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Database (Oxford). 2019 Jan 1;2019. pii: baz070. doi: 10.1093/database/baz070.

MepmiRDB: a medicinal plant microRNA database.

Yu D1, Lu J1,2, Shao W1,2, Ma X1, Xie T3,4, Ito H5, Wang T6, Xu M1,2, Wang H1,2, Meng Y1,2.

Author information

1
College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 310036, China.
2
Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou, 310036, China.
3
Department of Pharmacology, Holistic Integrative Pharmacy Institutes, College of Medicine, Hangzhou Normal University, Hangzhou, 311121, China.
4
Key Laboratory of Elemene Class Anti-cancer Chinese Medicine of Zhejiang Province and Engineering Laboratory of Development and Application of Traditional Chinese Medicine from Zhejiang Province, Hangzhou Normal University, Hangzhou, 311121, China.
5
Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan.
6
Key Laboratory of Microbiological Technology and Bioinformatics Research in Zhejiang Province, Hangzhou, 310012, China.

Abstract

MicroRNAs (miRNAs) have been recognized as a key regulator in plant development and metabolism. Recent reports showed that the miRNAs of medicinal plants not only act as a critical modulator in secondary metabolism but also had a great potential of performing cross-kingdom gene regulation. Although several plant miRNA repositories have been publicly available, no miRNA database specific for medicinal plants has been reported to date. Here, we report the first version of MepmiRDB (medicinal plant microRNA database), which is freely accessible at http://mepmirdb.cn/mepmirdb/index.html. This database accommodates thousands of miRNA candidates belonging to 29 medicinal plant species. The miRNA information on sequences, expression patterns and regulatory networks has been included in the functional modules of the database. Specifically, the 'Sequence' module provides the sequences of the mature miRNAs and their precursors, and the structure information of the precursors. Moreover, the processing and small RNA accumulation signals on the miRNA precursors are also included in the 'Sequence' module. The organ/growth condition-specific expression information of the mature miRNAs has been stored in the 'Expression' module. The 'Interaction' module offers the information of the degradome-validated miRNA-target pairs of eight plant species. The 'Search' module enables users to search for the miRNAs by plant species and miRNA families, or by sequences. All data in this database are available for download. Taken together, the functional modules of MepmiRDB ensure its importance and timeliness for mechanistic and functional studies on the medicinal plant miRNAs.

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