Background: Small RNAs (sRNAs) are hypothesized to contribute to plant defense responses by increasing the overall genetic diversity and regulating gene expression; however, their origins and functional importance in plant defense remain unclear. Here, we use Illumina sequencing to assess how sRNA populations vary in the Chinese white poplar (Populus tomentosa) during a rust fungus (Melampsora larici-populina) infection. We sampled sRNAs from the biotrophic growth phase (T02; 48 h post infection) and the urediniospore formation and release phase (T03; 168 h), two essential stages associated with plant colonization and biotrophic growth in rust fungi.
Results: The proportion of siRNA clusters located in pseudogenes and transposons was significantly larger than would be expected by chance and infection-stage-specific differences in siRNAs primarily originated from those in the transposon regions. We also found that the abundance of clusters comprising 24-nt siRNAs located in the transposon and intergenic regions underwent more substantial changes as the infection progressed. A target analysis revealed that 95% of fungal genes were predicted to be targets of Populus sRNAs. Pathogen effector genes were targeted by more sRNAs identified during the biotrophic growth and urediniospores formation and release phases than in the control plants, suggesting a clear selection for sRNA-target interactions. Compared with the miRNAs conserved between different plant species, a significantly higher proportion of Populus-specific miRNAs appeared to target NB-LRR genes.
Conclusions: This integrated study on the plant colonization and biotrophic growth in rust fungi profiles could provide evolutionary insights into the origin and potential roles of the sRNAs in plant defense, coevolution with pathogens, and functional innovation.