Submitted to: Phytopathology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: June 17, 2012
Publication Date: November 1, 2012
Repository URL: http://handle.nal.usda.gov/10113/57061
Citation: Lakshman, D.K., Roberts, D.P., Alkharouf, N., Mitra, A., Natarajan, S.S. 2012. Gene expression profiling of the plant pathogenic basidiomycetous fungus Rhizoctonia solani AG 4 reveals putative virulence factors. Phytopathology. 104(5):1020-1035. Interpretive Summary: Rhizoctonia solani is a an ubiquitous soilborne fungal pathogen causing damping off of vegetables and nursery seedlings, brown patches of turfgrasses, aerial blights and postharvest diseases, etc. Some isolates of Rhizoctonia are also beneficially associated with orchids and other may serve as biological control agents or survive as saprophytes with roles in decaying and recycling of soil organic matter. Despite their economic importance, the fungus is poorly characterized at the molecular level. Very few genes of R. solani have been reported, limiting investigations using advanced high throughput molecular approaches. R. solani AG 4 is a wide host range pathogen. In order to obtain a snapshot of genes, we have constructed two expressed gene (Expressed Sequence Tag or EST) libraries of the R. solani AG 4 isolate Rs 23A, grown under different nutrient conditions to mimic both virulent and hypovirulent conditions. For the first time in R. solani, DNA sequencing and bioinformatic analyses of ESTs revealed several genes with putative roles in pathogenicity, mating, drug resistance, lignin degradation, bioremediation and morphological differentiation. Further analysis of ESTs may provide insights into virulence mechanisms as well as roles of these genes in development, saprophytic ability and ecological adaptation of this important fungal plant pathogen.
Technical Abstract: Rhizoctonia solani is a ubiquitous basidiomycetous soilborne fungal pathogen causing damping off of seedlings, aerial blights and postharvest diseases. To gain insight into the molecular mechanisms of pathogenesis a global approach based on analysis of expressed sequence tags (ESTs) was undertaken. In order to get broad gene expression coverage, two normalized EST libraries were developed from mycelia grown under high nitrogen-induced virulent and low nitrogen-methylglucose-induced hypovirulent conditions. A pilot scale assessment of gene diversity was made from the sequence analyses of the two libraries. A total of 2280 cDNA clones were sequenced that corresponded to 220 unique sequence sets or clusters (contigs) and 541 singlets, making up a total of 761 unique genes identified from the two virulence-differentiated cDNA libraries. From the total sequences, 295 (38.7%) genes exhibited strong similarities with genes in public databases and categorized into eleven functional groups. Approximately 61.3% of the R. solani ESTs have no apparent homologs in the publicly available fungal genome databases and are considered unique genes. We have identified several cDNAs with reported roles in fungal pathogenicity, virulence, signal transduction components, vegetative incompatibility and mating, drug resistance, lignin degradation, bioremediation and morphological differentiation. A codon usage table has been formulated based on 14694 R. solani EST codons. Further analysis of ESTs may provide insights into virulence mechanisms as well as roles of these genes in development, saprophytic colonization and ecological adaptation of this important fungal plant pathogen.