PtncRNAdb: plant transfer RNA-derived non-coding RNAs (tncRNAs) database

3 Biotech. 2022 May;12(5):105. doi: 10.1007/s13205-022-03174-7. Epub 2022 Apr 7.

Abstract

Specific endonucleolytic cleavage of tRNA molecules leads to the biogenesis of heterogeneously sized fragments called tRNA-derived non-coding RNAs (tncRNAs). The role of tncRNAs is well studied in human processes, and diseases including different types of cancers and other ailments. They are also generated under stress conditions in plants. Considering the potential role of tncRNAs in the plant system, we have developed a user-friendly, open-access web resource, PtncRNAdb (https://nipgr.ac.in/PtncRNAdb). PtncRNAdb consists of 4,809,503 tncRNA entries identified from ~ 2500 single-end small RNA-seq libraries from six plants, viz., Arabidopsis thaliana, Cicer arietinum, Zea mays, Oryza sativa, Medicago truncatula, and Solanum lycopersicum. It is provided with assorted options to search, browse, visualize, interpret, and download tncRNAs data. Users can perform query search using 'BLASTN' against PtncRNAdb entries. Highcharts have been included for better statistical PtncRNAdb data readability to the users. Additionally, PtncRNAdb includes 'DE tncRNAs' module for differentially expressed tncRNAs under various conditions. Their secondary structure, putative targets, interactive networks of target enrichment, and related publications are also incorporated for further interpretation of their biological functions. PtncRNAdb is an efficient, user-friendly, and exhaustive database, which will aid the ongoing research in plant tncRNAs as well as help in deciphering their role in gene regulation. We hope that it provides a promising platform for researchers to facilitate the understanding of tncRNAs, and their involvement in numerous pathways related to plant development and stress tolerance.

Supplementary information: The online version contains supplementary material available at 10.1007/s13205-022-03174-7.

Keywords: Database; NGS; Regulatory RNAs; Small RNAs; tRNA; tncRNAs.