Research Articles (Biochemistry, Genetics and Microbiology (BGM))

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Orthosiphon stamineus Benth. (Lamiaceae) : a bibliometric analysis of its antidiabetic properties
Akwu, Nneka Augustina; Banji-Onisile, Folasade; Kayode, Adeoye John; Rambau, Unarine; Mendez, Melisa; Nnadozie, Ijeoma; Ansori, Arif Nur Muhammad; Purnobasuki, Hery (Universidade Estadual de Maringa, 2025)
The use of medicinal plants for the management of diabetes is gaining rapid attention. There are several reports on the antidiabetic properties of Orthosiphon stamineus Benth. There has been no previous bibliometric analysis review conducted on O. stamineus as an antidiabetic agent to date. Therefore, this review is centred on gathering information about the potential sources of antidiabetic properties from O. stamineus. A bibliometric analysis on the antidiabetic properties of O. stamineus was conducted following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. Scientific publications in the SCOPUS database were retrieved using the search strings ‘Orthosiphon stamineus’ OR ‘Orthosiphon aristatus’ OR ‘Kumis Kucing’ OR ‘Misai Kucing’ OR ‘Java tea’ AND ‘diabetes’ OR ‘diabetes mellitus’ OR ‘dm’ OR ‘antidiabetic’ OR ‘hypoglycemic’ OR ‘diabetic complications’ OR ‘insulin’ OR ‘glucose’. 76 articles related to O. stamineus and diabetes were included after the exclusion criteria. The bibliometric analysis spanning from 1991 and 2023 sheds light on the dynamic and collaborative research landscape surrounding O.stamineus. It highlights several aspects of the plant's multifaceted exploration for potential antidiabetic properties, including a surge in activity in 2006 and 2012, international contributions, a diverse distribution across journals, and a broad spectrum of keyword concepts.
Whole genome sequencing of Yersinia pestis isolates from Central Asian natural plague foci revealed the role of adaptation to different hosts and environmental conditions in shaping specific genotypes
Abdirassilova, Aigul A.; Yessimseit, Duman T.; Kassenova, Altynai K.; Abdeliyev, Beck Z.; Zhumadilova, Zauresh B.; Tokmurziyeva, Gulnara Zh.; Kovaleva, Galina G.; Abdel, Ziyat Zh.; Meka-Mechenko, Tatiyana V.; Umarova, Saule K.; Begimbayeva, Elmira Zh.; Agzam, Sanzhar D.; Motin, Vladimir L.; Reva, Oleg N.; Rysbekova, Altyn K. (Public Library of Science, 2025-09-12)
The genetic diversity and biovar classification of Yersinia isolates from Central Asia were investigated using whole-genome sequencing. In total, 98 isolates from natural plague foci were sequenced using the MiSeq platform. Computational pipelines were developed for accurate assembly of Y. pestis replicons, including small cryptic plasmids, and for identifying genetic polymorphisms. A panel of 99 diagnostic polymorphisms was established, enabling the distinction of dominant Medievalis isolates derived from desert and upland regions. Evidence of convergent evolution was observed in polymorphic allele distributions across genetically distinct Y. pestis biovars, Y. pseudotuberculosis, and other Y. pestis strains, likely driven by adaptation to similar environmental conditions. Genetic polymorphisms in the napA, araC, ssuA, and rhaS genes, along with transposon and CRISPR-Cas insertion patterns, were confirmed as suitable tools for identifying Y. pestis biovars, although their homoplasy suggests limited utility for phylogenetic inference. Notably, a novel cryptic plasmid, pCKF, previously associated with the strain of the population 2.MED0 from the Central-Caucasus high-altitude autonomous plague focus, was detected in a genetically distinct isolate of 2.MED1 population from the Ural-Embi region, indicating potential plasmid transfer across the 2.MED lineage. These findings emphasize the need for ongoing genomic surveillance to monitor the spread of virulence-associated genetic elements and to improve our understanding of Y. pestis evolution and ecology.
Draft genome sequence of Elsinoe masingae : the causal agent of Eucalyptus scab in South Africa
Pham, Nam Q.; Wingfield, Michael J.; Duong, Tuan A.; Wingfield, Brenda D. (Springer, 2026-02)
Elsinoe masingae is a recently described fungal pathogen causing Eucalyptus scab and shoot malformation in South African plantations. Here we present the draft genome sequence of the ex-holotype isolate (CMW 58888 = CMW-IA 1800). Illumina paired-end sequencing generated approximately 24.6 million reads, yielding a 24.8 Mb assembly comprising 176 scaffolds with an N50 of 0.47 Mb and a GC content of 51.04%. BUSCO analysis using the dothideomycetes_odb10 dataset indicated 93.70% completeness, and funannotate predicted 8 883 protein-coding genes. Phylogenetic inference based on ITS, LSU, TEF1 and RPB2 sequences confirmed the identity of the sequenced isolate as E. masingae. The availability of this genome provides an essential resource for developing molecular tools to study the population diversity, epidemiology, and evolutionary history of E. masingae, and enables comparative analyses of pathogenicity and host adaptation among Elsinoe species affecting Eucalyptus and other crops.
