title: PlanTE-MIR DB: a database for transposable element-related microRNAs in plant genomes.
abstract: Transposable elements (TEs) comprise a major fraction of many plant genomes and are known to drive their organization and evolution. Several studies show that these repetitive elements have a prominent role in shaping noncoding regions of the genome such as microRNA (miRNA) loci, which are components of post-transcriptional regulation mechanisms. Although some studies have reported initial formation of miRNA loci from TE sequences, especially in model plants, the approaches that were used did not employ systems that would allow results to be delivered by a user-friendly database. In this study, we identified 152 precursor miRNAs overlapping TEs in 10 plant species. PlanTE-MIR DB was designed to assemble this data and deliver it to the scientific community interested in miRNA origin, evolution, and regulation pathways. Users can browse the database through a web interface and search for entries using various parameters. This resource is cross-referenced with repetitive element (Repbase Update) and miRNA (miRBase) repositories, where sequences can be checked for further analysis. All data in PlanTE-MIR DB are publicly available for download in several file formats to facilitate their understanding and use. The database is hosted at http://bioinfo-tool.cp.utfpr.edu.br/plantemirdb/ .
authors.affiliation: Graduation Program in Genetics and Molecular Biology, Universidade Estadual de Londrina, UEL, Londrina, Brazil.
authors.forename: Alan P
authors.initials: AP
authors.lastname: R Lorenzetti
authors.affiliation: Bioinformatics Laboratory, Universidade Tecnológica Federal do Paraná, UTFPR, Cornélio, Procópio, Brazil.
authors.forename: Gabriel Y
authors.initials: GY
authors.lastname: A de Antonio
authors.affiliation: Bioinformatics Laboratory, Universidade Tecnológica Federal do Paraná, UTFPR, Cornélio, Procópio, Brazil.
authors.forename: Alexandre R
authors.initials: AR
authors.lastname: Paschoal
authors.affiliation: Department of Botany, Instituto de Biociências, Universidade Estadual Paulista, UNESP, Rio Claro, Brazil. doug@rc.unesp.br.
authors.forename: Douglas S
authors.initials: DS
authors.lastname: Domingues
mesh_terms: D004251:DNA Transposable Elements / Q000235:genetics*; D030541:Databases, Genetic; D018506:Gene Expression Regulation, Plant / Q000235:genetics*; D018745:Genome, Plant; D020407:Internet; D035683:MicroRNAs / Q000235:genetics*; D012091:Repetitive Sequences, Nucleic Acid / Q000235:genetics; D012984:Software
chemical_list: D004251:DNA Transposable Elements; D035683:MicroRNAs
keywords: Database; MicroRNAs; Plant genomes; Transposable elements