MITEs in the promoters of effector genes allow prediction of novel virulence genes in Fusarium oxysporum

Authors

Sarah M. Schmidt, University of Amsterdam, Netherlands
Petra M. Houterman, University of Amsterdam, Netherlands
Ines Schreiver, University of Amsterdam, Netherlands
Lisong Ma, University of Amsterdam, Netherlands
Stefan G. Amyotte, University of KentuckyFollow
Biju Chellappan, University of Amsterdam, Netherlands
Sjef Boeren, Wageningen University, Netherlands
Frank L. W. Takken, University of Amsterdam, Netherlands
Martijn Rep, University of Amsterdam, Netherlands

Abstract

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.

Document Type

Article

Publication Date

2-22-2013

Notes/Citation Information

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.

Digital Object Identifier (DOI)

http://dx.doi.org/10.1186/1471-2164-14-119

Repository Citation

Schmidt, Sarah M.; Houterman, Petra M.; Schreiver, Ines; Ma, Lisong; Amyotte, Stefan G.; Chellappan, Biju; Boeren, Sjef; Takken, Frank L. W.; and Rep, Martijn, "MITEs in the promoters of effector genes allow prediction of novel virulence genes in Fusarium oxysporum" (2013). Plant Pathology Faculty Publications. 16.
https://uknowledge.uky.edu/plantpath_facpub/16