Genomic Differences Between Two Fusarium oxysporum Formae Speciales Causing Root Rot in Cucumber

The host specificity of <i>Fusarium oxysporum</i> (<i>Fox</i>) formae speciales has been reported to be linked to effector proteins known as Secreted in Xylem (SIX). These genes are associated with the non-autonomous mobile element miniature impala (<i>mimp</i>), normally distributed on the accessory chromosomes. The pattern of <i>mimp</i> associated with effector genes has been used to predict candidate effector profiles which characterize <i>Fox</i> formae speciales. In this study, we demonstrate the pathogenicity of strains <i>Fusarium oxysporum</i> f.sp. <i>radicis-lycopersici</i> (<i>Forl</i>) ZUM2407 and <i>Fusarium oxysporum</i> f.sp. <i>radicis-cucumerinum</i> (<i>Forc</i>) V03-2g in a common host plant (cucumber) and compare their genomes. The <i>Forl</i> ZUM2407 genome lacks <i>SIX</i> genes and their homologs, in contrast to <i>Forc</i> V03-2g. We predicted the total number of <i>mimp</i> elements in the genome of <i>Forl</i> ZUM2407 to be three-fold less than that of <i>Forc</i> V03-2g (10 and 36 copies, respectively). The <i>mimp</i> distribution pattern in <i>Forl</i> ZUM2407 was completely different from that present in <i>Forc</i> V03-2g. Candidate effector profile analysis did not predict that <i>Forl</i> ZUM2407 was able to infect cucumber plants like <i>Forc</i> V03-2g. Therefore, we assume that <i>Forl</i> ZUM2407 has a different type of genome organization associated with pathogenicity, whose effector profile cannot be described using the <i>mimp</i>-based approach.