Biology subjects

van Kan, J. A. L.

Publications and source records attributed to van Kan, J. A. L..

10 recordsLinked to original sources

bioRxiv2026

A finished, telomere-to-telomere assembly for Botrytis cinerea strain B05.10

We present an improved genome assembly of Botrytis cinerea strain B05.10 which serves as a reference isolate for most labs active in the Botrytis research. The existing assembly dating from 2017 was extended by adding 8 telomeric regions and a small number of minor errors was corrected. The new assembly contains telomeres on each chromosome end, except for Chr4 carrying the rDNA repeat. The unannotated assembly is deposited in NCBI and manual curation of gene models is ongoing. The new assembly will be hosted on Ensembl-Fungi after completion of the structural curation.

genomics↗

bioRxiv2026

Cheating (re)shapes pathogen virulence and antifungal resistance

Filamentous fungi grow as fused, multinucleate networks that share secreted public goods vs private goods. We asked whether this sharing enables "cheater" nuclei to increase in frequency by exploiting goods produced by other nuclei, and whether such social conflict shapes virulence and antifungal resistance. We tested this in the gray mold pathogen Botrytis cinerea by contrasting an extracellular detoxification trait, a public good (enzymatic hydrolysis of the tomato saponin alpha-tomatine) with an intracellular antibiotic resistance trait, a private good (hygromycin phosphotransferase). In pairwise competitions, tomatinase-deficient nuclei gained advantage when rare against a constitutive producer, both in vitro and in planta, even though producers drive lesion expansion. An ordinary differential equation model fitted to the competition outcomes identified antibiotic gradients as the key driver of frequency-dependent selection and predicted stable coexistence of producer and non-producer nuclei across multinucleate bottlenecks. Cheating within fungal syncytia can therefore decouple virulence from reproduction and buffer the selection on antifungal resistance.

genetics↗

bioRxiv2026

Multiple nuclei means multiple chromosome sets in Botrytis cinerea and Neurospora crassa

We often think of fungi as mysterious organisms that do not follow the general principles of other eukaryotes. Thus, when exciting results are found, these organisms do not always receive the rigorous level of scrutiny seen in other fields. For many fungal species, dispersal and reproduction relies on spores, either sexual or asexual. These spores can either have a single nucleus, or multiple nuclei, and the purpose of these presumably mitotic copies was unclear. Recently it was described that the multiple nuclei in these spores are not mitotic duplicates, but instead they share a single haploid set of chromosomes distributed across nuclei. Here, we provide fluorescent microscopy and UV mutagenesis data that is inconsistent with this hypothesis. Contrasting these previous results, we observe multiple sets of chromosomes in spores of both B. cinerea and N. crassa. We also observed a strong linear relationship between the number of nuclei in spores and the total acriflavine fluorescence, further supporting mitotic copies. Genome sequencing of colonies arising from UV-irradiated colonies also recovered variants at intermediate frequences, instead of the fixed 100% expected from the new model proposed. This evidence suggests that, as long suspected, these nuclei are indeed mitotic copies, and that a re-evaluation of fungal biology is not currently necessary.

genetics↗

bioRxiv2026

Pathogen-induced red pigmentation uncovers a conserved floral defense in Asteraceae

Flower colour is predominantly selected for visual appeal and pollinator-driven evolution, however its role in plant-pathogen interaction remains unclear. Here, we investigated the relationship between anthocyanin accumulation and resistance to the necrotrophic pathogen Botrytis cinerea in Chrysanthemum morifolium. Using a unique set of spontaneous colour mutants sharing a common genetic background, we demonstrate that higher anthocyanin levels are associated with enhanced resistance to B. cinerea. Furthermore, we also observed pathogen induced anthocyanin accumulation at pathogen penetration sites in the white cultivars. Transcriptomics and metabolomics analyses revealed shift in metabolic pathways from flavonols towards flavone and anthocyanin biosynthesis during infections. A broader survey of taxonomically distant flowering species identified pathogen-induced red pigmentation is largely restricted to the members of the Asteraceae family. Notably, we observed divergence between wild and domesticated species, where the wild species retained the inducible pigmentation response and exhibited resistant to B. cinerea, whereas the cultivated species showed loss of this response, correlating with its increased susceptibility. Overall, our findings indicate that breeding for ornamental traits may have inadvertently selected against floral immunity.

plant biology↗

bioRxiv2026

The role of two GLYCOALKALOID METABOLISM genes in α-tomatine biosynthesis and basal defense in tomato

