Biology subjects

Ponts, N.

Publications and source records attributed to Ponts, N..

5 recordsLinked to original sources

bioRxiv2026

Strain-level diversity shapes competitive outcomes in Fusarium: a multi-omic synthesis of fungal warfare

Fusarium head blight (FHB) is driven by co-occurring Fusarium species. Yet the molecular bases of their competitive interactions, particularly at the strain level, remain largely unknown. We performed an integrated multi-omic investigation of four Fusarium isolates cultivated in monoculture, self-confrontation (SC) and inter-specific confrontation (C) assays: two Fusarium graminearum strains FgrI349 and FgrPH-1, and two Fusarium avenaceum strains FaveI494 and FaLH03. Light microscopy and quantitative colorimetry revealed marked phenotypic heterogeneity. the F. graminearum strains formed expansive, red-pigmented colonies with rapid radial growth, whereas the F. avenaceum isolates grew more slowly and displayed distinct colony morphologies and pigmentation patterns. Untargeted LC-HRMS detected 1,008 metabolites in monocultures and 938 metabolites in confrontation zones. Species-level chemical signatures were confirmed, and strain-specific metabolite sets were identified, with FaLH03 producing more than 60 % of the metabolites being made exclusively by a single strain, highlighting its exceptionally unique metabolic profile. RNA-seq uncovered extensive transcriptional reprogramming during competition. In self-confrontations, strain-specific differences persisted but no major morphological or metabolic shifts were observed. Inter-specific confrontations elicited partner-dependent responses: FgrI349 up-regulated 1,492 genes against FaveI494 (including secondary-metabolite biosynthesis, oxidoreductase activity and transport) but only 407 genes against FaLH03, while down-regulating secondary-metabolite genes in the conspecific confrontation. Conversely, the F. avenaceum isolates showed opposite trends; FaLH03 strongly repressed ribosome-biogenesis and cell-wall genes while inducing oxidative-metabolism pathways, whereas FaveI494 displayed a modest transcriptional response dominated by down-regulation of cell-division and chromosome-segregation genes. Gene-ontology enrichment highlighted an opponent-specific reversal of the secondary-metabolite biosynthetic process category in F. graminearum: down-regulated in intra-specific confrontation but up-regulated in both inter-specific encounters. Collectively, our results demonstrate that competitive outcomes are shaped more by strain identity than by species identity, with each strain deploying a distinct molecular arsenal, ranging from metabolite-mediated antagonism to targeted transcriptional shutdown, when confronted with a specific opponent. These findings refine our understanding of Fusarium community dynamics and provide a framework for developing strain-targeted biocontrol strategies against FHB.

microbiology↗

bioRxiv2026

Hi-C data from the filamentous fungus Podospora anserina and associated 3D models to visualize the spatial organization of its chromosomes

ObjectivesModel species are essential for fundamental research in biology. While a complete genomic sequence is a prerequisite for genetic studies, it is not enough on its own. Understanding the three-dimensional organization of the genome is also important, allowing researchers to gain a more realistic understanding of the mechanisms governing genome function. In the fungal model Podospora anserina, although the genomic sequence has been established for a long time, the three-dimensional organization remained unknown. Here we obtained the first Hi-C datasets and present associated 3D models, providing the research community with a valuable resource for better multi-omics data integration. Data descriptionHi-C experiments were performed in duplicate, using nuclei purified from wild-type fungal mycelium. Four FASTQ files were obtained (two per replicate) and used as inputs for the 3DGB workflow with four different output resolutions, to observe the genome organization of P. anserina at different levels of detail (50 kb, 20 kb, 10 kb, and 5 kb). In a context where researchers already have, for this species, a large amount of traditional omics data (ChIP-seq, RNA-seq, etc.), these 3D models are helpful for complementing the linear representation of the genome, which is traditionally used in bioinformatic analyses.

