Submitted to: Plant Journal
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/18/2012
Publication Date: 3/8/2012
Citation: Li, F., Orban, R., Baker, B.J. 2012. SoMART, a web server for miRNA, tasiRNA and target gene analysis in Solanaceae plants. Genome Research. 70:891-901. Interpretive Summary: Small RNA molecules mediate many aspects of gene regulation. We have developed a bioinformatic web server linked to Solanaceae sequence databases to find the small RNAs, their precurser RNA molecules, the genes that encode the small RNAs as well as the genes that are targetted by the small RNAs. The web server will be an important tool for those working with potato and tomato genomes.
Technical Abstract: Plant micro(mi)RNAs and trans-acting small interfering (tasi)RNAs mediate posttranscriptional silencing of genes and play important roles in a variety of biological processes. Although bioinformatics prediction and small (s)RNA cloning are the key approaches used for identification of miRNAs, tasiRNAs and their targets, these resources are not readily available for application to researchers studying non-model plant species. We developed a publically available webserver for Solanaceae miRNA/tasiRNA Analysis Resources and Tools (SMART), comprised of four bioinformatic tools linked to Solanaceae sequence databases. The server is designed to identify miRNAs and tasiRNAs that potentially regulate Solanaceae genes of interest. The webserver tools detect sRNAs, precursor miRNA (MIR) and tasiRNA (TAS) genes, cleavage products of miRNA and tasiRNAs, and map sRNAs onto input genes. These tools in conjunction with their associated databases can be used individually or in combination to identify and characterize MIR and TAS genes that target one or many genes of interest in Solanaceae species.