Comparative genomics of geographically distant Fusarium fujikuroi isolates revealed two distinct pathotypes correlating with secondary metabolite profiles

Abstract

Fusarium fujikuroi causes bakanae (“foolish seedling”) disease of rice which is characterized by hyper-elongation of seedlings resulting from production of gibberellic acids (GAs) by the fungus. This plant pathogen is also known for production of harmful mycotoxins, such as fusarins, fusaric acid, apicidin F and beauvericin. Recently, we generated the first de novo genome sequence of F. fujikuroi strain IMI 58289 combined with extensive transcriptional, epigenetic, proteomic and chemical product analyses. GA production was shown to provide a selective advantage during infection of the preferred host plant rice. Here, we provide genome sequences of eight additional F. fujikuroi isolates from distant geographic regions. The isolates differ in the size of chromosomes, most likely due to variability of subtelomeric regions, the type of asexual spores (microconidia and/or macroconidia), and the number and expression of secondary metabolite gene clusters. Whilst most of the isolates caused the typical bakanae symptoms, one isolate, B14, caused stunting and early withering of infected seedlings. In contrast to the other isolates, B14 produced no GAs but high amounts of fumonisins during infection on rice. Furthermore, it differed from the other isolates by the presence of three additional polyketide synthase (PKS) genes (PKS40, PKS43, PKS51) and the absence of the F. fujikuroi-specific apicidin F (NRPS31) gene cluster. Analysis of additional field isolates confirmed the strong correlation between the pathotype (bakanae or stunting/withering), and the ability to produce either GAs or fumonisins. Deletion of the fumonisin and fusaric acid-specific PKS genes in B14 reduced the stunting/withering symptoms, whereas deletion of the PKS51 gene resulted in elevated symptom development. Phylogenetic analyses revealed two subclades of F. fujikuroi strains according to their pathotype and secondary metabolite profiles.

Set1 and Kdm5 are antagonists for H3K4 methylation and regulators of the major conidiation‐specific transcription factor gene ABA1 in Fusarium fujikuroi

“…Most F. fujikuroi strains cause bakanae disease when infecting rice plants as a result of their secretion of GAs, a group of highly bioactive phytohormones (Niehaus et al, 2017a). Since the GA 3 production in axenic culture was fully abolished in Δset1 and significantly decreased in Δkdm5 (Fig.…”

“…In order to compare the genome-wide impact of SET1 and KDM5 deletion on transcription, we performed a microarray expression analysis. For this, the WT, Δset1 and Δkdm5 mutants were cultivated in synthetic ICI liquid medium with limiting (6 mM, N−) or saturating (60 mM, N+) amounts of glutamine (Gln), conditions that were previously shown to either induce or repress the expression of several SM genes in F. fujikuroi Niehaus et al, 2017a). Based on the selection criteria of a fourfold change in expression (log 2 fold change ≥ 2 or ≤ −2) at the 95% confidence interval (false discovery rate < 0.05), 2282 of the 14,816 annotated genes (15.4%) were affected in a Set1-and/or Kdm5-dependent manner in at least one condition.…”

“…The formation of asexual spores is an important way for filamentous, pathogenic fungi to proliferate and spread. The F. fujikuroi WT IMI58289 used in this work produces only microconidia (here simply referred to as 'conidia'), while other strains produce micro-and macroconidia (with several septa), or predominantly macroconidia (Niehaus et al, 2017a). As conidiation-related genes are Fig.…”

“…7B). BrlA seems to be absent from the genus Fusarium (Son et al, 2014a;Niehaus et al, 2017a). Single deletion mutants were generated for the F. fujikuroi orthologs, designated ABA1, FLB2-FLB5 and WET1, and the mutants were tested for their ability to produce conidia.…”

“…As indicated above, F. fujikuroi IMI58289 analyzed so far produces only microconidia, while the sequenced strain F. fujikuroi E282 produces macroconidia (Niehaus et al, 2017a). To elucidate whether Aba1 might be also required for macroconidia formation in E282, the respective ABA1 ortholog FFE2_00769 was deleted also in the E282 background.…”