Different phenotypes, similar genomes: three newly sequenced Fusarium fujikuroi strains induce different symptoms in rice depending on temperature

Bakanae, caused by the hemibiotrophic fungus Fusarium fujikuroi, is one of the most important diseases of rice, causing up to 75% of losses, depending on strain and environmental conditions. Some strains cause elongation and thin leaves, while others induce stunting and chlorotic seedlings. Differences in symptoms are attributed to genetic differences in the strains. F. fujikuroi strains Augusto2, CSV1 and I1.3 were sequenced with Illumina MySeq, and pathogenicity trials were conducted on rice cv. Galileo, susceptible to bakanae. By performing gene prediction, SNP calling and structural variant analysis with a reference genome, we show how an extremely limited number of polymorphisms in genes not commonly associated with bakanae disease can cause strong differences in phenotype. CSV1 and Augusto2 are particularly close, with only 21,887 SNPs between them, but they differ in virulence, reaction to temperature, induced symptoms, colony morphology and color, growth speed, fumonisin and gibberellin production. Genes potentially involved in the shift in phenotype are identified. Furthermore, we show how temperature variation may result in different symptoms even in rice plants inoculated with the same F. fujikuroi strain. Moreover, all the F. fujikuroi strains became more virulent at higher temperatures. Significant differences were likewise observed in gibberellic acid production and in the expression of both fungal and plant gibberellin biosynthetic genes.