title: De Novo transcriptome sequencing reveals important molecular networks and metabolic pathways of the plant, Chlorophytum borivilianum.
abstract: Chlorophytum borivilianum, an endangered medicinal plant species is highly recognized for its aphrodisiac properties provided by saponins present in the plant. The transcriptome information of this species is limited and only few hundred expressed sequence tags (ESTs) are available in the public databases. To gain molecular insight of this plant, high throughput transcriptome sequencing of leaf RNA was carried out using Illumina's HiSeq 2000 sequencing platform. A total of 22,161,444 single end reads were retrieved after quality filtering. Available (e.g., De-Bruijn/Eulerian graph) and in-house developed bioinformatics tools were used for assembly and annotation of transcriptome. A total of 101,141 assembled transcripts were obtained, with coverage size of 22.42 Mb and average length of 221 bp. Guanine-cytosine (GC) content was found to be 44%. Bioinformatics analysis, using non-redundant proteins, gene ontology (GO), enzyme commission (EC) and kyoto encyclopedia of genes and genomes (KEGG) databases, extracted all the known enzymes involved in saponin and flavonoid biosynthesis. Few genes of the alkaloid biosynthesis, along with anticancer and plant defense genes, were also discovered. Additionally, several cytochrome P450 (CYP450) and glycosyltransferase unique sequences were also found. We identified simple sequence repeat motifs in transcripts with an abundance of di-nucleotide simple sequence repeat (SSR; 43.1%) markers. Large scale expression profiling through Reads per Kilobase per Million mapped reads (RPKM) showed major genes involved in different metabolic pathways of the plant. Genes, expressed sequence tags (ESTs) and unique sequences from this study provide an important resource for the scientific community, interested in the molecular genetics and functional genomics of C. borivilianum.
authors.affiliation: Department of Biotechnology, Panjab University, Chandigarh, India.
authors.forename: Shikha
authors.initials: S
authors.lastname: Kalra
authors.affiliation: G N Ramachandran Knowledge Center, Institute of Genomics and Integrative Biology (Council of Scientific and Industrial Research), New Delhi, India.
authors.forename: Bhanwar Lal
authors.initials: BL
authors.lastname: Puniya
authors.affiliation: G N Ramachandran Knowledge Center, Institute of Genomics and Integrative Biology (Council of Scientific and Industrial Research), New Delhi, India.
authors.forename: Deepika
authors.initials: D
authors.lastname: Kulshreshtha
authors.affiliation: Department of Biotechnology, Panjab University, Chandigarh, India.
authors.forename: Sunil
authors.initials: S
authors.lastname: Kumar
authors.affiliation: Department of Biotechnology, Panjab University, Chandigarh, India.
authors.forename: Jagdeep
authors.initials: J
authors.lastname: Kaur
authors.affiliation: G N Ramachandran Knowledge Center, Institute of Genomics and Integrative Biology (Council of Scientific and Industrial Research), New Delhi, India.
authors.forename: Srinivasan
authors.initials: S
authors.lastname: Ramachandran
authors.affiliation: Department of Biotechnology, Panjab University, Chandigarh, India.
authors.forename: Kashmir
authors.initials: K
authors.lastname: Singh
mesh_terms: D000470:Alkaloids / Q000096:biosynthesis; D001046:Aphrodisiacs / Q000302:isolation & purification; D001482:Base Composition; D003577:Cytochrome P-450 Enzyme System / Q000235:genetics / Q000378:metabolism; D018900:Dinucleotide Repeats; D056727:Endangered Species; D020224:Expressed Sequence Tags; D005419:Flavonoids / Q000096:biosynthesis; D018506:Gene Expression Regulation, Plant; D016695:Glycosyltransferases / Q000235:genetics / Q000378:metabolism; D019668:Liliaceae / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D053858:Metabolic Networks and Pathways / Q000235:genetics*; D058977:Molecular Sequence Annotation; D018515:Plant Leaves / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D010940:Plant Proteins / Q000235:genetics* / Q000378:metabolism; D010946:Plants, Medicinal; D012503:Saponins / Q000096:biosynthesis; D059467:Transcriptome
chemical_list: D000470:Alkaloids; D001046:Aphrodisiacs; D005419:Flavonoids; D010940:Plant Proteins; D012503:Saponins; D003577:Cytochrome P-450 Enzyme System; D016695:Glycosyltransferases