De novo transcriptome analysis deciphered polyoxypregnane glycoside biosynthesis pathway in Gymnema sylvestre
- 88 Downloads
Gymnema sylvestre is an important medicinal plant containing antidiabetic activity. Through de novo transcriptomic study, the pathways of polyoxypregnane glycosides were explored and candidate genes of these pathways were identified in G. sylvestre. High-quality raw reads were assembled into transcripts which resulted in 193,615 unigenes. These unigenes further decoded 58,274 coding DNA sequences (CDSs). Functional annotation of predicted CDSs was carried out using the protein databases, i.e., NCBI’s non-redundant, Uniprot and Pfam. Eukaryotic orthologous group (KOG) classification and transcription factor analysis has revealed most CDS-enriched categories as “Signal transduction mechanism” and “Basic Helix loop helix” (bHLH) transcription factor family, respectively. A total of 16,569 CDSs were assigned minimum one Gene Ontology (GO) term. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis disclosed 235 CDSs which represented total 27 genes of pregnane glycoside pathways and 19 CDSs represented 10 important enzymes of polyoxypregnane glycoside biosynthesis, i.e., sterol 24-C-methyltransferase, cycloeucalenol cycloisomerase, Δ14-sterol reductase, C-8,7 sterol isomerase, sterol methyltransferase 2, C-5 sterol desaturase, sterol Δ7 reductase, Δ24 sterol reductase, 3β-hydroxysteroid dehydrogenase and progesterone 5β reductase (5βPOR). This transcriptome analysis provided an important resource for future functional genomic studies in G. sylvestre.
KeywordsGymnema sylvestre Next generation sequencing Pregnane glycosides RNA sequencing
We acknowledge the funding through FAP Scheme 2015–16, sanctioned dated 23.09.2016 from GSBTM, Govt. of Gujarat, Gujarat, India, the ICAR-DMAPR, Anand and the ICAR, New Delhi for providing the basic facilities for this research work, all germplasm explorers who collected this germplasm and all curators who maintained this genotype at our research farm.
KK conceived the project, designed the experiment, analyzed the data and drafted the MS. DM analyzed the data and drafted the MS. PM explored the germplasm used, gave overall technical and administrative support in this study.
Compliance with ethical standards
Availability of data and materials
The data generated or analyzed during this study are included in this published article, its supplementary information files, and publicly available repositories. The transcriptome raw data are deposited at NCBI under submission ID: SUB2977090, sample ID: GSLFDGS03 and SRA accession ID: SRR5965322.
Conflict of interest
The authors declare no competing financial interests.
- Benveniste P (2002) Sterol metabolism. In: Somerville CR, Meyerowitz EM (eds) The arabidopsis book, vol 1. American Society of Plant Biologists, RockvilleGoogle Scholar
- Bode HB, Zeggel B, Silakowski B, Wenzel SC, Reichenbach H, Muller R (2003) Steroid biosynthesis in prokaryotes: identification of myxobacterial steroids and cloning of the first bacterial 2,3(S)-oxidosqualene cyclase from the myxobacterium Stigmatella aurantiaca. Mol Microbiol 47:471–481CrossRefPubMedGoogle Scholar
- Conesa A, Gotz S (2007) Blast2GO: a comprehensive suite for functional analysis in plant genomics. Int J Plant Genom 2008:1–12Google Scholar
- Gershenzon J, Kreis W (1999) Biochemistry of plant secondary metabolism: annual plant reviews, vol 2. Sheffield Academic Press, SheffieldGoogle Scholar
- Gupta SS, Seth CB, Variyar MC (1962) Experimental studies on pituitary-diabetes. Part I. Inhibitory effect of a few Ayurvedic antidiabetic remedies on anterior pituitary extract induced hyperglycemia in albino rats. J Med Res 50:73–81Google Scholar
- Haas BJ, Papanicolaou A, Yassour M, Grabherr M, Blood PD, Bowden J, Couger MB, Eccles D, Li B, Lieber M, MacManes MD, Ott M, Orvis J, Pochet N, Strozzi F, Weeks N, Westerman R, William T, Dewey CN, Henschel R, Le Duc RD, Friedman N, Regev A (2013) De novo transcript sequence reconstruction from RNA-Seq: reference generation and analysis with Trinity. Nat Protoc 8(8):1494–1512CrossRefPubMedGoogle Scholar
- Kreis W, Müller-Uri F (2013) Cardenolide aglycone formation in Digitalis, isoprenoid synthesis in plants and microorganisms. Springer, New York, pp 425–438Google Scholar
- Luckner M, Wichtl M (2000) Digitalis. WVG, Stuttgart. ISBN 3804717055Google Scholar
- Pandey A, Swarnkar V, Pandey T, Srivastava P (2016) Transcriptome and Metabolite analysis reveal candidate genes of the cardiac glycoside biosynthetic pathway from Calotropis procera. Sci Rep 6(34464):1–14Google Scholar