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

PubWeight™: 0.77‹?›

🔗 View Article (PMID 27378356)

Published in Plant Cell Rep on July 04, 2016

Authors

Amit Rai1, Michimi Nakamura2, Hiroki Takahashi3, Hideyuki Suzuki4, Kazuki Saito2, Mami Yamazaki5

Author Affiliations

1: Metabolites Biology Lab, Department of Biological Sciences, National University of Singapore, Singapore 117543 (A.R., S.U., M.R., L.B.K., J.A.S.B., S.S.);Synthetic Biology Research Consortium (A.R., S.S.) and Singapore Centre for Environmental Life Science Engineering (S.U., S.S.), National University of Singapore, Singapore 117456;NUS Environmental Research Institute, National University of Singapore, Singapore 117411 (S.U., M.R., L.B.K., S.S.); andSingapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore 637551 (S.S.).
2: Graduate School of Pharmaceutical Sciences, Chiba University, Inohana 1-8-1, Chuo-ku, Chiba, 260-8675, Japan.
3: Medical Mycology Research Center, Chiba University, Chiba, Japan.
4: Department of Research and Development, Kazusa DNA Research Institute, Chiba, Japan.
5: Graduate School of Pharmaceutical Sciences, Chiba University, Inohana 1-8-1, Chuo-ku, Chiba, 260-8675, Japan. mamiy@faculty.chiba-u.jp.

Articles cited by this

Basic local alignment search tool. J Mol Biol (1990) 659.07

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol (2009) 235.12

MEGA6: Molecular Evolutionary Genetics Analysis version 6.0. Mol Biol Evol (2013) 112.81

Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res (2002) 76.95

Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol (2011) 53.86

Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics (2005) 46.40

Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics (2014) 44.23

Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics (2006) 43.68

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol (2014) 27.48

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinformatics (2011) 25.76

Data, information, knowledge and principle: back to metabolism in KEGG. Nucleic Acids Res (2013) 15.13

Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgare L.). Theor Appl Genet (2002) 12.60

InterProScan 5: genome-scale protein function classification. Bioinformatics (2014) 8.52

CD-HIT: accelerated for clustering the next-generation sequencing data. Bioinformatics (2012) 8.32

Gene Ontology Consortium: going forward. Nucleic Acids Res (2014) 7.76

Genic microsatellite markers in plants: features and applications. Trends Biotechnol (2005) 7.70

Blast2GO: A comprehensive suite for functional analysis in plant genomics. Int J Plant Genomics (2008) 7.12

THE IMPORTANCE OF MINUTE CHEMICAL CONSTITUENTS (INFINIMENT PETITS CHIMIQUES) OF BIOLOGICAL PRODUCTS: NICKEL, COBALT AND INSULIN. Science (1926) 4.25

Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species. Gigascience (2013) 4.11

Comparing de novo assemblers for 454 transcriptome data. BMC Genomics (2010) 3.49

Assessment of transcript reconstruction methods for RNA-seq. Nat Methods (2013) 3.11

InterPro and InterProScan: tools for protein sequence classification and comparison. Methods Mol Biol (2007) 3.05

In silico analysis on frequency and distribution of microsatellites in ESTs of some cereal species. Cell Mol Biol Lett (2002) 3.04

SOAPdenovo-Trans: de novo transcriptome assembly with short RNA-Seq reads. Bioinformatics (2014) 2.82

The grapevine transcription factor VvMYBPA1 regulates proanthocyanidin synthesis during fruit development. Plant Physiol (2007) 2.33

UGT73C6 and UGT78D1, glycosyltransferases involved in flavonol glycoside biosynthesis in Arabidopsis thaliana. J Biol Chem (2003) 1.78

Three enzyme systems for galactoglycerolipid biosynthesis are coordinately regulated in plants. J Biol Chem (2004) 1.66

Chemical genetic interrogation of natural variation uncovers a molecule that is glycoactivated. Nat Chem Biol (2007) 1.56

