ORIGINAL RESEARCH article
Front. Plant Sci.
Sec. Plant Bioinformatics
Volume 16 - 2025 | doi: 10.3389/fpls.2025.1586268
SmilODB: A Multi-Omics Database for the Medicinal Plant Danshen (Salvia miltiorrhiza, Lamiaceae)
Provisionally accepted
- Zhejiang Provincial Key Laboratory of Plant Secondary Metabolism Regulation, School of Life Science and Medicine, Zhejiang Sci-Tech University, Hangzhou, Jiangsu Province, China
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Danshen (Salvia miltiorrhiza Bunge) is a medicinal plant with significant therapeutic value for treating cardiovascular and inflammatory diseases. Despite the availability of multi-omics resources, there remains an urgent need for an integrated platform to harmonize genomic, transcriptomic, metabolomic, and proteomic data. To address this gap, we developed the S. miltiorrhiza Multi-omics Database (SmilODB, http://www.isage.top:56789/), an integrative platform based on the genomic, transcriptomic, metabolomic, and proteomic information of S. miltiorrhiza. SmilODB provides comprehensive data on gene expression, metabolic compound composition, and protein coding. It includes multi-omics resources encompassing: (i) two publicly available genome assemblies (ii) 48 tissue-specific transcriptome datasets spanning root, leaf, and other vegetative tissues, (iii) annotated metabolic pathways for key bioactive compounds (tanshinones, salvianolic acids, and related secondary metabolites), and (iv) 2,967 high-confidence protein structural models predicted using the RoseTTAFold algorithm. The corresponding information is presented intuitively through heat maps, line charts and histograms. Additionally, SmilODB incorporates tools such as genome browsers, BLAST, and gene heatmaps to support sequence analysis and gene exploration. This resource serves as a valuable platform for advancing S. miltiorrhiza research and unlocking its therapeutic potential.
Keywords: S. miltiorrhiza, multi-omics database, Gene Expression, Transcriptomics, 3D structure, deep learning
Received: 02 Mar 2025; Accepted: 22 Apr 2025.
Copyright: © 2025 Liu, Zeng, Tao, Du, Yu, Qi and Yang. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
* Correspondence:
Zhechen Qi, Zhejiang Provincial Key Laboratory of Plant Secondary Metabolism Regulation, School of Life Science and Medicine, Zhejiang Sci-Tech University, Hangzhou, Jiangsu Province, China
Dongfeng Yang, Zhejiang Provincial Key Laboratory of Plant Secondary Metabolism Regulation, School of Life Science and Medicine, Zhejiang Sci-Tech University, Hangzhou, Jiangsu Province, China
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