De novo transcriptome sequencing facilitates genomic resource generation in Tinospora cordifolia

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 (...

Full description

Saved in:
Bibliographic Details
Published in:Functional & integrative genomics 2016-09, Vol.16 (5), p.581-591
Main Authors: Singh, Rakesh, Kumar, Rajesh, Mahato, Ajay Kumar, Paliwal, Ritu, Singh, Amit Kumar, Kumar, Sundeep, Marla, Soma S., Kumar, Ashok, Singh, Nagendra K.
Format: Article
Language:English
Subjects:
Animal Genetics and Genomics
Biochemistry
Bioinformatics
Biomedical and Life Sciences
Biosynthesis
Cell Biology
Databases, Genetic
Expressed Sequence Tags
Flavonoids
Genetic Variation
Genomes
Genomics
High-Throughput Nucleotide Sequencing
Life Sciences
Microbial Genetics and Genomics
Microsatellite Repeats - genetics
Molecular Sequence Annotation
Original Article
Plant Genetics and Genomics
Tinospora - genetics
Transcriptome - genetics
Citations: Items that this one cites
Items that cite this one
Online Access:Get full text
Tags: Add Tag
No Tags, Be the first to tag this record!
Description
Summary: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.
ISSN:1438-793X
1438-7948
DOI:10.1007/s10142-016-0508-x