KMID : 0381120220440060699
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Genes and Genomics 2022 Volume.44 No. 6 p.699 ~ p.707
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SmGDB: genome database of Salvia miltiorrhiza, an important TCM Plant
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Zhou Changhao
Lin Caicai Xing Piyi Li Xingfeng Song Zhenqiao
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Abstract
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Background: Salvia miltiorrhiza is an important traditional Chinese medicinal (TCM) plant and a model plant in the genetic study of TCM. A series of omics related to Danshen have been published. Integrating, managing, storing, and sharing data has become an urgent problem to be solved in S. miltiorrhiza genetic studies.
Objectives: The genome database is the link for the exchange, acquisition, and use of different omics data between data producers and users, maximizing value and utilization of data.
Methods: The genome database included DSS3 genome and five RNA-Seq data. The back-end performs data search and retrieval through the LAMP (Linux, Apache, MySQL, PHP) framework.
Results: Here, we present SmGDB (S. miltiorrhiza genome database; http://8.140.162.85/), which houses the latest version of genome sequence and annotation data for S. miltiorrhiza, combining three unpublished RNA-Seq data from our group and two released RNA-Seq data. We also identified a novel gene cluster including seven CYP71D genes involved in the tanshinone synthesis pathway based on genome sequences and expression data. Besides, SmGDB provides user-friendly web interfaces for querying and browsing gene annotation, structure, location, and expression profiles for concerned genes. Popular bioinformatics tools such as ¡®BLAST', ¡®Search', ¡®Heatmap', ¡®JBrowse', etc., were also provided in SmGDB.
Conclusions: SmGDB will provide utility for characterizing the structure of the S. miltiorrhiza genome and better understanding gene functions and biological processes underlying complex secondary metabolism in Danshen.
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KEYWORD
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