Genomic and phenotypic insights into the expanding phylogenetic landscape of the Cryptococcus genus
Coelho , Marco A.; David-Palma, Márcia; Kachalkin, Aleksey V.; Kolařík, Miroslav; Turchetti, Benedetta; Sampaio, José Paulo; Wingfield, Michael J.; Fisher , Matthew C.; Yurkov, Andrey M.; Heitman, Joseph (Public Library of Science, 2025-11-10)
The fungal genus Cryptococcus includes several life-threatening human pathogens as well as diverse saprobic species whose genome architecture, ecology, and evolutionary history remain less well characterized. Understanding how some lineages evolved into major pathogens remains a central challenge and may be advanced by comparisons with their nonpathogenic counterparts. Integrative approaches have become essential for delimiting species and reconstructing evolutionary relationships, particularly in lineages with cryptic diversity or extensive chromosomal rearrangements. Here, we formally characterize six Cryptococcus species representing distinct evolutionary lineages, comprising both newly discovered and previously recognized but unnamed taxa, through a combination of phylogenomic analyses, divergence metrics, chromosomal comparisons, mating assays, and phenotypic profiling. Among pathogenic taxa, we formally name Cryptococcus hyracis sp. nov., corresponding to the previously characterized VGV lineage within the C. gattii complex. In parallel, we describe five saprobic, nonpathogenic species isolated from fruit, soil, and bark beetle galleries, spanning four phylogenetic clades. We identify a strong ecological association with bark beetles for Cryptococcus porticicola sp. nov., the only newly described nonpathogenic species with multiple sequenced strains from diverse sites. In this species, we detect strain-level chromosomal variation and evidence of sexual reproduction, along with population-level signatures of recombination. Across the genus, chromosome-level comparisons reveal extensive structural variation, including species- and strain-specific rearrangements that may restrict gene flow. We also identify multiple instances of chromosome number reduction, often accompanied by genomic signatures consistent with centromere inactivation or loss of centromeric identity. Comparative metabolic profiling with Biolog phenotype microarrays reveals clade-level differentiation and distinct substrate preferences, which may reflect metabolic divergence and habitat-specific diversification. Notably, we confirm that thermotolerance is restricted to clinically relevant taxa. These findings refine the species-level taxonomy of Cryptococcus, broaden its known genomic and ecological diversity, and strengthen the framework for investigating speciation, adaptation, and the emergence of pathogenicity within the genus.
An inter-specific Amaranthus pangenome captures genetic variation potentially underlying key leafy vegetable traits in this underutilised crop
De Kinderen, Maud A.J.; Ma, Xiao; Vaistij, Fabian E.; Chang, Jiyang; Larson, Tony; Li, Yi; Dinssa, Fekadu; Lin, Chen-yu; Suchak, Tulsi; Smit, Samuel J.; Jeffares, Daniel C.; Van Deynze, Allen; Jansen van Rensburg, Willem S.; Gerrano, Abe S.; Bairu, Michael W.; Venter, Sonja L.; Schafleitner, Roland; Van de Peer, Yves; Denby, Katherine (Wiley, 2026)
Amaranthus species (particularly Amaranthus cruentus, Amaranthus hypochondriacus, Amaranthus tricolor and Amaranthus caudatus) are traditional underutilised crops with the potential to contribute to sustainable, healthy food systems. We focus on amaranth as a leafy vegetable aiming to develop improved lines for cultivation by smallholder farmers in Sub-Saharan Africa. We demonstrate differences in leaf yield and metabolites relevant to human nutrition across eight amaranth accessions: four A. cruentus and four A. hypochondriacus. These accessions are founders of an inter-specific multi-parent advanced generation inter-cross population. We generated high-quality genome assemblies and annotations for these founder lines and identified sequence and structural variants (SVs) compared with a reference A. cruentus genome. Pangenome analysis (also including A. cruentus, A. hypochondriacus and A. tricolor reference genomes) identified core, dispensable and private gene families. Fifty per cent of gene families were core, highlighting the value, in terms of gene discovery, of sequencing additional accessions and the inclusion of three Amaranthus species. A graphical pangenome was constructed using SVs and demonstrated variation in copy number of genes with a likely role in disease resistance. This inter-specific pangenome will be highly valuable for future research on amaranth and facilitate usage of SVs in trait mapping and causal gene discovery.
