Condition-dependent co-regulation of genomic clusters of virulence factors in the grapevine trunk pathogen Neofusicoccum parvum

Authors: MASSONNET, MELANIE - University Of California; MORALES-CRUZ, ABRAHAM - University Of California; FIGUEROA-BALDERAS, ROSA - University Of California; Lawrence, Daniel; Baumgartner, Kendra; CANTU, DARIO - University Of California

Submitted to: Molecular Plant Pathology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/2/2016
Publication Date: 2/11/2018
Citation: Massonnet, M., Morales-Cruz, A., Figueroa-Balderas, R., Lawrence, D.P., Baumgartner, K., Cantu, D. 2018. Condition-dependent co-regulation of genomic clusters of virulence factors in the grapevine trunk pathogen Neofusicoccum parvum. Molecular Plant Pathology. 19:490-503. https://doi.org/10.1111/mpp.12491.
DOI: https://doi.org/10.1111/mpp.12491

Interpretive Summary: The fungal grapevine pathogen Neofusicoccum parvum, which causes the disease of Botryosphaeria dieback, is a serious threat to grape production worldwide. The fungus decomposes the woody tissue of the grapevine as a food source and produces toxins that kill plant cells. Here, we describe the genetic basis of such ‘virulence factors’ in experiments that tracked gene expression as the fungus fed on different nutrient sources and colonized the woody stem. First, we sequenced all fungal genes (i.e., the transcriptome), comparing gene expression when the fungus was grown on two artificial nutrient sources (potato dextrose agar or medium amended with grape wood as substrate) versus when the fungus was inoculated to live plants. Statistical analyses revealed that physically clustered genes coding for putative virulence functions were induced in function depending on nutrient source or stage of plant infection. Co-expressed gene clusters were significantly enriched not only in genes associated with secondary metabolism, but also in cell-wall degradation, suggesting that dynamic co-regulation of transcriptional networks contribute to multiple aspects of N. parvum virulence. In most of the co-expressed clusters, all genes shared at least a common motif in their promoter region indicative of co-regulation by the same transcription factor. Co-expression analysis also identified chromatin regulators with correlated expression with inducible clusters of virulence factors, suggesting a complex, multi-layered regulation of the virulence repertoire of N. parvum.

Technical Abstract: The ascomycete Neofusicoccum parvum, one of the causal agents of Botryosphaeria dieback, is a destructive wood-infecting fungus and a serious threat to grape production worldwide. The capability of colonizing woody tissue combined with the secretion of phytotoxic compounds is thought to underlie its pathogenicity and virulence. Here, we describe its repertoire of virulence factors and their transcriptional dynamics as the fungus feeds on different substrates and colonizes the woody stem. First, we assembled and annotated a highly contiguous genome using single molecule real-time DNA sequencing. Transcriptome profiling by RNA-sequencing determined the genome-wide patterns of expression of virulence factors both in vitro (potato dextrose agar or medium amended with grape wood as substrate) and in planta. Pairwise statistical testing of differential expression followed by co-expression network analysis revealed that physically clustered genes coding for putative virulence functions were induced in function depending on substrate or stage of plant infection. Co-expressed gene clusters were significantly enriched not only in genes associated with secondary metabolism, but also in cell-wall degradation, suggesting that dynamic co-regulation of transcriptional networks contribute to multiple aspects of N. parvum virulence. In most of the co-expressed clusters, all genes shared at least a common motif in their promoter region indicative of co-regulation by the same transcription factor. Co-expression analysis also identified chromatin regulators with correlated expression with inducible clusters of virulence factors, suggesting a complex, multi-layered regulation of the virulence repertoire of N. parvum.