Abstract
BackgroundThe 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.ResultsTo 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.ConclusionsEffector 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.
Highlights
The plant-pathogenic fungus Fusarium oxysporum f.sp.lycopersici (Fol) has accessory, lineage-specific (LS) chromosomes that can be transferred horizontally between strains
Non-transposable elements (TEs) genes on the forma specialis lycopersisci (Fol) pathogenicity chromosome group into a small set of functional classes Non-TE open reading frames (ORFs) occupy only 13% of the DNA space on the pathogenicity chromosome of Fol, which consists of four supercontigs in the most recent Fol genome assembly (Li-Jun Ma, personal communication, Table 1)
Proteins encoded on the Fol pathogenicity chromosome that are likely involved in secondary metabolism [1] include methyl transferases (6), cytochrome P450s (6) and glycosyltransferases (3)
Summary
The plant-pathogenic fungus Fusarium oxysporum f.sp.lycopersici (Fol) has accessory, lineage-specific (LS) chromosomes that can be transferred horizontally between strains. Eleven of the 15 chromosomes of the sequenced strain (Fol4287) are syntenic with chromosomes of the sister species Fusarium verticilloides and the more distantly related Fusarium graminearum, displaying high sequence similarity and conservation of gene order [1] These core chromosomes contain all housekeeping genes and few transposable elements (TEs). Spp. are monophyletic, others are composed of several clonal lineages that appear to have independently acquired the ability to infect the same host plant [4,5,6] This polyphyletic origin was likely caused by horizontal transfer of chromosomes encoding host specific virulence genes between Fo lineages, thereby allowing the distinction of members of a f. This polyphyletic origin was likely caused by horizontal transfer of chromosomes encoding host specific virulence genes between Fo lineages, thereby allowing the distinction of members of a f. sp., not by overall genetic relatedness, but by the presence or absence of certain LS chromosomes [1]
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