Metatranscriptomic comparison of endophytic and pathogenicFusarium–Arabidopsis interactions reveals plant transcriptional plasticity

Abstract

Plants are continuously exposed to beneficial and pathogenic microbes, but how plants recognize and respond to friends versus foes remains poorly understood. Here, we compared the molecular response of Arabidopsis thaliana independently challenged with a Fusarium oxysporum endophyte Fo47 versus a pathogen Fo5176. These two Fusarium oxysporum strains share a core genome of about 46 Mb, in addition to unique 1,229 and 5,415 accessory genes. Metatranscriptomic data reveal a shared pattern of expression for most plant genes (~80%) in responding to both fungal inoculums at all time points from 12 to 96 h post inoculation (HPI). However, the distinct responding genes depict transcriptional plasticity, as the pathogenic interaction activates plant stress responses and suppresses plant growth/development related functions, while the endophytic interaction attenuates host immunity but activates plant nitrogen assimilation. The differences in reprogramming of the plant transcriptome are most obvious in 12 HPI, the earliest time point sampled and are linked to accessory genes in both fungal genomes. Collectively, our results indicate that the A. thaliana and F. oxysporum interaction displays both transcriptome conservation and plasticity in the early stages of infection, providing insights into the fine-tuning of gene regulation underlying plant differential responses to fungal endophytes and pathogens.

Inactivation of tomato WAT1 leads to reduced susceptibility to Clavibacter michiganensis through downregulation of bacterial virulence factors

“…To definitely conclude, however, that auxin directly affects the expression of bacterial genes after supplementation of cultures with IAA could be monitored. Moreover, meta-transcriptomics analysis through RNA-seq on infected SlWAT1 inactivated plants and their susceptible background could be deployed in different experimental timepoints, in order to elucidate the complete pathways involved in the molecular interaction of the organisms (Guo et al, 2021). Future studies on how Cm responds to IAA, as well as the production of IAA non-responsive Cm mutants, could allow us to fully study and understand the role of auxin as a signaling molecule in the pathosystem.…”

Conservation and Expansion of Transcriptional Factor Repertoire in theFusarium oxysporumSpecies Complex

“…The RNA-seq datasets were previously described (Guo et al 2021;Redkar et al 2022) and deposited by those authors to the NCBI Short Read Archive with accession number GSE87352 and to the ArrayExpress database at EMBL-EBI (www.ebi.ac.uk/arrayexpress) under accession number E-MTAB-10597, respectively. For data reprocessing, reads were mapped to reference genomes of Arabidopsis [annotation version Araport11 (Cheng et al 2017)], Fo5176 (Fokkens et al 2021), Fo47 (Wang et al 2020) and Fol4287 (Ma et al 2010) using HISAT2 version 2.0.5 (Kim et al 2019).…”

“…Interestingly, all expanded HSFs are phylogenetically close to Hsf1, which cluster together with the Hsf1 paralog of Fusarium solani, suggesting their horizontal transfer origin (Figure 3A). We then examined the Hsf1 expression during the plant colonization (Guo et al 2021).…”

“…To understand the functional importance of FOSC TFs, we take advantage of two recently reported transcriptomics datasets (Redkar et al 2022;Guo et al 2021), including pathogenic interactions (Fo5176 infecting Arabidopsis and Fol4287…”

“…Figure 4. Unique expansion of some TFs, driven by ACs, may provide clues to host-specific adaptation.RNA-seq data were previously described(Guo et al, 2021; Redkar et al, 2021). (A) Ftf1, the TF involved in the tomato pathogenicity is most significantly expanded (10 copies of accessory FTFs) in the tomato pathogen Fol4287 genome and the expression of eight out of 10 were induced during plant colonization.…”