1. CsMPDB 1.0: An interactive web application for visualizing and exploring the microRNAs and phasiRNAs of tea plant (Camellia sinensis var. sinensis 'Shuchazao').
- Author
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Zhao S, Qiao D, Zhang R, Jing T, and An Y
- Subjects
- RNA, Plant genetics, Gene Expression Regulation, Plant, Computational Biology methods, Databases, Genetic, RNA, Small Untranslated genetics, User-Computer Interface, MicroRNAs genetics, Camellia sinensis genetics, Internet, Software
- Abstract
The microRNAs and phasiRNAs of plant are small non-coding RNAs with important functions through regulating gene expression at the post-transcriptional level. However, identifying miRNAs, phasiRNAs and their target genes from numerous sequencing raw data requires multiple software and command-line operations, which are time-consuming and labor-intensive for non-model plants. Therefore, we present CsMPDB (miRNAs and phasiRNAs database of Camellia sinensis), an interactive web application with multiple analysis modules developed to visualize and explore miRNA and phasiRNA in tea plants based on 259 sRNA-seq samples and 24 degradome-seq samples in NCBI. The source code for the CsMPDB was written in R/shiny. It is compatible, extendable, and portable to be easily set up on different operating systems, and can be accessed at http://myshiny.cpolar.io/CsMPDB. This application plays an important role in accelerating the functional study of sRNAs in the transcriptional regulation of tea plants, and has important reference value for the development of sRNA databases of other species., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2025 Elsevier B.V. All rights reserved.)
- Published
- 2025
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