SmGDB: genome database of Salvia miltiorrhiza, an important TCM Plant

• Published in: Genes & genomics 2022, 44(6), , pp.699-707
• Main Authors: Zhou, Changhao, Lin, Caicai, Xing, Piyi, Li, Xingfeng, Song, Zhenqiao
• Format: Article
• Language: English
• Subjects: Analysis; Animal Genetics and Genomics; Bioinformatics; Biomedical and Life Sciences; Browsing; Database management systems; Genes; Genomes; Genomics; Human Genetics; Interfaces; Life Sciences; Medicinal plants; Medicine, Chinese; Microbial Genetics and Genomics; Nucleotide sequence; Plant Genetics and Genomics; Research Article; Ribonucleic acid; RNA; RNA sequencing; Salvia miltiorrhiza; 생물학
• ISSN: 1976-9571; 2092-9293
• DOI: 10.1007/s13258-022-01251-y

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), which houses the latest version of genome sequence and annotation data for S. miltiorrhiza , combining three unpublished RNA-Seq data from our group and two released RNA-Seq data.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.