BACKGROUND: The plant-pathogenic fungus Fusarium oxysporum f.sp.lycopersici (Fol) has accessory, lineage-specific (LS) chromosomes that can be transferred horizontally between strains. A single LS chromosome in the Fol4287 reference strain harbors all known Fol effector genes. Transfer of this pathogenicity chromosome confers virulence to a previously non-pathogenic recipient strain. We hypothesize that expression and evolution of effector genes is influenced by their genomic context.

RESULTS: To gain a better understanding of the genomic context of the effector genes, we manually curated the annotated genes on the pathogenicity chromosome and identified and classified transposable elements. Both retro- and DNA transposons are present with no particular overrepresented class. Retrotransposons appear evenly distributed over the chromosome, while DNA transposons tend to concentrate in large chromosomal subregions. In general, genes on the pathogenicity chromosome are dispersed within the repeat landscape. Effector genes are present within subregions enriched for DNA transposons. A miniature Impala (mimp) is always present in their promoters. Although promoter deletion studies of two effector gene loci did not reveal a direct function of the mimp for gene expression, we were able to use proximity to a mimp as a criterion to identify new effector gene candidates. Through xylem sap proteomics we confirmed that several of these candidates encode proteins secreted during plant infection.

CONCLUSIONS: Effector genes in Fol reside in characteristic subregions on a pathogenicity chromosome. Their genomic context allowed us to develop a method for the successful identification of novel effector genes. Since our approach is not based on effector gene similarity, but on unique genomic features, it can easily be extended to identify effector genes in Fo strains with different host specificities.

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Published in BMC Genomics, v. 14, 119.

© 2013 Schmidt et al; licensee BioMed Central Ltd.

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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1471-2164-14-119-s1.xls (143 kB)
Detailed annotation of the Fol4287 pathogenicity chromosome.

1471-2164-14-119-s2.pptx (1101 kB)
A putative secondary metabolite gene cluster of Fol is expressed during tomato infection.

1471-2164-14-119-s3.doc (74 kB)
Significance of the association between the TCGGCA element and upstream regions of effector genes.

1471-2164-14-119-s4.doc (38 kB)
Complex repeat structure in SIX8, SIX8b and SIX14 upstream regions.

1471-2164-14-119-s5.doc (185 kB)
Newly identified TEs of Fol.

1471-2164-14-119-s6.xlsx (8 kB)
Primers used in this study.