title: De novo transcriptome sequencing facilitates genomic resource generation in Tinospora cordifolia.
abstract: Tinospora cordifolia is known for its medicinal properties owing to the presence of useful constituents such as terpenes, glycosides, steroids, alkaloids, and flavonoids belonging to secondary metabolism origin. However, there is little information available pertaining to critical genomic elements (ESTs, molecular markers) necessary for judicious exploitation of its germplasm. We employed 454 GS-FLX pyrosequencing of entire transcripts and altogether ∼25 K assembled transcripts or Expressed sequence tags (ESTs) were identified. As the interest in T. cordifolia is primarily due to its secondary metabolite constituents, the ESTs pertaining to terpenoids biosynthetic pathway were identified in the present study. Additionally, several ESTs were assigned to different transcription factor families. To validate our transcripts dataset, the novel EST-SSR markers were generated to assess the genetic diversity among germplasm of T. cordifolia. These EST-SSR markers were found to be polymorphic and the dendrogram based on dice similarity index revealed three distinct clustering of accessions. The present study demonstrates effectiveness in using both NEWBLER and MIRA sequence read assembler software for enriching transcript-dataset and thus enables better exploitation of EST resources for mining candidate genes and designing molecular markers.
authors.affiliation: Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, New Delhi, 110 012, India. rakesh.singh2@icar.gov.in.
authors.forename: Rakesh
authors.identifier: http://orcid.org/0000-0001-7269-6420
authors.initials: R
authors.lastname: Singh
authors.affiliation: Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, New Delhi, 110 012, India.
authors.forename: Rajesh
authors.initials: R
authors.lastname: Kumar
authors.affiliation: ICAR-National Research Centre on Plant Biotechnology, New Delhi, 110 012, India.
authors.forename: Ajay Kumar
authors.initials: AK
authors.lastname: Mahato
authors.affiliation: Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, New Delhi, 110 012, India.
authors.forename: Ritu
authors.initials: R
authors.lastname: Paliwal
authors.affiliation: Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, New Delhi, 110 012, India.
authors.forename: Amit Kumar
authors.initials: AK
authors.lastname: Singh
authors.affiliation: Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, New Delhi, 110 012, India.
authors.forename: Sundeep
authors.initials: S
authors.lastname: Kumar
authors.affiliation: Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, New Delhi, 110 012, India.
authors.forename: Soma S
authors.initials: SS
authors.lastname: Marla
authors.affiliation: Germplasm Evaluation Division, ICAR-National Bureau of Plant Genetic Resources, New Delhi, 110 012, India.
authors.forename: Ashok
authors.initials: A
authors.lastname: Kumar
authors.affiliation: ICAR-National Research Centre on Plant Biotechnology, New Delhi, 110 012, India.
authors.forename: Nagendra K
authors.initials: NK
authors.lastname: Singh
mesh_terms: D030541:Databases, Genetic; D020224:Expressed Sequence Tags; D014644:Genetic Variation; D023281:Genomics; D059014:High-Throughput Nucleotide Sequencing; D018895:Microsatellite Repeats / Q000235:genetics*; D058977:Molecular Sequence Annotation; D031610:Tinospora / Q000235:genetics*; D059467:Transcriptome / Q000235:genetics*
keywords: EST-SSR; Terpenes; Tinospora; Transcription factor; Transcriptome