Steroidal glycoalkaloids and saponins are plant cholesterol-based steroid metabolites with antimicrobial activities and potential pharmacological value. The saponin uttroside B from black nightshade (Solanum nigrum) plays an important role in defense against herbivorous insect and exhibits anti-hepatocellular carcinoma activity. The tomato (S. lycopersicum) glycoalkaloid -tomatine has been studied because of its antinutritional effects, however, its role in protecting plants from fungal pathogens remains understudied. The biosynthetic pathway of -tomatine involves multiple clustered genes designated as glycoalkaloid metabolism (GAME) genes. In this study, we generated single knockout mutants of SlGAME4 and SlGAME2 by CRISPR/Cas9-based genome editing. The SlGAME4 mutants did not accumulate glycoalkaloids but instead redirected resources towards steroidal saponin (uttroside B) synthesis. SlGAME2 mutants contained unaltered -tomatine contents indicating that the SlGAME2 gene, previously reported to catalyze the transfer of xylose to {beta}1-tomatine, is not involved in -tomatine biosynthesis. Infection assays with four fungal tomato pathogens demonstrated that the SlGAME4 mutant plants were slightly more susceptible to Botrytis cinerea, but equally susceptible to the other three fungi. Up-regulation of -tomatine-responsive genes in B. cinerea was observed during infection on SlGAME4 mutant tomato, as well as on S. nigrum suggesting that uttroside B induces a fungal transcriptional response similar to -tomatine. Furthermore, we observed that tolerance mechanisms to plant saponins mediated by glycosyl hydrolases and a glycosyltransferase contribute to virulence of B. cinerea on SlGAME4 mutant plants and S. nigrum. This indicates that also uttroside B contributes to defense against fungal pathogens and can be detoxified by B. cinerea.

plant biology↗

bioRxiv2025

When flowers turn red: Pathogen induced flavonoid and anthocyanin biosynthesis in Chrysanthemum seticuspe confers resistanceto Botrytis cinerea

Botrytis cinerea is a major threat to ornamental crops, yet floral defence responses remain poorly understood. In Chrysanthemum seticuspe, we found that flower petals, unlike leaves, mount a localized resistance response resulting in red spots appearing at fungal penetration sites. We observed an intensification of the coloured response as infections progressed. To investigate the basis of this phenotype, we performed a time-course paired transcriptomic and metabolomic analysis on mock-inoculated vs B. cinerea-inoculated petals and leaves. Infection triggered strong transcriptional reprogramming in petals, with clear induction of phenylpropanoid and flavonoid/anthocyanin pathway genes and candidate regulators, consistent with the visible pigmentation. Metabolite profiles reflected this response, showing time-dependent accumulation of infection induced flavonoids such as quercetin, tilianin, and their derivatives, as well as cyanidin-based anthocyanins in infected petals. Integrating both omics datasets with MEANtools highlighted an anthocyanin-associated transcript-metabolite module, including a module putatively involved in the synthesis of polyyne-type phytoalexins. Antifungal assays demonstrated that selected flavonoids and cyanidin derivatives inhibit B. cinerea in a dose-dependent manner, supporting a direct antifungal role of these compounds. Altogether, our results show that C. seticuspe petals deploy a spatially confined, multi-layered chemical defence in which pathogen-induced flavonoids and anthocyanins operate as active components of resistance against a necrotrophic pathogen. We anticipate that future paired omics analyses in combination with spatial omics and bioactivity assays will yield insights into the role of specialised defence molecules in response to biotic and abiotic stresses. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=75 SRC="FIGDIR/small/695701v1_ufig1.gif" ALT="Figure 1"> View larger version (29K): org.highwire.dtl.DTLVardef@e5dbeborg.highwire.dtl.DTLVardef@c94bd1org.highwire.dtl.DTLVardef@190c030org.highwire.dtl.DTLVardef@39a7b5_HPS_FORMAT_FIGEXP M_FIG C_FIG

plant biology↗

bioRxiv2022

A multifunctional LysM effector of Botrytis cinerea contributes to plant infection

O_LILysM effectors are suppressors of chitin-triggered plant immunity in biotrophic and hemibiotrophic fungi. Their role in necrotrophic fungi is unclear as these last are known to activate plant defenses and induce cell death. C_LIO_LITo characterize the role of the BcLysM1 gene encoding a putative LysM effector in the necrotrophic fungus Botrytis cinerea, its expression was followed by transcriptional fusion and by RT-qPCR in planta. Two tagged-recombinant proteins were produced, and two independent deletion strains were constructed and characterized. C_LIO_LIBcLysM1 is induced in the early phase of infection, and more specifically in multicellular appressoria called infection cushions. The BcLysM1 protein binds the chitin in the fungus cell wall and protects hyphae against degradation by external chitinases. It is also able to sequester chitooligosaccharides and to prevent them from inducing ROS production in A. thaliana. Using mycelium as inoculum, deletion strains show a delay in infection initiation and a default in adhesion to bean leaf surfaces. C_LIO_LIThis study demonstrates for the first time a dual role for a LysM effector in mycelium adhesion on the plant and in host defenses suppression, both of them occurring during the asymptomatic phase of infection by a necrotrophic fungus. C_LI

microbiology↗

bioRxiv2022

Botrytis cinerea infection accelerates ripening and cell wall disassembly to promote disease in tomato fruit

