Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

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: Mami Yamazaki

PROVIDER: E-GEOD-80057 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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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

<h4>Key message</h4>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 lac ...[more]

PMID: 27378356

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Project description:Southern California (USA) populations of the intertidal marine snail Chlorostoma (formerly Tegula) funebralis are generally exposed to higher air and water temperatures than northern California populations. Previous studies have shown that southern populations are more tolerant of heat stress than northern populations. To assess the potential role of gene regulation in these regional differences, we examined transcriptome responses to thermal stress in two southern and two northern populations of C. funebralis. Snails from the four populations were acclimated to a common lab environment, exposed to a heat stress representative of natural low tide conditions, and then analyzed using RNA-Seq to characterize changes in gene expression associated with stress and differences in expression across geographic regions. Changes in expression following stress were dominated by genes involved in apoptosis, the inflammatory response, response to mis and unfolded proteins, and ubiquitination of proteins. Heat shock proteins (Hsps) were up-regulated in both northern and southern populations. However, while the magnitude of the response was significantly greater in northern populations for the majority of Hsp70s, the southern populations showed a greater up-regulation for roughly half of the Hsp40s, which are co-chaperones for Hsp70s. Differential expression analysis of the control versus treatment genes in the northern and southern populations respectively revealed that 56 genes, many involved in the inflammation and immune response, responded to heat stress only in the northern populations. Moreover, several of the molecular chaperones and antioxidant genes that were not differentially expressed in the southern populations instead showed higher constitutive expression under control conditions compared to the northern populations. The expression levels of some of these constitutive genes such as superoxide dismutase were also found to positively correlate with survival following heat stress. This suggests that expression of these genes has evolved a degree of M-bM-^@M-^\frontloadingM-bM-^@M-^] that may contribute to the higher thermal tolerance of southern populations. mRNA profiles of northern and southern California heat-stressed and control C. funebralis were generated by 100bp paired end sequencing, in duplicate, using Illumina HiSeq2000.

Dataset Information

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

Publications

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

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