Optimizing de novo common wheat transcriptome assembly using short-read RNA-Seq data. BMC Genomics (2012) 1.54

N-glucosylation of cytokinins by glycosyltransferases of Arabidopsis thaliana. J Biol Chem (2004) 1.46

The seco-iridoid pathway from Catharanthus roseus. Nat Commun (2014) 1.40

An evolutionary view of functional diversity in family 1 glycosyltransferases. Plant J (2011) 1.26

Development and mapping of simple sequence repeat markers for pearl millet from data mining of expressed sequence tags. BMC Plant Biol (2008) 1.18

Swertia (Gentianaceae): chemical and pharmacological aspects. Chem Biodivers (2004) 1.17

Cutoffs and k-mers: implications from a transcriptome study in allopolyploid plants. BMC Genomics (2012) 1.17

Tetraoxygenated naturally occurring xanthones. Phytochemistry (2000) 1.17

Combining transcriptome assemblies from multiple de novo assemblers in the allo-tetraploid plant Nicotiana benthamiana. PLoS One (2014) 1.15

Simple sequences in a "minimal' genome. Nat Genet (1996) 1.01

Evaluation of the in-vivo activity and toxicity of amarogentin, an antileishmanial agent, in both liposomal and niosomal forms. J Antimicrob Chemother (1999) 0.98

Historical perspective of traditional indigenous medical practices: the current renaissance and conservation of herbal resources. Evid Based Complement Alternat Med (2014) 0.97

A web-based resource for the Arabidopsis P450, cytochromes b5, NADPH-cytochrome P450 reductases, and family 1 glycosyltransferases (http://www.P450.kvl.dk). Phytochemistry (2009) 0.97

Natural products derived from plants as a source of drugs. J Adv Pharm Technol Res (2012) 0.97

Bellidifolin: a potent hypoglycemic agent in streptozotocin (STZ)-induced diabetic rats from Swertia japonica. Planta Med (1994) 0.94

Plant-derived medicines: a novel class of immunological adjuvants. Int Immunopharmacol (2010) 0.93

Phytochemical genomics--a new trend. Curr Opin Plant Biol (2013) 0.91

Constructing de novo biosynthetic pathways for chemical synthesis inside living cells. Biochemistry (2011) 0.91

The use of abscisic acid analogues to analyse the substrate selectivity of UGT71B6, a UDP-glycosyltransferase of Arabidopsis thaliana. FEBS Lett (2005) 0.90

Biosynthesis of camptothecin. In silico and in vivo tracer study from [1-13C]glucose. Plant Physiol (2003) 0.90

Anti-diabetic activity of swertiamarin is due to an active metabolite, gentianine, that upregulates PPAR-γ gene expression in 3T3-L1 cells. Phytother Res (2012) 0.90

Prevention of liver carcinogenesis by amarogentin through modulation of G1/S cell cycle check point and induction of apoptosis. Carcinogenesis (2012) 0.87

Introgression of Swertia mussotii gene into Bupleurum scorzonerifolium via somatic hybridization. BMC Plant Biol (2011) 0.87

Swertiamarin attenuates inflammation mediators via modulating NF-κB/I κB and JAK2/STAT3 transcription factors in adjuvant induced arthritis. Eur J Pharm Sci (2014) 0.86

AFLP markers for identification of Swertia species (Gentianaceae). Genet Mol Res (2010) 0.86

Phenolic-linked biochemical rationale for the anti-diabetic properties of Swertia chirayita (Roxb. ex Flem.) Karst. Phytother Res (2012) 0.85

Anticholinergic action of Swertia japonica and an active constituent. J Ethnopharmacol (1991) 0.83

Effect of methanolic extract of Enicostemma littorale on Dalton's ascitic lymphoma. J Ethnopharmacol (2000) 0.83

[Biologically active principles of crude drugs: pharmacological actions of Swertia japonica extracts, swertiamarin and gentianine (author's transl)]. Yakugaku Zasshi (1978) 0.83

