Small RNA-Producing Genes in Plants: Improved Methods and Novel Discoveries

Plants produce an extraordinary variety of regulatory small RNAs, which include microRNAs (miRNAs) and short interfering RNAs (siRNAs). miRNAs and siRNAs are a major factor in plant gene regulation and affect nearly every phenotype of interest. A given plant genome produces miRNAs from many hundreds of genes, and siRNAs from many thousands of genes. However, the methods for finding and annotating these genes have been uneven, and the current state of miRNA and siRNA gene annotation is poor. I will describe our novel, open-source methods for miRNA and siRNA gene discovery using high-throughput small RNA-seq data. I will then describe how we have used these methods to make novel small RNA discoveries in several plant species, including Arabidopsis, maize, Physcomitrella patens, and most recently in several parasitic plant species.