Equipped for success : genomes and metabolomes of the European Amanita muscaria are conserved in its novel South African range
Nickles, Grant R.; Stokes, Cecelia K.; Narh, Deborah L; Lynn, Kira Mary Theresa; Fuqua, Savannah R.; Bryan, Corbin; Allen, Brooke M.; Bivins, Christopher P.; Woo Bok, Jin; Brewer, J. Stephen; Buthelezi, Sikelela T.; Clark, Jahiya P.R.M.; Coon, Kerri L.; Corby, Lauren R.; Coetzee, Martin Petrus Albertus; Dewing, Claudette; Duong, Tuan A.; Harris, Mathew Andrew; Keller, Nancy P.; Kopotsa, Katlego; Lane, Frances Alice; Nichols, Holly L.; Nieuwoudt, Alandie; Nunez, Martin A.; Medina Munoz, Miguel E.; Park, Sung Chul; Pham, Nam Q.; Ryan, Kaetlyn T.; Solis, Myriam; Vilgalys, Rytas; Wallace, Jasmine Marea; Wang, Yen-Wen; Wingfield, Brenda D.; Wingfield, Michael J.; Worley, Travis K.; Zallek, Taylor A.; Zamanian, Mostafa; Hoeksema, Jason D.; Drott, Milton T.; Pringle, Anne (Wiley, 2026-05)
• Plants and soils have been moved around the world for centuries, but invasive mushrooms receive scant attention. The Amanita muscaria species complex was introduced to South Africa in the context of forestry, but its origins, ecology and recent evolution are unstudied. • We sequenced the genomes of 24 Northern and Southern Hemisphere A. muscaria, built phylogenies and reconstructed its South African history. We identified the biosynthetic gene clusters (BGCs) encoding specialized metabolites (SMs). We subsequently extracted mushrooms' metabolites and used mass spectrometry data to group SMs into unique molecular families (MFs). We tested metabolites for bioactivity against diverse microbes and animals. • We identify Europe as the origin of South African A. muscaria. A highly conserved group of BGCs is found in nearly all European and African genomes, and only 13 of 273 MFs are unique to South Africa. Metabolites extracted from all mushrooms kill nematodes, while microbes and flies appear unaffected. • The nearly global distribution of the fly agaric results from multiple introductions of a single European clade to the Southern Hemisphere. Despite its long history in South Africa, the fungus has not lost any of its BGCs, suggesting a conservation of function(s) across multiple continents.
Purple garlic (Allium sativum) peel anthocyanins are potent inhibitors of the diabetes-related enzyme,α--glucosidase
Samson, Sana; Rabbad, Ali H.; Gama, Ntombenhle Hlengiwe; Malgas, Samkelo (Elsevier, 2026-06)
Type 2 diabetes management may benefit from inhibiting α-amylase and α-glucosidase to lower blood glucose levels. Acarbose, a known α-glucosidase inhibitor (AGI), can excessively inhibit α-amylase, leading to side effects from undigested starch fermentation in the colon. This study explored anthocyanins from purple garlic (Allium sativum) peels as potential α-glucosidase inhibitors (AGIs). Extracted using ultrasound-assisted acidified methanol, yielding a 2 % (w/w) extract, the anthocyanin-enriched purple garlic peel extract (PGPE) showed an IC50 similar to acarbose (≈0.2 mg/ml) and acted as a non-competitive inhibitor of α-glucosidase without inhibiting α-amylase, unlike acarbose. Molecular docking and molecular dynamics (MD) simulation revealed stable complexes formed between anthocyanins and α-glucosidase through hydrogen bonding and hydrophobic interactions. Subsequent deactivation studies corroborated the in silico and enzyme kinetics studies, indicating that anthocyanins preferably bind to α-glucosidase alone compared to the α-glucosidase-substrate complex. Amylolytic enzyme (α-amylase and α-glucosidase) inhibition studies demonstrated that the extract significantly reduced residual starch and glucose release compared to acarbose. Additionally, cytotoxicity tests indicated the extract was biocompatible with Caco-2 intestinal cells. Overall, anthocyanins may be effective AGIs with fewer side effects, as they may reduce residual starch that may be destined for fermentation in the colon. Future research should explore how PGPE affects gut microbiota and examine the potential side effects of AGIs, especially in relation to gas production. HIGHLIGHTS • Purple garlic peel anthocyanins were extracted and characterised by LC-MS. • Anthocyanins from garlic peels inhibited α-glucosidase more than α-amylase. • Anthocyanins inhibited glucose release and significantly reduced residual starch. • The anthocyanins can potentially mitigate gastrointestinal side effects of AGIs.