Phytochemical genomics on the way. Plant Cell Physiol (2013) 0.82

High-Throughput Sequencing and De Novo Assembly of Red and Green Forms of the Perilla frutescens var. crispa Transcriptome. PLoS One (2015) 0.82

Improved resistance to oxidative stress by a loss-of-function mutation in the Arabidopsis UGT71C1 gene. Mol Cells (2008) 0.82

RP-HPLC analysis of seco-iridoid glycoside swertiamarin from different Swertia species. Nat Prod Res (2015) 0.81

IPRStats: visualization of the functional potential of an InterProScan run. BMC Bioinformatics (2010) 0.79

Omics data input for metabolic modeling. Curr Opin Biotechnol (2015) 0.79

Swertia spp: a source of bitter compounes for medicinal use. Anc Sci Life (1996) 0.79

Xanthones with anti-hepatitis B virus activity from Swertia mussotii. Planta Med (2013) 0.78

RNA-seq Transcriptome Analysis of Panax japonicus, and Its Comparison with Other Panax Species to Identify Potential Genes Involved in the Saponins Biosynthesis. Front Plant Sci (2016) 0.78

Hepatoprotective principles of Swertia japonica Makino on D-galactosamine/lipopolysaccharide-induced liver injury in mice. Chem Pharm Bull (Tokyo) (1997) 0.77

Simple sequence repeat marker development and genetic mapping in quinoa (Chenopodium quinoa Willd.). J Genet (2008) 0.77

Contents of therapeutic metabolites in Swertia chirayita correlate with the expression profiles of multiple genes in corresponding biosynthesis pathways. Phytochemistry (2015) 0.77

Combined de novo and genome guided assembly and annotation of the Pinus patula juvenile shoot transcriptome. BMC Genomics (2015) 0.77

Xanthones from Swertia punctata. Phytochemistry (2002) 0.77

Effects of Swertia japonica extract and its main compound swertiamarin on gastric emptying and gastrointestinal motility in mice. Fitoterapia (2011) 0.76

Antimutagenicity of Japanese traditional herbs, gennoshoko, yomogi, senburi and iwa-tobacco. Biofactors (2004) 0.76

Phylogenetic examination of crude drugs derived from Yunnanese Swertia plants. J Nat Med (2013) 0.76

Phytochemical investigation of crude methanol extracts of different species of Swertia from Nepal. BMC Res Notes (2015) 0.75

Studies on the constituents of Swertia japonica. IV. Isolation and structure of xanthones. Chem Pharm Bull (Tokyo) (1969) 0.75

[Studies on the constituents of Swertia japonica. 3. On the flavonoid constituents of the plants of Swertia spp]. Yakugaku Zasshi (1968) 0.75

Xanthones from Swertia mussotii as multitarget-directed antidiabetic agents. ChemMedChem (2014) 0.75

Studies on the constituents of Swertia japonica MAKINO I. On the structures of new secoiridoid diglycosides. Chem Pharm Bull (Tokyo) (2004) 0.75

Xanthones from the herb of Swertia elata and their anti-TMV activity. Nat Prod Res (2015) 0.75

Studies on the constituents of Swertia japonica Makino II. On the structures of new glycosides. Chem Pharm Bull (Tokyo) (2005) 0.75

Medicinal plants in the prevention and treatment of chronic diseases 2013. Evid Based Complement Alternat Med (2014) 0.75

Analysis of swertiamarin in Swertia herb and preparations containing this crude drug by capillary electrophoresis. Anal Sci (2001) 0.75

Senburiside II, a New Iridoid Glucoside from Swertia japonica. Planta Med (1987) 0.75

Iridoid Glucoside of Swertia japonica. Planta Med (1985) 0.75

[The active constituents of Swertia patens]. Zhong Yao Tong Bao (1984) 0.75

[Studies on the constituents of Swertia japonica. V. On the xanthone constituents of the plants of Swertia ssp]. Yakugaku Zasshi (1969) 0.75