Conserved and Divergent Features of Land Plant miRNAs and Endogenous siRNAs

microRNAs and other endogenous small RNAs are present in both animals and plants, although key aspects of their biogenesis and functions are somewhat different. Within the land plants it has been proposed that just a small cohort of miRNAs are highly conserved, while many other miRNAs are much less conserved and often species-specific. Recent observations have challenged this model by suggesting that inaccurate miRNA annotations may have inflated counts of species-specific miRNAs. In addition, miRNAs that have no obvious similarities may indeed be orthologs due to extensive divergence in sequence. Besides miRNAs, a major type of endogenous small RNA in plants are 24 nt heterochromatic siRNAs that serve to guide deposition of repressive histone and DNA modifications. The extent of conservation of the heterochromatic siRNA pathway within the land plants has been the subject of some debate. In my talk, I will summarize our recent efforts to clarify miRNA and heterochromatic siRNA conservation patterns in plants through the analysis of extensive small RNA-seq data from multiple species. I will also outline methodological developments that enable robust analyses of these data.