The complex evolution and genomic dynamics of mating-type loci in Cryptococcus and Kwoniella
Coelho, Marco A.; David-Palma, Márcia; Marincowitz, Seonju; Aylward, Janneke; Pham, Nam Q.; Yurkov, Andrey M.; Wingfield, Brenda D.; Wingfield, Michael J.; Sun, Sheng; Heitman, Joseph (Public Library of Science, 2025-10-03)
Sexual reproduction in basidiomycete fungi is governed by MAT loci (P/R and HD), which exhibit remarkable evolutionary plasticity, characterized by expansions, rearrangements, and gene losses often associated with mating system transitions. The sister genera Cryptococcus and Kwoniella provide a powerful framework for studying MAT loci evolution owing to their diverse reproductive strategies and distinct architectures, spanning bipolar and tetrapolar systems with either linked or unlinked MAT loci. Building on recent comparative genomic analyses, we generated additional chromosome-level assemblies, uncovering distinct trajectories shaping MAT loci organization. Contrasting with the small-scale expansions and gene acquisitions observed in Kwoniella, our analyses revealed independent expansions of the P/R locus in tetrapolar Cryptococcus, possibly driven by pheromone gene duplications. Notably, these expansions coincided with a pronounced GC-content reduction best explained by reduced GC-biased gene conversion following recombination suppression, rather than relaxed codon usage selection. Diverse modes of MAT locus linkage were also identified, including three previously unrecognized transitions: one resulting in a pseudobipolar arrangement and two leading to bipolarity. All three transitions involved translocations. In the pseudobipolar configuration, the P/R and HD loci remained on the same chromosome but genetically unlinked, whereas the bipolar transitions additionally featured rearrangements that fused the two loci into a nonrecombining region. Mating assays confirmed a sexual cycle in Cryptococcus decagattii, demonstrating its ability to undergo mating and sporulation. Progeny analysis in Kwoniella mangrovensis revealed substantial ploidy variation and aneuploidy, likely stemming from haploid–diploid mating, yet evidence of recombination and loss of heterozygosity indicates that meiotic exchange occurs despite irregular chromosome segregation. Our findings underscore the importance of continued diversity sampling and provide further evidence for convergent evolution of fused MAT loci in basidiomycetes, offering new insights into the genetic and chromosomal changes driving reproductive transitions.
Importance of measuring and reporting environmental conditions across plant science subdisciplines
Vincent, Christopher; Leisner, Courtney P.; Locke, Anna M.; Pelech, Elena; Schmiege, Stephanie C.; Sharkey, Thomas D.; Tejera-Nieves, Mauricio; Alade, Dorcas Olufunke; Cardoso, Amanda A.; Teshome, Demissew Tesfaye (Oxford University Press, 2025-10)
Understanding plant responses to the environment is based on research performed across several scales and subdisciplines. However, the interpretation and repeatability of experimental results depend on careful reporting of experimental procedures and environmental conditions. These conditions include light intensity and quality, temperature, relative humidity and vapor pressure deficit, soil water potential or volumetric water content, and pot size, which interact on plant physiological responses across biological and experimental scales regardless of whether they are the focus of the experiment. To ascertain how effectively and consistently these conditions are reported, we reviewed more than 200 plant science research articles on vascular plants published from 2020 through 2024. Environmental condition data were often not reported, including cases where the specific environmental variable was the focus of the study. This situation hampers both replicability and interpretability of results and hinders progress in understanding plant physiological responses across subdisciplines. The Environmental and Ecological Plant Physiology section of the American Society of Plant Biologists recommends several best practices to measure and report environmental conditions in plant physiology experiments, such as measuring and reporting actual environmental conditions, especially of control variables, to enable replication and comparative interpretation among experiments. These guidelines can aid authors in experimental design and manuscript preparation and assist reviewers in evaluating submitted manuscripts. Following such guidelines will enhance the dynamic progress of sound plant science within our community by improving replicability and enabling cross-disciplinary interpretation of results.
The Fusarium fujikuroi species complex in Korea : taxonomic revision, new records, and description of Fusarium ipomoeicola sp. nov.
Thao, Le Dinh; Choi, Yunhee; Yang, Jung-Wook; Yilmaz, Neriman; Lee, Jae Sung; Mageswari, Anbazhagan; Lee, Daseul; Kang, Donghun; Sossah, Frederick Leo; Choi, In-Young; Hong, Seung-Beom (Asian Network for Scientific Information (ANSINET), 2025-12)
The Fusarium fujikuroi species complex (FFSC) includes numerous phytopathogenic and mycotoxigenic species of significant agricultural importance. In this study, 81 Korean isolates within the FFSC from the Korean Agricultural Culture Collection (KACC) were re-identified using multi-locus sequence analyses of partial gene fragments of the translation elongation factor 1-alpha (tef1), beta-tubulin (tub2), calmodulin (CaM), RNA polymerase II largest subunit (rpb1), and RNA polymerase II second largest subunit (rpb2). Phylogenetic analyses clarified the taxonomic identities of these isolates, revealing that many strains previously reported as F. proliferatum, F. subglutinans, and F. circinatum were re-identified as F. annulatum, F. dendrobii, and a novel species, F. ipomoeicola sp. nov., respectively. In total, eight species were confirmed within the FFSC, including seven known species (F. annulatum, F. concentricum, F. dendrobii, F. elaeagni, F. fujikuroi, F. planum, and F. thapsinum) and one novel species described herein. Notably, the taxonomic status of four recently described species was revised, indicating that F. hipposidericola, F. jacksoniae, F. xishuangbannaense, and F. oryzigenum are synonyms of F. annulatum, F. babinda, F. hechiense, and F. planum, respectively. In addition, F. annulatum, F. dendrobii, F. elaeagni, and F. planum are reported for the first time in Korea, and 22 previously undocumented fungus-host associations from Korea were identified, including 15 novel combinations not previously reported worldwide. However, the pathogenicity of these fungal species on their respective hosts was not confirmed in this study.
