GSE138039
Global transcriptome of Helianthus annuus, Beta vulgaris, Ricinus communis and Phaseolus vulgaris healthy plants and plant infected by the fungal pathogen Sclerotinia sclerotiorum (strain 1980)
Quantitative disease resistance (QDR) is a form of plant immunity conserved across species able to limit infections caused by a broad range of pathogens. QDR has a complex genetic determinism, the bases of which are not fully understood. The number of genes contributing to the QDR response and the extent to which molecular components of the QDR response vary across plant species remain elusive. The fungal pathogen Sclerotinia sclerotiorum, causal agent of white mold disease on hundreds of plant species, triggers QDR responses in host populations. To document the diversity of plant responses to S. sclerotiorum at the molecular level, we analyzed the complete transcriptome of six plant species spanning the Pentapetalae group inoculated by the same strain of S. sclerotiorum.  We identified 48,910 genes differentially expressed (DEGs) upon infection across six species, enriched in 286 gene ontologies and 148 PFAM domains. DEGs represented ~32% of the plant genome, with an excess of down-regulated over up-regulated genes in all species. DEGs were enriched among orthologous gene groups conserved in all six species (core) compared to other orthologous groups and lineage-specific groups. Although 86.9% of core orthogroups included DEGs, only 5.5% included DEGs from all six species, revealing a high degree of regulatory divergence at the interspecific level. Focusing on a group of ABCG/PDR transporters with up-regulated members in all species, we propose that an ancestral function of AtPDR12 in acclimation to abiotic stress was exapted into QDR against S. sclerotiorum through reinforcement of pathogen responsiveness at the transcriptional level. Our results suggest that exaptation by cis-regulatory divergence contributed to the evolution of QDR and support an infinitesimal model of QDR determinism. It provides resources for functional studies on gene regulation and QDR molecular bases across the Pentapetalae clade. Overall design: Periphery of S. sclerotiorum disease lesions (Ss) and uninfected plants grown together (control), Ss and control samples collected simultaneously in three independent replicates