Transcriptome-wide analysis of the genome regulation and pathogenicity mechanisms of a fungal pathogen. Verticillium dahliae

Transcriptome sequencing is a powerful approach to globally delineate both the transcriptional and post-transcriptional genome regulation in human and other higher eukaryotes. This study sequenced the transcriptomes of two pathogenicity-differential strains of the plant wilt pathogen Verticillium dahliae. Although they showed no growth difference in vitro, hundreds of V. dahliae genes including those synthesizing aflatoxin were preferentially expressed at in the high-virulence strain. Using both the Pfam and GO annotation strategies, some of these putative virulence genes were ambiguously clustered into several known pathogenic mechanisms including hydrophobins secreted from fungal cells and acting as phytotoxin, biosynthesis of melanin protecting the fungal pathogen against host immune responses, membrane proteins of CFEM and major facilitator superfamily MFS1 with known functions in pathogenesis and multi-drug resistance, respectively. These results suggest that some pathogenicity pathways are pre-activated at the transcriptional level prior to the fungal infection of host plants. We developed two algorithms to confidently identify 1518 alternative splicing events in 1,259 Verticillium genes, representing 15.1% of multi-exonic genes. Among the events, 43.5% involving in novel splice sites were classified into nine AS types, the others belong to intron retention. Verticillium AS genes were exclusively enriched in the regulatory biological processes such as mycelium development, reproduction, morphogenesis, cell communication and signal transduction, predicting a primary function of AS regulation when the pathogen infecting its host. This work presents a transcriptome-wide approach for identifying the fungal virulence genes and pathogenicity mechanisms; both the methodology and mechanisms could be generally applicable to other fungal pathogens. Overall design: Transcriptome analysis of two Verticillium dahliae strains