title: DsTRD: Danshen Transcriptional Resource Database.
abstract: Salvia miltiorrhiza has been comprehensively studied as a medicinal model plant. However, research progress on this species is significantly hindered by its unavailable genome sequences and limited number of expressed sequence tags in the National Center for Biotechnology Information database. Thus, a transcript database must be developed to assist researchers to browse, search, and align sequences for gene cloning and functional analysis in S. miltiorrhiza. In this study, the Danshen Transcriptional Resource Database (DsTRD) was built using 76,531 transcribed sequences assembled from 12 RNA-Seq transcriptomes. Among these 12 RNA-seq data, ten were downloaded from NCBI database. The remaining two were enced on the Hiseq2000 platform using the stem and hairy-root of S. miltiorrhiza. The transcripts were annotated as protein-coding RNAs, long non-coding RNAs, microRNA precursors, and phased secondary small-interfering RNA genes through several bioinformatics methods. The tissue expression levels for each transcript were also calculated and presented in terms of RNA-Seq data. Overall, DsTRD facilitates browsing and searching for sequences and functional annotations of S. miltiorrhiza. DsTRD is freely available at http://bi.sky.zstu.edu.cn/DsTRD/home.php.
authors.affiliation: Institute of Bioengineering, College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou, 310018, China.
authors.forename: Yuxuan
authors.initials: Y
authors.lastname: Shao
authors.affiliation: Institute of Bioengineering, College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou, 310018, China.
authors.forename: Jiabo
authors.initials: J
authors.lastname: Wei
authors.affiliation: Institute of Bioengineering, College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou, 310018, China.
authors.forename: Fangli
authors.initials: F
authors.lastname: Wu
authors.affiliation: Institute of Bioengineering, College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou, 310018, China.
authors.forename: Haihua
authors.initials: H
authors.lastname: Zhang
authors.affiliation: Institute of Bioengineering, College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou, 310018, China.
authors.forename: Dongfeng
authors.initials: D
authors.lastname: Yang
authors.affiliation: Institute of Bioengineering, College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou, 310018, China.
authors.forename: Zongsuo
authors.initials: Z
authors.lastname: Liang
authors.affiliation: Institute of Bioengineering, College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou, 310018, China.
authors.forename: Weibo
authors.initials: W
authors.lastname: Jin
mesh_terms: D030561:Databases, Nucleic Acid; D018749:RNA, Plant / Q000096:biosynthesis / Q000235:genetics*; D027561:Salvia miltiorrhiza / Q000235:genetics* / Q000378:metabolism; D014158:Transcription, Genetic
chemical_list: D018749:RNA, Plant