systemic release of key phytohormones in tomato affecting the behavior and herbivory of P. absoluta. As D. gelechiidivoris uses odor cues to locate P. absoluta, we therefore investigated the chemical basis of interactions between D. gelechiidivoris, the tomato plant with and without endophyte and P. absoluta through bioassay-guided chemical analysis. Y-tube olfactometer bioassays showed that the parasitoid was significantly attracted to P. absoluta-infested tomato plants but did not show preference to colonized and colonized-infested plants. Coupled GC–MS analyses revealed both qualitative and quantitative differences in volatile emission between non-colonized, colonized, non-colonized infested and colonized-infested plants, where volatile emission rate increased with increasing infestation level. Methyl salicylate (MeSA) emission was significantly higher in colonized-infested than in colonized and non-colonized infested plants. Subsequent bioassays revealed attraction of the parasitoid to synthetic MeSA emitted at its natural release rate from endophytically-colonized infested plants. Our findings highlight the significant role played by MeSA, which mediates the attraction of D. gelechiidivoris thereby indirectly assisting tomato plants in combatting P. absoluta.
An evidence-based protocol for developing lists for tree planting
Potgieter, Luke J.; Cadotte, Marc W.; Kumschick, Sabrina; Paap, Trudy; Roets, Francois; Wilson, John R.U.; Richardson, David M. (Pensoft Publishers, 2025-11)
Tree-planting is increasingly being promoted for urban greening, carbon sequestration, and to enhance biodiversity. However, poorly planned and executed tree-planting schemes can inadvertently contribute to biological invasions with detrimental effects on local ecosystems, economies, and human well-being. Therefore, sustainable, rigorous, repeatable, and transparent species selection strategies are needed. We developed a strategic decision protocol for identifying tree taxa suitable for planting schemes, using a multi-criterion approach that integrates national lists of regulated invasive plant species, global evidence of invasiveness, and susceptibility to key pests. Using the Polyphagous Shot Hole Borer (PSHB) invasion in the City of Cape Town, South Africa as a case study, we illustrate the protocol’s application and potential for informing planting decisions. 444 tree taxa currently planted in Cape Town were assessed. Of these, 85 are regulated nationally as invasive species (and are prohibited from use), while 49 met all suitability criteria and were identified as candidates for a planting list (i.e., a safe list). This protocol provides evidence-based guidance for tree-planting to mitigate the risk of tree invasions and to reduce the spread and impact of associated pests and pathogens. This protocol is replicable and adaptable for use in other regions and can support environmental planners and managers in making informed decisions to safeguard ecosystems and optimise ecosystem services (e.g., which trees to plant in restoration initiatives).
Advancing the taxonomy of Sclerotinia (Helotiales, Sclerotiniaceae) : a review and recommendations for an important plant-pathogenic genus
Thomas, Chanel; Wilken, Pieter Markus; Coetzee, Martin Petrus Albertus; Visagie, Cobus M. (Pensoft Publishers, 2026)
Sclerotinia is a fungal genus of significant agricultural and scientific importance, as it includes multiple plant pathogens and provides an informative case study for mechanisms of host generalism. However, the taxonomy of this group remains unsettled, which hinders research on these pathogens. The last monographic treatment of Sclerotinia was published more than 40 years ago and was centered on the morphological data available at that time. Here, we examine that revision alongside other pivotal publications to trace the taxonomic history of Sclerotinia and to evaluate the morphological traits used to identify Sclerotinia species. We also briefly assess the composition of genera in the family Sclerotiniaceae, emphasising the need for a modern taxonomic investigation of the broader group. Thirteen new Sclerotinia species have been described since the last taxonomic revision, including Sclerotinia antarctica, S. asari, S. atrostipitata, S. cirsii-spinosissimi, S. ginseng, S. glacialis, S. himalayensis, S. nivalis, S. pseudoplatani, S. subarctica, S. tetraspora, S. trillii, and S. verrucispora. These species are evaluated here. Finally, several recommendations are made regarding how future taxonomic research on Sclerotinia should incorporate molecular data. We highlight potential obstacles and opportunities for this research, including the limitations of the internal transcribed spacer rDNA region (ITS) as a DNA barcode and the untapped potential of genomic data for the genus. By outlining the gaps that need to be addressed, this review charts a course toward a clearer understanding of taxonomic relationships among Sclerotinia species. This understanding will facilitate research into other aspects, such as pathogenicity and host generalism, and may ultimately contribute to improved management of the devastating diseases caused by these pathogens.
