Striking genetic similarity between races of Fusarium oxysporum f. sp. ciceris confirms a monophyletic origin and clonal evolution of the chickpea vascular wilt pathogen

Eight pathogenic races, determined based on the virulence displayed on differential chickpea cultivars, have been recognized in Fusarium oxysporum f. sp. ciceris, the causal agent of Fusarium wilt of chickpea. In order to elucidate the genetic relationships between these races and understand how virulence evolved, we analyzed the sequences of 32 genomic regions for each of the eight races. Twelve of these regions were newly-designed microsatellite markers polymorphic for the F. oxysporum complex (10 displaying polymorphisms in the number of core repeats, and two displaying polymorphic nucleotides in the microsatellite flanking regions), developed from a microsatellite enriched genomic library. The translation elongation factor 1-α (TEF), internal transcribed spacer region of the rDNA (ITS), five mitochondrial regions, a xylanase gene (xyl4) and its transcriptional activator (xlnR), two F. oxysporum f. sp. ciceris sequence characterized amplified regions (SCAR) and 11 microsatellites were completely identical for all races. Only a few polymorphisms were observed between and sometimes within races for the β-tubulin gene, intergenic spacer of the ribosomal DNA (IGS), endopolygalacturonase pg1 and exopolygalacturonase pgx4 genes, and six microsatellite regions (four loci with repeat number variations and two loci with polymorphisms in flanking regions). In a previous study, race 3 of F. oxysporum f. sp. ciceris was reported to be Fusarium proliferatum based on TEF data of one isolate. However, our sequence analyses using TEF and other regions showed that the race 3 isolates in our study belong to F. oxysporum. The high degree of similarity among races supports a monophyletic origin of this forma specialis and a subsequent development of pathogenic races within the lineage.