Abstract
Transposable elements (TEs) play an essential role in the genetic variability of eukaryotic species. In plants, they may comprise up to 90% of the total genome. Non-coding RNAs (ncRNAs) are known to control gene expression and regulation. Although the relationship between ncRNAs and TEs is known, obtaining the organized data for sequenced genomes is not straightforward. In this study, we describe the PlaNC-TE (http://planc-te.cp.utfpr.edu.br), a user-friendly portal harboring a knowledgebase created by integrating and analysing plant ncRNA-TE data. We identified a total of 14 350 overlaps between ncRNAs and TEs in 40 plant genomes. The database allows users to browse, search and download all ncRNA and TE data analysed. Overall, PlaNC-TE not only organizes data and provides insights about the relationship between ncRNA and TEs in plants but also helps improve genome annotation strategies. Moreover, this is the first database to provide resources to broadly investigate functions and mechanisms involving TEs and ncRNAs in plants.
Highlights
Transposable elements (TEs) are DNA sequences capable of moving from one position to another in its own genome.They are classified into Classes, Superfamilies and Families based on structural characteristics and mechanisms of transposition [1, 2]
In five genomes (Glycine max, Gossypium raimondii, Hordeum vulgare, Phaseolus vulgaris and Prunus persica), we identified non-coding RNAs (ncRNAs) and TE entries in Ensembl Plants, but we did not find ncRNA-TE overlaps (Table S3)
Several effort has been done to general annotation and organization of genomic data but few works are devoted to making sense of it
Summary
Transposable elements (TEs) are DNA sequences capable of moving from one position to another in its own genome. They are classified into Classes, Superfamilies and Families based on structural characteristics and mechanisms of transposition [1, 2]. NcRNAs are sequences that are not translated into proteins and have influence on great variations in biological functions [9,10,11]. They are important for gene expression regulation at post-transcriptional levels, RNA processing and translation [12]. The most studied are transporter RNA (tRNA), ribosomal RNA (rRNA), microRNA (miRNA), small nuclear RNA (snRNA), small nucleolar RNA (snoRNA) and long ncRNA (lncRNA)
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