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

Autor: Jing Liu, Xiaonan Liu, Siju Zhang, Shanshan Liang, Weijiang Luan, Xuan Ma
Jazyk: angličtina
Rok vydání: 2021
Předmět:
Zdroj: BMC Genomics, Vol 22, Iss 1, Pp 1-12 (2021)
Druh dokumentu: article
ISSN: 1471-2164
DOI: 10.1186/s12864-021-07680-5
Popis: Abstract Background In 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. Results Here, 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 . Conclusions In summary, TarDB serves as a useful web resource for exploring relatively high-confidence miRNA targets and miRNA-triggered phasiRNAs in plants.
Databáze: Directory of Open Access Journals