A weighted gene co-expression network analysis characterises the common defence responses of Eucalyptus to diverse biotic challenges
Swanepoel, Shae; Naidoo, Sanushka (Nature Research, 2026-02)
Eucalyptus is a globally important forestry genera cultivated for paper, pulp and biofuel production. These trees are increasingly threatened by a range of emerging pests and pathogens. While previous studies have focused on the transcriptomes of single Eucalyptus-pathogen interactions, the core transcriptional networks underlying defence across multiple biotic challenges remain poorly understood. Here we integrated 180 Eucalyptus-biotic stress RNA-sequencing libraries to characterise the common defence gene network during interactions with five distinct pathosystems. We constructed a comprehensive weighted gene co-expression network and identified 38 modules of highly co-expressed genes consisting of between 40 and 3,328 genes. The network revealed distinct modules that were induced by pathogen infection, enriched for defence responses including salicylic acid signalling and secondary metabolite biosynthesis and notably nitrate transport and responses, suggesting a potential link between nitrogen metabolism and immunity. Transcription factor enrichment analysis highlighted WRKY family genes as key regulators of induced responses, with WRKY6 emerging as a candidate hub gene in broad-spectrum resistance. Together, this study provides the first integrative transcriptome network of Eucalyptus responses to diverse biotic stressors, and offers candidate genes and pathways for future functional validation to enhance disease resistance resource in long-lived trees.
Pinus-derived membrane vesicles disrupt pathogenic metabolism in fungi
Kunene, Sithembile; Mmushi, Tshepo Joseph; Steenkamp, Emma Theodora; Motaung, Thabiso Eric (Wiley, 2026)
• Much of what we know about the biological impacts of vesicles (MVs) is derived from Arabidopsis thaliana. Our study focused on vesicles from species in the non-model plant group, Pinus (pine) (P. elliottii, P. radiata, and P. patula × Pinus tec (hybrid)). These plants have tougher tissues and strong, acicular-shaped leaves (needles). • Herein, we first developed a protocol to guide effective collection of juice fluid from needles and roots in a clean and efficient manner. The effects of these vesicles were characterized in terms of the global nutrient profile of the pine pitch canker fungus, Fusarium circinatum, generated from growing fungal spores on ~400 substrates embedded across BioLog phenotypic microarray (PM) plates (PM1, PM2A: carbon sources; PM3B: nitrogen sources; PM9: osmolytes/pH; PM24C: chemicals). • Our findings revealed that MVs, specifically needle-derived MVs (ndMVs) from P. elliottii, disrupt metabolite assimilation in several important pathways, including carbon and nitrogen metabolism. The PM data were also strongly correlated with observed phenotypic effects, including reduced viability and germination of spores in liquid media, as well as impaired filamentous growth on solid media. Importantly, these MV-induced phenotypic effects were reproducible in other filamentous pathogens (e.g., Botrytis cinerea, Chrysoporthe cubensis and F. graminearum) and during a glasshouse trial conducted with F. circinatum-infected P. elliottii seedlings, demonstrating the stable biological effects of ndMVs. • Cumulatively, our results suggest that plant-derived vesicles can disrupt metabolism in pathogenic fungi and, therefore, serve as a cost-effective and sustainable source of novel plant protection molecules.
Genome resources of Xanthomonas vasicola strains from various hosts : reference-guided chromosome and plasmid assemblies for enhanced pathogen genomics
Zim, Nomakula Y.; Yssel, Anna E.J.; Coutinho, Teresa A. (Springer, 2026)
No abstract available.
Genome and transcriptome-based identification and expression profiling of chemosensory gene families across developmental stages and tissues in Sirex noctilio (Hymenoptera: Siricidae)
Postma, Alisa; Klynsmith, Leandri; Duong, Tuan A.; Allison, Jeremy D.; Smidt, Werner; Waterhouse, Robert M.; Lesny, Peter; Oeyen, Jan Philip; Petersen, Malte; Martin, Sebastian; Liu, Shanlin; Zhou, Xin; Ziesmann, Tanja; Donath, Alexander; Mayer, Christoph; Misof, Bernhard; Niehuis, Oliver; Peters, Ralph S.; Podsiadlowski, Lars; Coetzee, Martin Petrus Albertus; Joubert, Fourie; Slippers, Bernard (Wiley, 2026)
The Sirex woodwasp (Sirex noctilio; Hymenoptera: Siricidae) is among the most destructive invasive pests affecting Pinus plantations worldwide. Chemosensory systems offer promising targets for pest control strategies. The identification and characterization of chemosensation genes in non-model, economically significant insects such as S. noctilio, is an important first step towards the development of such control methods. Here we sequenced and assembled a draft genome of S. noctilio and performed RNA-sequencing of 15 olfactory and non-olfactory tissues to study the expression patterns of chemosensation-related genes. Specific genes, such as SnocOR16 and SnocSNMP1, displayed tissue- and sex-specific expression patterns, making them particularly intriguing for their potential roles in chemosensation and oviposition. As woodwasps and their related lineages form a sister group to the majority of other Hymenoptera, including Apocrita, insights into their gene repertoires are crucial for tracing the evolutionary history of chemosensory multigene families of this ecologically and economically significant insect order. This study enhances our understanding of the molecular mechanisms underlying S. noctilio chemosensation, paving the way for further research in chemical ecology and the functional characterization of S. noctilio chemosensation genes.
