Transcriptomics

Dataset Information

236

De novo Assembly and Characterization of Swertia japonica Transcriptome for the Identification of Candidate Genes Involved in the Biosynthesis of Therapeutic Metabolites


ABSTRACT: Here, we performed deep transcriptome sequencing for the aerial-tissues and the roots of S. japonica, generating over 2 billion raw reads with an average length of 101 nt by using an Illumina paired-end sequencing by HiSeq2000 platform. Using a combined approach of three popular assemblers, de novo transcriptome assembly for S. japonica was obtained, yielding in 81,729 unigenes with an average length as 884bps and N50-value as 1,452bps, with 46,963 unigenes being annotated based on the sequence similarity against NCBI-nr protein database. Transcriptome profiling of the aerial-tissues and the roots of Swertia japonica

ORGANISM(S): Swertia japonica  

SUBMITTER: Amit Rai   Kazuki Saito  Hiroki Takahashi  Mami Yamazaki  Hideyuki Suzuki  Michimi Nakamura 

PROVIDER: E-GEOD-80057 | ArrayExpress | 2016-07-01

SECONDARY ACCESSION(S): SRP073028GSE80057PRJNA317748

REPOSITORIES: GEO, ArrayExpress, ENA

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Publications

High-throughput sequencing and de novo transcriptome assembly of Swertia japonica to identify genes involved in the biosynthesis of therapeutic metabolites.

Rai Amit A   Nakamura Michimi M   Takahashi Hiroki H   Suzuki Hideyuki H   Saito Kazuki K   Yamazaki Mami M  

Plant cell reports 20160704 10


Here, we report potential transcripts involved in the biosynthesis of therapeutic metabolites in Swertia japonica , the first report of transcriptome assembly, and characterization of the medicinal plant from Swertia genus. Swertia genus, representing over 170 plant species including herbs such as S. chirata, S. hookeri, S. longifolia, S. japonica, among others, have been used as the traditional medicine in China, India, Korea, and Japan for thousands of years. Due to the lack of genomic and tra  ...[more]

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