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Species-Specific Regulatory Complexes Shape Quan ta ve Resistance to a Necrotrophic Pathogen in Wild Tomatoes.

ABSTRACT: Wild relatives of crop species possess diverse levels of quantitative disease resistance (QDR) to biotic stresses, yet the genomic and regulatory mechanisms underlying these differences are not well understood. In particular, how QDR against a generalist necrotrophic pathogen evolved and whether it is driven by conserved or species-specific regulatory networks remains unclear. Here, we examined the transcriptomic responses of five diverse wild tomato species that span a gradient of QDR. we initially hypothesized that conserved regulatory modules might control QDR. Instead, Using differential gene expression analysis and weighted gene co-expression network analysis (WGCNA), we find instead that species-specific regulatory features, encompassing both infection-induced and constitutively expressed genes, predominantly shape QDR levels. Although we identified an ethylene response factor (ERF-D6) among candidate genes for QDR-regulation, it did not fully account for the phenotypic variation. To further dissect the evolutionary basis of these regulatory patterns, we performed phylotranscriptomic analyses on gene co-regulatory networks. Strikingly, QDR-associated gene sets were enriched for evolutionarily older genes, suggesting that ancient gene functions have been co-opted rather than derived from recent gene family expansions. These results provide new insights into the evolutionary and regulatory complexity governing QDR and underscore the importance of species-specific gene regulation in shaping resistance against a cosmopolitan necrotrophic pathogen.

ORGANISM(S): Solanum habrochaites Solanum chilense Solanum pennellii Solanum lycopersicoides Solanum pimpinellifolium

PROVIDER: GSE288242 | GEO | 2025/12/02

REPOSITORIES: GEO

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Project description:Worldwide, 20-25% of all harvested fruit and vegetables are lost annually in the field and throughout the postharvest supply handling chain due to spoilage by fungal pathogens. Most impactful postharvest pathogens exhibit necrotrophic lifestyles, resulting in rotting of the host tissues and complete loss of marketable commodities. Necrotrophic fungi can readily infect ripe fruit leading to the rapid establishment of disease symptoms. However, these pathogens generally fail to infect unripe fruit, or remain quiescent until host and environmental conditions stimulate a successful infection. Current research on necrotrophic infections of fruit was mainly focused on the host by characterizing genetic and physicochemical factors that inhibit or promote the disease. However, the pathogenicity and virulence strategies employed by necrotrophic pathogens in ripe and unripe fruit are mostly understudied. Here, we provide a first comparative transcriptomics study of fungal postharvest pathogens: Botrytis cinerea, Rhizopus stolonifer and Fusarium acuminatum, all of which display necrotrophic behavior when infecting fruit. We de novo assembled and annotated the transcriptomes of R. stolonifer, and F. acuminatum and performed a differential gene expression analysis comparing the three fungal transcriptomes during fruit infection with that of fungal in-vitro growth. Analysis of the differentially expressed genes for enrichment of functional annotations revealed shared strategies of the three fungi during infection of compatible (ripe fruit) and incompatible (unripe fruit) hosts. We furthermore selected candidate genes that are involved in these strategies to characterize their expression during infection of unripe and ripe-like fruit of the non-ripening (nor) tomato mutant, both of which are physiologically and biochemically similar to unripe wildtype fruit. By enabling a better understanding of fungal necrotrophic infection strategies, we move closer to generating accurate models of fruit diseases and development of early detection tools and effective management strategies.

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Species-Specific Regulatory Complexes Shape Quan ta ve Resistance to a Necrotrophic Pathogen in Wild Tomatoes.

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