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

Abstract

BackgroundSeveral 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.ResultsComparative 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.ConclusionsThe 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 materialThe online version of this article (doi:10.1186/1471-2164-15-743) contains supplementary material, which is available to authorized users.

Genome-wide comparative analysis in Solanaceous species reveals evolution of microRNAs targeting defense genes inCapsicumspp.

“…Previous studies revealed that miR6024 acts as a trigger of phasiRNA biogenesis, by targeting the I2 gene in tomato and Rx1 gene in potato. 20 , 65 The length of miR6024 is 22 nucleotides in tomato and potato, but 21 nucleotides in pepper ( Supplementary Table S1 ). Because phasiRNA triggers are typically 22 nucleotides in length, 9 can-miR6024-derived phasiRNA biogenesis might not occur in pepper.…”

Dramatic Number Variation of R Genes in Solanaceae Species Accounted for by a Few R Gene Subfamilies

“…Comparative analysis revealed that presence/absence (P/A) polymorphism is prevalent between species [ 5 , 9 , 19 , 20 ]. An integrated map of R gene loci for a plant family will be helpful to understand the distribution of P/A polymorphism as well as their evolutionary mechanism, and it is also useful for future mapping and cloning of R genes [ 3 , 5 ].…”

“…An integrated map of R gene loci for a plant family will be helpful to understand the distribution of P/A polymorphism as well as their evolutionary mechanism, and it is also useful for future mapping and cloning of R genes [ 3 , 5 ]. R gene family represents the most divergent gene family in plant genome, with considerable copy number variation, P/A polymorphism as well as sequence variation caused by various evolutionary mechanisms [ 5 , 18 , 20 , 21 ].…”

The NLR Protein Encoded by the Resistance Gene Ty-2 Is Triggered by the Replication-Associated Protein Rep/C1 of Tomato Yellow Leaf Curl Virus

“…Ty-2 is a CC-NBS-LRR (CNL) type of gene belonging to the I-2 like subclass of CNL genes. I2-like genes in tomato and potato show high divergence (Wei et al, 2014) and distinctly segregates in sequence and function from other CNLs (Bentham et al, 2018). The resistance mechanism of this subclass of CNLs is unknown (Kourelis and van der Hoorn, 2018).…”