Characterization of the defense transcriptome responsive to Fusarium oxysporum-infection in Arabidopsis using RNA-seq

We analyzed the dynamic defense transcriptome responsive to Fusarium oxysporum infection in Arabidopsis using a strand-specific RNA-sequencing approach. Following infection, 177 and 571 genes were up-regulated, 30 and 125 genes were down-regulated at 1 day-post-inoculation (1DPI) and 6DPI, respectively. Of these genes, 116 were up-regulated and seven down-regulated at both time points, suggesting that most genes up-regulated at the early stage of infection tended to be constantly up-regulated at the later stage whereas the landscape of the down-regulated genes differed significantly at the two time points investigated. In addition to genes known to be part of the defense network in various plant–pathogen interactions, many novel disease responsive genes, including non-coding RNAs, were identified. Disease inoculation experiments with mutants of the AtROBH genes showed that AtROBHD and AtROBHF have opposite effects on disease development and provided new insights into the functions of the genes encoding NADPH oxidase in fungal disease resistance.

► Dynamic transcriptomes responsive to F. oxysporum were analysed in Arabidopsis
► The ET-signaling pathway was activated earlier than the JA- and SA-signaling ones
► Transcription factors induced at 1DPI tend to be induced at 6DPI as well
► Several MIRNAs and pseudogenes were found to be F. oxysporum responsive
► AtROBHD and AtROBHF have opposite effect on fungal disease development