Recombination between diverged clusters of the tomato Cf-9 plant disease resistance gene family

The tomato Cf-4 and Cf-9 genes are the founder members of a large gene fami ly of homologues of Cladosporium fulvum resistance gene Cf-9 (Hcr9 genes), several of which confer resistance against C. fulvum through recognition of different pathogen-encoded avirulence determinants. Three loci of tandemly repeated Hcr9 genes-Southern Cross (SC), Milky Way (MW), and Northern Ligh ts (NL)-are located on the short arm of tomato chromosome 1, Comparisons be tween 2 SC-Hcr9s, 11 from MW and 5 from NL implicated sequence exchange bet ween gene family members in their evolution. The extent to which novel vari ants can be generated by recombination depends on the degree of sequence po lymorphism available within the gene family. Here we show that physical sep aration of Hcr9 genes can be associated with elevated sequence divergence. Two diverged subclasses of Hcr9s could be defined. These are physically sep arated from each other, with members of one class exclusively residing at N orthern Lights. One exceptional Hcr9 at Northern Lights carried sequence fe atures specific for Hcr9s at other loci, suggesting a recent transfer of th is gene by an interlocus recombination event. As members of diverged subcla sses are brought into physical vicinity within a tandem repeat, a larger sp ectrum of sequence variants can potentially be generated by subsequent inte rhomologue sequence exchange.