Biology subjects

Tobian Herreno, A.

Publications and source records attributed to Tobian Herreno, A..

4 recordsLinked to original sources

bioRxiv2026

Standing genetic variation buffers field populations of Zymoseptoria tritici against seasonal and fungicide selection

Zymoseptoria tritici is a fungal wheat pathogen whose exceptionally large effective population sizes and frequent sexual recombination enable rapid adaptation and the breakdown of disease control strategies, yet the relative contributions of demographic turnover and fungicide selection to within-season genomic change remain unresolved at the field scale. We analysed whole-genome sequences from five wheat fields sampled during epidemic progression, including paired untreated and fungicide-treated populations, to separate seasonal demographic change from fungicide effects on genome-wide diversity allowing us to compare minor allele frequency spectra and diversity statistics to disentangle these effectswithin individual fields. Field populations were locally differentiated yet nested within the broader European gene pool; within-season demographic turnover consistently shifted allele frequency spectra towards more shared, common alleles; whereas nucleotide diversity and adaptive potential remained largely unchanged. Seasonal demographic turnover accounted for most short-term genomic change, while fungicide effects were comparatively small, field-specific and acted primarily on pre-existing resistance alleles and standing genetic variation. Our results show that short-term adaptation is driven primarily by the redistribution rather than depletion of standing genetic variation, highlighting pathogen population biology as a key determinant of disease-control durability and emphasizing the value of population-informed genomic surveillance.

evolutionary biology↗

bioRxiv2026

Deletion of 29 cell death-inducing proteins and phytotoxin biosynthetic genes does not completely abolish virulence of Botrytis cinerea

Botrytis cinerea is a necrotrophic plant pathogen with an extremely wide host range. During invasion, the fungus induces rapid host cell death and proliferates in the necrotic tissue. Host killing involves secretion of lytic enzymes, phytotoxic metabolites and cell death inducing proteins (CDIPs), but their relative contributions are poorly understood. We have previously shown that the sequential knockout of up to 12 CDIPs leads to a substantial reduction of virulence of B. cinerea mutants. In this study, we identified additional CDIPs and generated an unprecedented series of multi-gene deletion mutants in a filamentous fungus, culminating in a 29x mutant carrying deletions of 27 CDIP-encoding genes and two genes required for the biosynthesis of the phytotoxins botrydial and botcinic acid. These multi-k.o. mutants were strongly reduced in virulence and almost unable to infect apple fruit tissue, but still induced slowly expanding necrosis on leaves, demonstrating that additional determinants of host killing remain to be identified. Overexpression of the highly phytotoxic Nep1 in a 22-fold CDIP mutant failed to increase its virulence. Reevaluation of several CDIPs previously described as virulence factors revealed for most of them only small or no significant contributions to pathogenesis. Generation of a mutant lacking all six predicted endo-polygalacturonases confirmed only for PG1 and PG2 a major role for cell wall degradation and infection. Our work demonstrates that necrotrophic pathogenesis in B. cinerea does not depend on a few primary virulence determinants, but rather on a highly redundant network of host damaging factors.

molecular biology↗

bioRxiv2025

Temporal Shifts in Gene Expression Drive Quantitative Resistance to a Necrotrophic Fungus in a Tomato Crop Wild Relative

Resistance breeding against generalist necrotrophic pathogens heavily relies on quantitative disease resistance (QDR). Lesion growth dynamics involve distinct phases (e.g., lag phase duration or lesion doubling time), each independently affecting the overall symptom severity. While the genetic and regulatory basis of lesion growth rate has been studied, the host-derived regulation of the lag-phase duration remains largely uncharacterised. In this study, we tested the regulatory response of Solanum pennellii genotypes exhibiting different lag-phase durations. We conducted a time-series gene expression profiling experiment dissecting genotype-specific regulatory responses to Sclerotinia sclerotiorum inoculation. We observed genotype-specific regulatory trajectories, with resistant plants displaying early activation of defence-related genes during the asymptomatic phase. These genes, regulated by a WRKY6-centered gene regulatory network, exhibited elevated basal expression in resistant genotypes and a fine-tuned longitudinal expression with induction before lesion onset. In contrast, susceptible genotypes lacked this early response, showing gene induction only post-infection. This study is the first to link host regulatory dynamics to lag-phase duration, suggesting that elevated basal expression of receptor genes and a WRKY6-mediated gene regulatory network may enhance QDR. These findings provide insights into the regulatory foundation of QDR and establish a functional basis for more focused breeding of QDR traits.

plant biology↗

bioRxiv2025

Zymoseptoria tritici show local differences in within-field diversity and effector variation

Zymoseptoria tritici is a cosmopolitan hemibiotrophic wheat pathogen with a high mutation rate and a mixed reproduction system, leading to challenges in traditional farming management. For successful integration of pest management, especially for early diagnostics of new aggressive or fungicide-resistant lineages, it is critical to understand population diversity in the field. We look at whole-genome sequence data for three datasets to differentiate within field diversity in fields of similar size: one dataset from a newly sampled field population from the United Kingdom and two publicly available datasets from fields from the United States and Switzerland. Inspection of population structure and diversity features, such as minor allele frequency distribution and clonality, show no within-field structure, the most abundant SNPs are present in low frequency, and European fields have higher clonality. Knowing that effectors play particularly important roles in (a)virulence, we specifically assess effector diversity characteristics. Whereas on a whole-genome scale, we can see separation of the populations at the regional scale, we do not find such separation for the effectors. Moreover, we find that multiple effector haplotypes can be found interspersed within the field and even occur within what has been considered clonal isolates or isolates from a single lesion. Our analyses highlight that within-field Z. tritici diversity is higher than previously reported. Our finding that multiple effector haplotypes can be found within a single lesion might explain the large resistance gene-breaking potential of Z. tritici.

microbiology↗