Postharvest fungal pathogens benefit from the increased host susceptibility that occurs during fruit ripening. In unripe fruit, pathogens often remain quiescent and unable to cause disease until ripening begins, emerging at this point into destructive necrotrophic lifestyles that quickly result in fruit decay. Here, we demonstrate that one such pathogen, Botrytis cinerea, actively induces ripening processes to facilitate infections and promote disease. Assessments of ripening progression revealed that B. cinerea accelerated external coloration, ethylene production, and softening in unripe fruit, while mRNA sequencing of inoculated unripe fruit confirmed the corresponding upregulation of host genes involved in ripening processes, such as ethylene biosynthesis and cell wall degradation. Furthermore, an ELISA-based glycomics technique to assess fruit cell wall polysaccharides revealed remarkable similarities in the cell wall polysaccharide changes caused by both infections of unripe fruit and ripening of healthy fruit, particularly in the increased accessibility of pectic polysaccharides. Virulence and additional ripening assessment experiments with B. cinerea knockout mutants showed that induction of ripening is dependent on the ability to infect the host and break down pectin. The B. cinerea double knockout{Delta} bcpg1{Delta}bcpg2 lacking two critical pectin degrading enzymes was found to be incapable of emerging from quiescence even long after the fruit had ripened at its own pace, suggesting that the failure to accelerate ripening severely inhibits fungal survival on unripe fruit. These findings demonstrate that active induction of ripening in unripe tomato fruit is an important infection strategy for B. cinerea. One-Sentence SummaryPhysiological, transcriptional, and glycomic evidence indicates Botrytis cinerea hastens tomato fruit ripening to facilitate infection by a mechanism dependent on the fungal enzymes Bcpg1 and Bcpg2.

plant biology↗

bioRxiv2020

Convergent evolution of distinct immune sensor systems for fungal polygalacturonases in Brassicaceae

Plant pattern recognition receptors (PRRs) facilitate recognition of microbial surface patterns and mediate activation of plant immunity. Arabidopsis thaliana RLP42, a leucine-rich repeat (LRR) receptor protein (LRR-RP), senses fungal endopolygalacturonases (PGs) through a ternary complex comprising RLP42, the adapter kinase SOBIR1, and SERK proteins. Several fungal PGs harbor a conserved 9-amino acid fragment pg9(At), which is sufficient to activate RLP42-dependent plant immunity. Domain swap experiments using RLP42 and paralogous RLP40 sequences revealed a dominant role of the island domain (ID) for ligand binding and PRR complex assembly. Involvement of the ID in plant receptor function is reminiscent of plant phytosulfokine (PSK) perception through the receptor, PSKR, a LRR receptor kinase. Sensitivity to pg9(At), which is restricted to A. thaliana, exhibits notable accession specificity as active RLP42 alleles were found in only 16 of 52 accessions tested. Arabidopsis arenosa and Brassica rapa, two Brassicaceae species closely related to A. thaliana, perceive plant immunogenic PG fragments pg20(Aa) or pg36(Bra), which are distinct from pg9(At). Our study unveils unprecedented complexity and dynamics of PG pattern recognition receptor evolution within a single plant family. PG perception systems may have evolved rather independently as a result of convergent evolution even among closely related species.

plant biology↗

bioRxiv2020

Red-light imaging for programmed cell death visualization and quantification in plant-pathogen interactions

Studies on plant-pathogen interactions often involve monitoring disease symptoms or responses of the host plant to pathogen-derived immunogenic patterns, either visually or by staining the plant tissue. Both these methods have limitations with respect to resolution, reproducibility and the ability to quantify the results. In this study we show that red light detection in a multi-purpose fluorescence imaging system that is probably available in many labs can be used to visualize plant tissue undergoing cell death. Red light emission is the result of chlorophyll fluorescence upon thylakoid membrane disassembly during the development of a programmed cell death process. The activation of programmed cell death can occur either during a hypersensitive response to a biotrophic pathogen or an apoptotic cell death triggered by a necrotrophic pathogen. Quantifying the intensity of the red light signal enables to evaluate the magnitude of programmed cell death and provides a non-invasive readout of the plant immune response in a faster and safer manner as compared to chemical staining methodologies previously developed. This application can be implemented to screen for differences in symptom severity in plant-pathogen interactions, and to visualize and quantify in a sensitive and objective manner the intensity of a plant response upon perception of a given immunological pattern. We illustrate the utility and versatility of the method using diverse immunogenic patterns and pathogens.

plant biology↗