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Background  Land plant genomes contain multiple members of a eukaryote-specific gene family encoding proteins with pentatricopeptide repeat (PPR) motifs. Some PPR proteins were shown to participate in post-transcriptional events involved in organellar gene expression, and this type of function is now thought to be their main biological role. Among PPR genes, restorers of fertility (Rf) of cytoplasmic male sterility systems constitute a peculiar subgroup that is thought to evolve in response to the presence of mitochondrial sterility-inducing genes. Rf genes encoding PPR proteins are associated with very close relatives on complex loci.    Results  We sequenced a non-restoring allele (L7rfo) of the  Rfo  radish locus whose restoring allele (D81Rfo) was previously described, and compared the two alleles and their PPR genes. We identified a ca 13 kb long fragment, likely originating from another part of the radish genome, inserted into the L7rfo sequence. The L7rfo allele carries two genes ( PPR-1  and  PPR-2 ) closely related to the three previously described PPR genes of the restorer D81Rfo allele ( PPR-A ,  PPR-B , and  PPR-C ). Our results indicate that alleles of the  Rfo  locus have experienced complex evolutionary events, including recombination and insertion of extra-locus sequences, since they diverged. Our analyses strongly suggest that present coding sequences of  Rfo  PPR genes result from intragenic recombination. We found that the 10 C-terminal PPR repeats in  Rfo  PPR gene encoded proteins result from the tandem duplication of a 5 PPR repeat block.    Conclusions  The  Rfo  locus appears to experience more complex evolution than its flanking sequences. The  Rfo  locus and PPR genes therein are likely to evolve as a result of intergenic and intragenic recombination. It is therefore not possible to determine which genes on the two alleles are direct orthologs. Our observations recall some previously reported data on pathogen resistance complex loci.

Sequence analysis of two alleles reveals that intra-and intergenic recombination played a role in the evolution of the radish fertility restorer (Rfo)