PASmiR: a literature-curated database for miRNA molecular regulation in plant response to abiotic stress

Abstract

BackgroundOver 200 published studies of more than 30 plant species have reported a role for miRNAs in regulating responses to abiotic stresses. However, data from these individual reports has not been collected into a single database. The lack of a curated database of stress-related miRNAs limits research in this field, and thus a cohesive database system should necessarily be constructed for data deposit and further application.DescriptionPASmiR, a literature-curated and web-accessible database, was developed to provide detailed, searchable descriptions of miRNA molecular regulation in different plant abiotic stresses. PASmiR currently includes data from ~200 published studies, representing 1038 regulatory relationships between 682 miRNAs and 35 abiotic stresses in 33 plant species. PASmiR’s interface allows users to retrieve miRNA-stress regulatory entries by keyword search using plant species, abiotic stress, and miRNA identifier. Each entry upon keyword query contains detailed regulation information for a specific miRNA, including species name, miRNA identifier, stress name, miRNA expression pattern, detection method for miRNA expression, a reference literature, and target gene(s) of the miRNA extracted from the corresponding reference or miRBase. Users can also contribute novel regulatory entries by using a web-based submission page. The PASmiR database is freely accessible from the two URLs of http://hi.ustc.edu.cn:8080/PASmiR, and http://pcsb.ahau.edu.cn:8080/PASmiR.ConclusionThe PASmiR database provides a solid platform for collection, standardization, and searching of miRNA-abiotic stress regulation data in plants. As such this database will be a comprehensive repository for miRNA regulatory mechanisms involved in plant response to abiotic stresses for the plant stress physiology community.

A combined microRNA and transcriptome analyses illuminates the resistance response of rice against brown planthopper

“…2a), many of which belonged to known miRNA families including miR156, miRNA160, miR166, miR169, miR1846, miR1861 and miR319 (Additional file 3: Table S2). Members of the miRNA families were reported to be involved not only in growth, development, grain size and hormone signaling, but also in response to biotic and abiotic stress [21][22][23][24][25][26][27][28][29][30][31]. These BPH6 responsive DEMs might be involved in response to BPH.…”

“…miRNAs specifically regulate target gene expression through binding complementary sequences to degrade mRNA or inhibit translation [19]. Plant miRNAs are involved in many development processes, including hormone signal transduction, and leaf, floral, shoot, root and vascular development [20][21][22], and play significant roles in abiotic and biotic stress responses [23][24][25][26][27][28]. miR160 is associated with local defense and systemic acquired resistance to potato late blight [24].…”

Emerging techniques to decipher microRNAs (miRNAs) and their regulatory role in conferring abiotic stress tolerance of plants

“…ustc.edu.cn:8080/PASmiR) and (http://pcsb.ahau.edu.cn: 8080/PASmiR)], providing a strong platform for the collection, standardization, and querying miRNA-abiotic stress regulation data in plants (Zhang et al 2013c). It is exhaustively literature-curated and covers the miRNAs involved in abiotic stress types ranging from hormonal, heavy metal stress, mechanical damage, nutritional starvation, oxygen stress, radiation stress, salinity, alkalinity, temperature stress, absence of trace elements, drought, and water-logging.…”

Role of microRNAs in rice plant under salt stress

“…A strong role for miRs has been established in fine tuning the gene expression in response to different environmental stresses and diseases (Sunkar & Zhu, ; Fujii et al, ; Phillips et al, ; Ruiz‐Ferrer & Voinnet, ; Sanan‐Mishra et al, ; Pérez‐Quintero et al, ; Zhou et al, ; Meng et al, ; Yu et al, ; Zeng et al, ; Mittal et al, ). A total of 1511 miRs are known to be involved in various abiotic stresses in different plant species (Zhang et al, ). There is also evidence for a converging functional role of miRs in managing abiotic and biotic stresses (Sanan‐Mishra et al, ).…”