Comparative Sequencing of Plant Small RNAs

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The goal of this project is to develop extensive sequence resources of plant small RNAs (21 to 24 nucleotides) and target mRNAs from representative species across the plant kingdom. These data will enable functional and evolutionary studies of microRNAs (miRNA) and short-interfering RNAs (siRNAs). Small RNAs have a demonstrated and important role in plant development, stress responses, and epigenetic regulation primarily through their role in transcriptional and post-transcriptional silencing of specific target genes and other loci. While most studies have been limited to Arabidopsis, the little that is known about small RNA diversity and evolution suggests that miRNAs are a well-conserved gene regulatory system dating back to lower plants and green algae. This project will develop a sequence dataset of plant small RNAs and target RNAs, based on the hypothesis that most if not all plants utilize important small RNA signaling networks. Different plant families are likely to have both common and lineage-specific miRNAs or other small RNAs with important biological roles. Comparative genomics approaches can be applied to distinguish potential miRNAs from siRNAs and to match the miRNAs to the target sequences; the target sequences will add value to the small RNA sequence data. This project will develop an unparalleled resource of millions of plant small RNAs for comparative analyses. The project includes sequencing of small RNAs from a diverse and agronomically-relevant set of plant species, focused analyses of important members of the Solanaceae and Poaceae, sequencing of miRNA target libraries from several species, and development of a small RNA database and web interface for public access and analysis of data. These data will allow the experimental characterization of the majority of biologically important small RNAs for a range of plant species, and will be tremendously useful to a broad set of plant biologists interested in development, stress responses, epigenetics, evolution, RNA biology and other traits impacted by small RNAs. Access to project outcomesSequence data will be deposited in GenBank (http://www.ncbi.nlm.nih.gov/) and browsable at http://mpss.udel.edu/at. A tutorial on small RNA biology and utilization of the resources generated by this project will make the data accessible to experts as well as those with little exposure to the field.