Genome analyses reveal two novel species of Seiridium from Acacia mearnsii
Aylward, Janneke; Visagie, Cobus M.; Roets, Francois; Wingfield, Brenda D.; Wingfield, Michael J. (Springer, 2026-02)
Seiridium is a genus of Sordariomycetes (Amphisphaeriales, Sporocadaceae), primarily known for species that cause cypress canker on Cupressaceae trees. However, most species in this genus have been reported from angiosperms, including many species in the native range of their hosts. Several unidentified Seiridium strains, collected > 20 years ago from Acacia mearnsii trees in eastern South Africa and southeastern Australia, were recently recovered from a collection of preserved cultures. We considered the phylogenetic position of these Seiridium strains and assessed their pathogenicity on A. mearnsii. Maximum likelihood analysis of three concatenated gene regions revealed four well-supported clades. Two closely related clades corresponded to Australian and South African origins, whereas two other clades representing South African isolates formed a monophyletic group with S. kartense, a species known from Eucalyptus cladocalyx on Kangaroo Island in Australia. Genome-wide average pairwise nucleotide identity and genetic differentiation analysis supported three species, including isolates considered conspecific with S. kartense and two that we consider to represent new species. These are described and named here as Seiridium mearnsii sp. nov. and Seiridium rouxiae sp. nov. Inoculations with South African isolates failed to produce evidence of pathogenicity. Seiridium species from A. mearnsii have likely been introduced into South Africa from Australia, along with the planting material used to establish A. mearnsii forestry.
A haplotype-resolved reference genome for Eucalyptus grandis
Lötter, Anneri; Bruna, Tomas; Duong, Tuan A.; Barry, Kerrie; Lipzen, Anna; Daum, Chris; Yoshinaga, Yuko; Grimwood, Jane; Jenkins, Jerry W.; Talag, Jayson; Borevitz, Justin; Lovell , John T.; Schmutz, Jeremy; Wegrzyn, Jill L.; Myburg, Alexander A. (Oxford University Press, 2025-07)
Eucalyptus grandis is a hardwood tree used worldwide as pure species or hybrid partner to breed fast-growing plantation forestry crops that serve as feedstocks of timber and lignocellulosic biomass for pulp, paper, biomaterials, and biorefinery products. The current v2.0 genome reference for the species served as the first reference for the genus and has helped drive the development of molecular breeding tools for eucalypts. Using PacBio HiFi long reads and Omni-C proximity ligation sequencing, we produced an improved, haplotype-phased assembly (v4.0) for TAG0014, an early-generation selection of E. grandis. The 2 haplotypes are 571 Mbp (HAP1) and 552 Mbp (HAP2) in size and consist of 37 and 46 contigs scaffolded onto 11 chromosomes (contig N50 of 28.9 and 16.7 Mbp), respectively. These haplotype assemblies are 70–90 Mbp smaller than the diploid v2.0 assembly but capture all except one of the 22 telomeres, suggesting that substantial redundant sequence was included in the previous assembly. A total of 35,929 (HAP1) and 35,583 (HAP2) gene models were annotated, of which 438 and 472 contain long introns (>10 kbp) in gene models previously (v2.0) identified as multiple smaller genes. These and other improvements have increased gene annotation completeness levels from 93.8 to 99.4% in the v4.0 assembly. We found that 6,493 and 6,346 genes are within tandem duplicate arrays (HAP1 and HAP2, respectively, 18.4 and 17.8% of the total) and >43.8% of the haplotype assemblies consists of repeat elements. Analysis of synteny between the haplotypes and the E. grandis v2.0 reference genome revealed extensive regions of collinearity, but also some major rearrangements, and provided a preview of population and pangenome variation in the species.

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