Extracellular vesicles modulate growth and stress adaptation in Fusarium circinatum
Ratsoma, Manchela Francinah; Mokoena, Nthabiseng Z.; Mpupa, Sokunene; Santana, Quentin C.; Wingfield, Brenda D.; Steenkamp, Emma Theodora; Motaung, Thabiso Eric (Wiley, 2025-09)
The molecular mechanisms influencing Fusarium circinatum, an important pine tree pathogen, remain partially understood. We recently reported a biofilm-mediated response in this fungus, which supports its adaptation to harsh conditions including heat stress. Here, we report that biofilm extracellular vesicles (EVs) play a key role in this adaptive response. The EVs were purified from planktonic and biofilm cells via differential ultracentrifugation and size exclusion chromatography. Their subsequent application to fungal cells revealed the capacity of biofilm-derived EVs (bEVs) to promote conidial viability and germination. When bEV-treated conidia were cultured in the presence of carbon sources (PM1), nitrogen sources (PM3B) and chemical sensitivity agents (PM21D), a delayed nutrient utilisation and adaptation to antimicrobial agents such as nystatin were observed. Furthermore, exogenous application of bEVs on mono- and polymicrobial biofilms significantly enhanced biomass and matrix production, with EVs derived from heat-stressed biofilm (45°C, 1 h) showing more effectiveness at promoting biomass production and resistance to the antifungal agent, tebuconazole. This is consistent with the biofilm's heat resistance previously reported for F. circinatum biofilms. Taken together, our work provides novel insights into the EV-mediated molecular interactions that modulate environmental responses in F. circinatum.
Botryosphaeriaceae associated with racemes, fruits and leaves of Macadamia in South Africa
Maduke, Ntaoleng Angel; Slippers, Bernard; Van der Linde, Elna J.; Wingfield, Michael J.; Fourie, Gerda (Wiley, 2025-08)
Species in the Botryosphaeriaceae are common in the endophytic microbiome of woody plants. Some of these are well known to cause branch die-back and decline of macadamia trees and have also been associated with diseases of their fruits and leaves. The aim of this study was to characterise species of Botryosphaeriaceae from asymptomatic and symptomatic tissues of macadamia fruits, leaves and racemes in South Africa. Symptomatic tissues included die-back of the racemes, husk rot on fruits and brown leaf blight. Eleven species were identified based on analysis of DNA sequence data for the rDNA internal transcribed spacer (ITS), tub2, tef-1α and rpb2 gene regions. These included Diplodia pseudoseriata, D. allocellula, Lasiodiplodia sp., L. euphorbicola, L. gonubiensis, L. pseudotheobromae, L. theobromae, Neofusicoccum australe, N. kwambonambiense, N. luteum and N. parvum. The results revealed a greater species diversity and isolation frequency from leaves compared to fruits and racemes, which highlights the important role that the species play in brown leaf blight. All isolates used in pathogenicity trials produced lesions on both fruits and leaves, but Neofusicoccum and Lasiodiplodia species were more aggressive. Considering the frequency of association with diseased tissues and the pathogenicity trials, L. pseudotheobromae, L. theobromae, N. parvum and N. kwambonambiense are the most important species to focus on for future disease resistance screening of planting material. This study provided new insights into the association of Botryosphaeriaceae species with important canopy diseases such as brown leaf blight and husk rot in South Africa and will contribute to their future management.
