title: RNA-Seq mediated root transcriptome analysis of Chlorophytum borivilianum for identification of genes involved in saponin biosynthesis.
abstract: Chlorophytum borivilianum is an important species of liliaceae family, owing to its vital medicinal properties. Plant roots are used for aphrodisiac, adaptogen, anti-aging, health-restorative and health-promoting purposes. Saponins, are considered to be the principal bioactive components responsible for the wide variety of pharmacological properties of this plant. In the present study, we have performed de novo root transcriptome sequencing of C. borivilianum using Illumina Hiseq 2000 platform, to gain molecular insight into saponins biosynthesis. A total of 33,963,356 high-quality reads were obtained after quality filtration. Sequences were assembled using various programs which generated 97,344 transcripts with a size range of 100-5,216 bp and N50 value of 342. Data was analyzed against non-redundant proteins, gene ontology (GO), and enzyme commission (EC) databases. All the genes involved in saponins biosynthesis along with five full-length genes namely farnesyl pyrophosphate synthase, cycloartenol synthase, β-amyrin synthase, cytochrome p450, and sterol-3-glucosyltransferase were identified. Read per exon kilobase per million (RPKM)-based comparative expression profiling was done to study the differential regulation of the genes. In silico expression analysis of seven selected genes of saponin biosynthetic pathway was validated by qRT-PCR.
authors.affiliation: Department of Biotechnology, Panjab University, Sector-25, Chandigarh, 160014, India.
authors.forename: Sunil
authors.initials: S
authors.lastname: Kumar
authors.affiliation: Department of Biotechnology, Panjab University, Sector-25, Chandigarh, 160014, India.
authors.forename: Shikha
authors.initials: S
authors.lastname: Kalra
authors.affiliation: Department of Biotechnology, Panjab University, Sector-25, Chandigarh, 160014, India.
authors.forename: Baljinder
authors.initials: B
authors.lastname: Singh
authors.affiliation: Department of Biotechnology, Panjab University, Sector-25, Chandigarh, 160014, India.
authors.forename: Avneesh
authors.initials: A
authors.lastname: Kumar
authors.affiliation: Department of Biotechnology, Panjab University, Sector-25, Chandigarh, 160014, India.
authors.forename: Jagdeep
authors.initials: J
authors.lastname: Kaur
authors.affiliation: Department of Biotechnology, Panjab University, Sector-25, Chandigarh, 160014, India. kashmirbio@pu.ac.in.
authors.forename: Kashmir
authors.initials: K
authors.lastname: Singh
mesh_terms: D003577:Cytochrome P-450 Enzyme System / Q000235:genetics / Q000378:metabolism; D017343:Genes, Plant; D051228:Geranyltranstransferase / Q000235:genetics / Q000378:metabolism; D005964:Glucosyltransferases / Q000235:genetics / Q000378:metabolism; D019751:Intramolecular Transferases / Q000235:genetics / Q000378:metabolism; D019668:Liliaceae / Q000235:genetics* / Q000378:metabolism; D010940:Plant Proteins / Q000235:genetics / Q000378:metabolism; D018517:Plant Roots / Q000378:metabolism; D012503:Saponins / Q000096:biosynthesis* / Q000235:genetics; D059467:Transcriptome
chemical_list: D010940:Plant Proteins; D012503:Saponins; D003577:Cytochrome P-450 Enzyme System; D005964:Glucosyltransferases; C085360:sterol 3-beta-glucosyltransferase; D051228:Geranyltranstransferase; D019751:Intramolecular Transferases; C039924:2,3-oxidosqualene-beta-amyrin-cyclase; C021923:cycloartenol synthase
keywords: Borivilianosides; Chlorophytum borivilianum; De novo transcriptome sequencing; Expression analysis; RPKM; Saponin biosynthesis; qRT-PCR