Genome duplication and transposon mediated gene alteration shapes the pathogenicity of Rhizoctonia solani AG1-IA

Rhizoctonia solani AG1-IA is a polyphagous basidiomycete fungal pathogen that causes sheath blight disease in rice. In a high-quality genome assembly-based analysis, we report a recent whole genome duplication in R. solani AG1-IA. Duplicated syntenic gene blocks showed presence of district clusters of transposable elements (TEs), which introduced disruption in the continuity of synteny and caused alterations in gene structures. Genome duplication followed by TE-mediated gene structure alterations caused neofunctionalization of genes associated with pathogenicity, as experimentally shown by variation in expression patterns and their involvement during plant colonization. High throughput genome sequencing of forty-two rice field isolates of R. solani AG1-IA from different agro-climatic zones of India profiled the population genetic structure of the Indian isolates and classified those into three distinct groups and a subgroup of admixture, emphasizing exchange of genetic material under field conditions. Genetic diversity analysis of this population predicted the regions that are that are targets for diversifying and purifying selections. Experimental evidence showed that the genes undergoing diversifying and purifying selections were essential for pathogenicity. Together, our data and the analysis revealed profound impact of genome duplication and the transposable elements on genomic diversity and evolution that shaped the pathogenicity of R. solani AG1- IA.