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PlanTE-MIR DB: a database for transposable element-related microRNAs in plant genomes

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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/.

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Acknowledgments

We thank Romain Guyot (Institute de recherche pour le développement - IRD, Montpellier, France) for insightful comments on the TE annotation methods and for his web interface suggestions. APRL received a CAPES fellowship, and GYAdA received a Fundaçāo Araucária fellowship. DSD studies on transposable elements are funded by a CAPES/CNPq “Science without boarders” grant (process 084/13). This manuscript was reviewed by a professional science editor and by a native English-speaking copy editor to improve readability.

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Correspondence to Douglas S. Domingues.

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R. Lorenzetti, A.P., A. de Antonio, G.Y., Paschoal, A.R. et al. PlanTE-MIR DB: a database for transposable element-related microRNAs in plant genomes. Funct Integr Genomics 16, 235–242 (2016). https://doi.org/10.1007/s10142-016-0480-5

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