genomics↗

bioRxiv2022

Metabotyping of Andean pseudocereals and characterization of emerging mycotoxins

Pseudocereals are best known for three crops derived from the Andes: quinoa (Chenopodium quinoa, Chenopods I), canihua (C. pallidicaule, Chenopods I), and kiwicha (Amaranthus caudatus). Their grains are recognized for their nutritional benefits; however, there is a higher level of polyphenism and the chemical foundation that would rely with such polyphenism has not been thoroughly investigated. Meanwhile, the chemical food safety of pseudocereals remains poorly documented. Here we applied untargeted and targeted metabolomics approach by LC-MS to achieve both: i) a comprehensive chemical mapping of pseudocereal samples collected in the Andes to classify them according to their chemotype; ii) a quantification of their contents in emerging mycotoxins. An inventory of the fungal community was also realized with the aims to better know the filamentous fungi present in these grains and try to parallel this information with the presence of the molecules produced, especially mycotoxins. Metabotyping permitted to add new insights into the chemotaxonomy of pseudocereals, confirming the previously established phylotranscriptomic clades: Chenopods I (clusters quinoa and canihua), and Amaranthaceae s.s. (cluster kiwicha). Moreover, we report for the first time the presence of mycotoxins in pseudocereals. Sixteen samples of Peru (out of 27) and one sample from France (out of one) were contaminated with Beauvericin, an emerging mycotoxin. There were several mycotoxigenic fungi detected, including Aspergillus sp., Penicillium sp., and Alternaria sp., but not Fusaria. Highlights{blacksquare} Twenty-seven grain samples of Andean pseudocereals were profiled by LC-HRMS. {blacksquare}Untargeted metabolomics was used to differentiate varieties from the whole metabolome dataset. {blacksquare}Five mycotoxins were quantify using targeted metabolomics. {blacksquare}Sixteen samples of Peru and one sample from France were contaminated with Beauvericin. {blacksquare}An inventory of the fungal community infesting the Andean pseudocereal samples was documented.

biochemistry↗

bioRxiv2021

Nucleosome patterns in four plant pathogenic fungi with contrasted genome structures

AO_SCPLOWBSTRACTC_SCPLOWFungal pathogens represent a serious threat towards agriculture, health, and environment. Control of fungal diseases on crops necessitates a global understanding of fungal pathogenicity determinants and their expression during infection. Genomes of phytopathogenic fungi are often compartmentalized: the core genome contains housekeeping genes whereas the fast-evolving genome mainly contains transposable elements and species-specific genes. In this study, we analysed nucleosome landscapes of four phytopathogenic fungi with contrasted genome organizations to describe and compare nucleosome repartition patterns in relation with genome structure and gene expression level. We combined MNase-seq and RNA-seq analyses to concomitantly map nucleosome-rich and transcriptionally active regions during fungal growth in axenic culture; we developed the MNase-seq Tool Suite (MSTS) to analyse and visualise data obtained from MNase-seq experiments in combination with other genomic data and notably RNA-seq expression data. We observed different characteristics of nucleosome profiles between species, as well as between genomic regions within the same species. We further linked nucleosome repartition and gene expression. Our findings support that nucleosome positioning and occupancies are subjected to evolution, in relation with underlying genome sequence modifications. Understanding genomic organization and its role in expression regulation is the next gear to understand complex cellular mechanisms and their evolution.

genomics↗

bioRxiv2020

QTL mapping for aggressiveness variation in F. graminearum revealed one causal mutation in FgVe1 velvet protein

Fusarium graminearum is one of the most frequent causal agents of the Fusarium Head Blight in the world, a cereal disease spread throughout the world, reducing grain production and quality. F. graminearum isolates are genetically and phenotypically highly diverse. Notably, remarkable variations of aggressiveness between isolates have been observed, which could reflect an adaptive potential of this pathogen. In this study, we aimed to characterize the genetic basis of aggressiveness variation observed in an F1 population, for which genome sequences of both parental strains are available. Aggressiveness was assessed by a panel of in planta and in vitro proxies during two phenotyping trials including, among others, disease severity and mycotoxin accumulation in wheat spike. One major and single QTL was mapped for all the traits measured, on chromosome I, that explained up to 90% of the variance for disease severity. The confidence interval at the QTL spanned 1.2 Mb and contained 428 genes on the reference genome. Of these, four candidates were selected based on the postulate that a non-synonymous mutation affecting protein function may be responsible for phenotypic differences. Finally, a mutation was identified and functionally validated in the gene FgVe1, coding for a velvet protein known to be involved in pathogenicity and secondary metabolism production in several fungi.

microbiology↗