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Background  Several resistance traits, including the  I2  resistance against tomato fusarium wilt, were mapped to the long arm of chromosome 11 of Solanum. However, the structure and evolution of this locus remain poorly understood.    Results  Comparative analysis showed that the structure and evolutionary patterns of the  I2  locus vary considerably between potato and tomato. The  I2  homologues from different Solanaceae species usually do not have orthologous relationship, due to duplication, deletion and frequent sequence exchanges. At least 154 sequence exchanges were detected among 76 tomato  I2  homologues, but sequence exchanges between  I2  homologues in potato is less frequent. Previous study showed that  I2  homologues in potato were targeted by miR482. However, our data showed that  I2  homologues in tomato were targeted by miR6024 rather than miR482. Furthermore, miR6024 triggers phasiRNAs from  I2  homologues in tomato. Sequence analysis showed that miR6024 was originated after the divergence of Solanaceae. We hypothesized that miR6024 and miR482 might have facilitated the expansion of the  I2  family in Solanaceae species, since they can minimize their potential toxic effects by down-regulating their expression.    Conclusions  The  I2  locus represents a most divergent resistance gene cluster in Solanum. Its high divergence was partly due to frequent sequence exchanges between homologues. We propose that the successful expansion of  I2  homologues in Solanum was at least partially attributed to miRNA mediated regulation.    Electronic supplementary material  The online version of this article (doi:10.1186/1471-2164-15-743) contains supplementary material, which is available to authorized users.

The I2 resistance gene homologues in Solanum have complex evolutionary patterns and are targeted by miRNAs