Transcriptional responses of Eucalyptus to infection by an aggressive leaf blight pathogen reveal the role of host secondary metabolites during pathogen germination
Solis, Myriam; Hammerbacher, Almuth; Wingfield, Michael J.; Naidoo, Sanushka (Springer, 2025-08)
Teratosphaeria leaf blight disease caused by Teratosphaeria destructans poses a serious threat to Eucalyptus plantations worldwide. The pathogen infects leaves via stomatal penetration from 24 to 72 h after inoculation. Symptoms are visible after two weeks and pathogen sporulation commonly occurs four weeks after inoculation of a susceptible host. We studied the responses of a susceptible Eucalyptus clone during the entire disease cycle to identify susceptibility factors. RNA from healthy and infected leaves was isolated at 3, 14 and 28 days post inoculation. Differential expression and gene enrichment analysis showed that members of the transcription factor family TGA and MYB, involved in the salicylic acid and abscisic acid pathways, and genes involved in these hormone signaling pathways, were up-regulated. Overall, plant defense response pathways were enriched only at the late stage of infection (28 dpi). In contrast, both gene expression and chemical analysis revealed that the synthesis of the major flavonoids in Eucalyptus leaves was enhanced during pathogen infection, while the synthesis of terpenoids and flavan-3-ols declined. The flavonols, rutin and quercetin enhanced spore germination in-vitro while, the terpenoid eucalyptol and the flavan-3-ol catechin inhibited germination. This study provides insights into the molecular and chemical responses at different stages of infection of a susceptible host by T. destructans, thereby improving the current understanding of the pathosystem.
In silico prediction method for plant nucleotide-binding leucine-rich repeat- and pathogen effector interactions
Fick, Alicia; Fick, Jacobus Lukas Marthinus; Swart, Velushka; Van den Berg, Noelani (Wiley, 2025-04)
Plant Nucleotide-binding leucine-rich repeat (NLR) proteins play a crucial role in effector recognition and activation of Effector triggered immunity following pathogen infection. Genome sequencing advancements have led to the identification of a myriad of NLRs in numerous agriculturally important plant species. However, deciphering which NLRs recognize specific pathogen effectors remains challenging. Predicting NLR-effector interactions in silico will provide a more targeted approach for experimental validation, critical for elucidating function, and advancing our understanding of NLR-triggered immunity. In this study, NLR-effector protein complex structures were predicted using AlphaFold2-Multimer for all experimentally validated NLR-effector interactions reported in literature. Binding affinities- and energies were predicted using 97 machine learning models from Area-Affinity. We show that AlphaFold2-Multimer predicted structures have acceptable accuracy and can be used to investigate NLR-effector interactions in silico. Binding affinities for 58 NLR-effector complexes ranged between -8.5 and -10.6 log(K), and binding energies between -11.8 and -14.4 kcal/mol-1, depending on the Area-Affinity model used. For 2427 "forced" NLR-effector complexes, these estimates showed larger variability, enabling identification of novel NLR-effector interactions with 99% accuracy using an Ensemble machine learning model. The narrow range of binding energies- and affinities for "true" interactions suggest a specific change in Gibbs free energy, and thus conformational change, is required for NLR activation. This is the first study to provide a method for predicting NLR-effector interactions, applicable to all pathosystems. Finally, the NLR-Effector Interaction Classification (NEIC) resource can streamline research efforts by identifying NLRs important for plant-pathogen resistance, advancing our understanding of plant immunity.
Genome analyses provide insights into Engelhardia’s adaptation to East Asia summer monsoon
Li, Min; Wu, Jing-Jing; Su, Ren-Ping; Fang, Ou-Yan; Cai, Xiang; Huang, Pei-Han; Gao, Xiao-Yang; Fu, Xin-Xing; Ma, Xiao-Hui; He, Lin-Yue; Song, Yi-Gang; Hu, Guo-Xiong; Zhou, Shi-Shun; Tan, Yun-Hong; Van de Peer, Yves; Li, Jie; Wu, Sheng-Dan; Meng, Hong-Hu (KeAi Publishing Communications Ltd., 2025-09)
Genetic information has been instrumental in elucidating the relationship between the East Asian Summer Monsoon (EASM) and subtropical evergreen broad-leaved forests (EBLFs). However, how the genomic insights of EBLFs’ species correspond to environmental shifts induced by the EASM remains limited. In this study, we investigated the adaptive mechanisms of evergreen Engelhardia species in response to the EASM through genome sequencing and comparative genomic analyses from the de novo genome assemblies of five closely related Engelhardia taxa and one Rhoiptelea species. Our findings revealed that the divergence of evergreen trees from their sister deciduous species is closely associated with the onset and intensification of the EASM. This genomic transition may have coincided with a significant expansion of the terpene synthase (TPS) gene family in E. fenzelii, driven by four distinct modes of gene duplication. This expansion enhances the biosynthesis of terpene volatiles, providing a defensive mechanism against potential herbivory in EASM affected environments. We also identified a shared whole-genome duplication (WGD) event across Engelhardia, along with substantial differences in transposable element (TE) composition and activity, which contributed to genome size variation between E. fenzelii and E. roxburghiana. In addition, demographic analyses revealed a continuous population decline over the past 10 million years, further exacerbated by recent human disturbance, underscoring the conservation urgency for these species. These results not only provide preliminary insights into the complex evolutionary dynamics within the Engelhardia genus from genomic insights (e.g., the intricate relationships between genomic variations, environmental changes, and adaptive responses driven by significant climatic events such as the EASM), but also provides valuable insights into the conservation significance of EBLFs.
