TarDB: an online database for plant miRNA targets and miRNA-triggered phased siRNAs

BMC Genomics

Jing Liu¹  Weijiang Luan¹  Xuan Ma¹  Siju Zhang¹  Shanshan Liang¹  Xiaonan Liu¹ 

[1] College of Life Sciences, Tianjin Key Laboratory of Animal and Plant Resistance, Tianjin Normal University, 300387, Tianjin, China;

关键词: Plant;    miRNA target;    PhasiRNA;    Degradome;    Database;   

DOI  :  10.1186/s12864-021-07680-5

来源: Springer

【 摘 要 】

BackgroundIn plants, microRNAs (miRNAs) are pivotal regulators of plant development and stress responses. Different computational tools and web servers have been developed for plant miRNA target prediction; however, in silico prediction normally contains false positive results. In addition, many plant miRNA target prediction servers lack information for miRNA-triggered phased small interfering RNAs (phasiRNAs). Creating a comprehensive and relatively high-confidence plant miRNA target database is much needed.ResultsHere, we report TarDB, an online database that collects three categories of relatively high-confidence plant miRNA targets: (i) cross-species conserved miRNA targets; (ii) degradome/PARE (Parallel Analysis of RNA Ends) sequencing supported miRNA targets; (iii) miRNA-triggered phasiRNA loci. TarDB provides a user-friendly interface that enables users to easily search, browse and retrieve miRNA targets and miRNA initiated phasiRNAs in a broad variety of plants. TarDB has a comprehensive collection of reliable plant miRNA targets containing previously unreported miRNA targets and miRNA-triggered phasiRNAs even in the well-studied model species. Most of these novel miRNA targets are relevant to lineage-specific or species-specific miRNAs. TarDB data is freely available at http://www.biosequencing.cn/TarDB.ConclusionsIn summary, TarDB serves as a useful web resource for exploring relatively high-confidence miRNA targets and miRNA-triggered phasiRNAs in plants.

【 授权许可】

CC BY