Abstract
The genome of Fusarium oxysporum (Fo) consists of a set of eleven ‘core’ chromosomes, shared by most strains and responsible for housekeeping, and one or several accessory chromosomes. We sequenced a strain of Fo f.sp. radicis-cucumerinum (Forc) using PacBio SMRT sequencing. All but one of the core chromosomes were assembled into single contigs, and a chromosome that shows all the hallmarks of a pathogenicity chromosome comprised two contigs. A central part of this chromosome contains all identified candidate effector genes, including homologs of SIX6, SIX9, SIX11 and SIX13. We show that SIX6 contributes to virulence of Forc. Through horizontal chromosome transfer (HCT) to a non-pathogenic strain, we also show that the accessory chromosome containing the SIX gene homologs is indeed a pathogenicity chromosome for cucurbit infection. Conversely, complete loss of virulence was observed in Forc016 strains that lost this chromosome. We conclude that also a non-wilt-inducing Fo pathogen relies on effector proteins for successful infection and that the Forc pathogenicity chromosome contains all the information necessary for causing root rot of cucurbits. Three out of nine HCT strains investigated have undergone large-scale chromosome alterations, reflecting the remarkable plasticity of Fo genomes.
Highlights
Fusarium oxysporum Schlechtend.: Fr. f.sp. radicis-cucumerinum Vakalounakis (Forc) is the causal agent of root and stem rot in cucurbits resulting in severe damage, in greenhouse cucumber (Cucumis sativus) and muskmelon (C. melo)
We found that Forc strains possess four Secreted In Xylem (SIX) gene homologs: SIX6, SIX9, SIX11 and SIX13, which encode small secreted proteins originally identified in tomato-infecting strains[10,11,12]
In order to obtain a better understanding of the genome composition of Forc, an HGAP.[3] de novo assembly was generated for Forc[016], a strain previously sequenced by Illumina[9]
Summary
Fusarium oxysporum Schlechtend.: Fr. f.sp. radicis-cucumerinum Vakalounakis (Forc) is the causal agent of root and stem rot in cucurbits resulting in severe damage, in greenhouse cucumber (Cucumis sativus) and muskmelon (C. melo). The aims of this study were to (i) determine the genome structure of Forc, (ii) investigate whether Forc, like wilt-causing strains of Fo, relies on effector proteins for successful colonization and (iii) identify which part(s) of the Forc genome are necessary for the root- and shoot-rot phenotype as well as the extended host range of Forc. To reach these aims, we applied SMRT sequencing of a representative strain of Forc (strain Forc016) as well as Fom (Fom[001]; NRRL26406) as a step towards answering the question what differentiates Forc from strains causing wilt
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