Comprehensive sampling of mitochondrial genomes substantiates the Neoproterozoic origin of land plants
Hu, Shuai-Ya; Shi, Gongle; Yang, Cheng-Ao; Van de Peer, Yves; Li, Zhen; Xue, Jia-Yu (Elsevier, 2025-09-05)
Molecular phylogenetics elucidates the evolution and divergence of green plants by analyzing sequence data from diverse sources. Notably, phylogenetic reconstruction based on mitochondrial genes often shows incongruence with results from nuclear and chloroplast genes. Although the uniparental inheritance and conservatively retained protein-coding genes of mitochondrial genomes inherently exclude certain confounding factors that affect phylogenetic reconstruction—such as hybridization and gene loss—the use of mitochondrial genomes for phylogeny and divergence-time estimation has remained limited. Here, we assembled a comprehensive dataset of 565 mitochondrial genomes representing all major lineages of green plants. Applying multiple partitions and phylogenetic models, our mitochondrial-based phylogenies support paraphyly in both bryophytes and charophytes, place hornworts (Anthocerotaceae) as sister to all tracheophytes, and recover stoneworts (Charophyceae) as sister to land plants. We systematically evaluated the influence of factors in mitochondrial coding sequences, including GC-content heterogeneity and codon-usage bias. Furthermore, by rigorously testing seven dating strategies, we assessed the impact of confounding elements affecting divergence-time estimates, such as fossil calibration number and prior settings, as well as rate heterogeneity among sites and across lineages. Our dating analyses support a Neoproterozoic origin (crown age) of land plants and a Triassic origin of angiosperms, consistent with nuclear evidence. In conclusion, we emphasize the importance of exploring alternative partitioning strategies and addressing among-lineage heterogeneity in both phylogenetic and dating analyses, with extended sampling and careful data pruning to minimize systematic error in phylogenetic inference.
Genomic characterisation of Bidens mottle virus in South Africa and an assessment of the impact on Helianthus annuus (sunflower) in an open field setting
Mapfumo, Phrasia; Archer, Emma Rosa Mary; Swanevelder, Dirk Z.H.; Wilken, Pieter Markus; Creux, Nicole Marie; Read, David Alan (Wiley, 2025-06)
Sunflower (Helianthus annuus) is an oilseed crop of global economic importance, and South Africa ranks among the 20 top producers worldwide. Sunflower production can be severely limited by fungal, viral and bacterial diseases. In South Africa, knowledge of viral diseases in sunflowers is particularly limited. During a disease survey of a field trial for a separate study, we observed symptoms not common in sunflowers in South Africa on several plants across the trial. This study aimed to identify the causal agent of these symptoms that were observed on sunflowers in two consecutive seasons at two experimental sites in South Africa (Pretoria and Potchefstroom). Illumina sequencing of total RNA from symptomatic leaves and reverse transcription-PCR confirmation showed the presence of bidens mottle virus (BiMoV) in infected plants. BiMoV is a widespread potyvirus that is vectored by aphids, with weeds acting as viral reservoirs. The effects of the viral infection on the floral, morphological and yield traits in sunflowers were investigated. Pollen viability was reduced by 17.0%, plant height by 16.7%, leaf number by 12.3% and overall yield by 80.6%. This study suggests the potential for a significant impact from BiMoV infection on sunflower development and yield in South Africa. This is only the second report of natural infection of BiMoV in sunflowers and the first report of BiMoV in sunflowers in South Africa. We present preliminary evidence for yield losses; management strategies and disease progression need to be further investigated.
Sunflower seed yield and quality stabilize across planting dates during hot, dry seasons under rainfed conditions in South Africa
Mapfumo, Phrasia; Archer, Emma Rosa Mary; Swanevelder, Dirk Z.H.; Wilken, Markus; Creux, Nicole Marie (EDP Sciences, 2026-04)
ABSTRACT : South Africa is a water-scarce country predominantly practicing dryland agriculture, relying on rainfall onset to determine planting date. Sunflower is commonly considered a substitute crop, planted when primary crops face delayed plantings. The interaction between crop development and environmental variability is critical in Southern Africa because projections indicate warming of up to twice the rate of the global average. We investigated sunflower planting dates and production across two austral summer seasons (2020/2021 and 2021/2022) and two provinces of South Africa. A widely grown cultivar was sown monthly through the summer (from November to March) in a split-plot design. Plant height and leaf number were recorded weekly. Plants were harvested at physiological maturity for morphological and yield assessments. The hotter, drier first season (2020/2021 austral summer) led to the plantings reaching physiological maturity approximately 25 days earlier than in the wetter, cooler season (2021/2022 austral summer). In the hot/dry season, seed yield and quality were lower but more stable across planting dates. In the wetter/cooler second season, there were sharp declines in yield (78.8 g/plant, equivalent to 3.2 tons/ha ) and greater variation in oleic acid (up to 59.9%) across planting dates. These results highlight sunflowers’ stability under hot, dry conditions, supporting their use as a substitute crop. RESUME : L’Afrique du Sud est un pays confronté à la rareté de l’eau mais pratiquant peu l’irrigation. Ainsi, la date de semis dépend du début des pluies. Le tournesol est souvent considéré comme une culture de substitution quand les semis des cultures principales sont retardés. L’interaction entre le développement des cultures et la variabilité environnementale est critique en Afrique australe, les projections indiquant un réchauffement jusqu’à deux fois plus rapide que la moyenne mondiale. Nous avons étudié les dates de semis et la production du tournesol sur deux saisons d’été austral (2020/2021 et 2021/2022) et dans deux provinces d’Afrique du Sud. Un cultivar largement cultivé a été semé mensuellement durant l’été (de novembre à mars) avec un plan en split-plot. La hauteur des plantes et le nombre de feuilles ont été enregistrés chaque semaine. Les plantes ont été récoltées à maturité physiologique pour des évaluations morphologiques et de rendement. Par rapport à une première saison (été austral 2020/2021) plus humide et plus fraîche, la maturité physiologique était environ 25 jours plus rapide la seconde saison (été austral 2021/2022) plus chaude et plus sèche avec des rendements en graines et qualités plus faibles mais plus stables entre dates de semis. Pour l’année humide et fraîche, il y avait des réductions significatives en rendement (78,8 g/plante, équivalent à 3,2 t/ha) et une plus grande variation de l’acide oléique (jusqu’à 59,9%) entre dates de semis. Ces résultats soulignent la stabilité du tournesol en conditions chaudes et sèches, soutenant son utilisation comme culture de substitution. HIGHLIGHTS : South Africa is a major sunflower producer in Africa. Southern Africa is warming at twice the rate of the global average, which positions South Africa as a sentinel site for climate change. We show that sunflower is a hardy, adaptable crop that can be used as a substitute under hot, dry conditions when cash crops such as maize or soy are expected to fail.
A sensitive real-time PCR-based assay for the identification of Colletotrichum in phytosanitary and clinical applications
Phurbu, Dorji; Duan, Weijun; Crous, Pedro W.; Cai, Lei; Liu, Fang (MDPI, 2026-03)
Colletotrichum species are major plant pathogens and emerging opportunistic human pathogens. Due to their vast genetic diversity, existing diagnostic tools often suffer from narrow specificity or labor-intensive workflows. In this study, we developed a rapid, universal, and highly sensitive genus-specific real-time PCR assay utilizing a TaqMan MGB probe targeting the conserved 28S rDNA region. The assay demonstrated exceptional specificity, with no cross-reactivity against closely related fungal taxa or common co-occurring pathogens. The method exhibited high sensitivity, achieving a limit of detection (LOD) of 680 fg of genomic DNA. Furthermore, the assay was successfully validated using simulated environmental samples, where it accurately identified Colletotrichum within complex fungal communities. By providing a robust platform for genus-level screening, this methodology significantly enhances the efficiency of phytosanitary inspections and clinical diagnostics, facilitating timely biosecurity interventions and therapeutic decisions.
Towards developing an integrated approach for the treatment of white root rot in commercial avocado orchards
Van den Berg, Noelani; Magagula, Phinda; Backer, Robert; Swart, Velushka (Springer, 2025-04)
In 2016, Dematophora necatrix, the causal agent of white root rot (WRR), was identified in an avocado orchard in South Africa. Since then, this pathogen has spread to all avocado-growing regions in the country. This study aimed to evaluate the in-field efficacy of the biological control product EXTRASOL (Bacillus subtilis and Bacillus amyloquefaciens subsp. plantarum) and the fungicide fluazinam against WRR in two commercial avocado orchards in Tzaneen, Limpopo, South Africa. Over two growing seasons (2022 and 2023), disease severity, the number of D. necatrix-positive baits, and leaf area index (LAI) were monitored. Results showed that fluazinam significantly improved the health of WRR-symptomatic trees. At the start of the trial, symptomatic trees exhibited an average disease severity score of 4, which significantly declined to near 0 after two years, with symptoms largely absent. LAI of symptomatic trees treated with Fluazinam was significantly higher (> 4) in both orchards after two years. The combination of fluazinam and EXTRASOL performed similarly to fluazinam alone, while EXTRASOL alone provided minor benefits. Fluazinam residues also fell below detectable limits in the fruit of treated trees as soon as 2 weeks following treatment. These findings support fluazinam as a safe and effective treatment for WRR in South African avocado orchards.

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