NDLI: De novo transcriptome sequencing facilitates genomic resource generation in Tinospora cordifolia

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De novo transcriptome sequencing facilitates genomic resource generation in Tinospora cordifolia

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De novo transcriptome sequencing facilitates genomic resource generation in Tinospora cordifolia

Content Provider	Springer Nature Link
Author	Singh, Rakesh Kumar, Rajesh Mahato, Ajay Kumar Paliwal, Ritu Singh, Amit Kumar Kumar, Sundeep Marla, Soma S. Kumar, Ashok Singh, Nagendra K.
Copyright Year	2016
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.
Starting Page	581
Ending Page	591
Page Count	11
File Format	PDF
ISSN	1438793X
Journal	Functional & Integrative Genomics
Volume Number	16
Issue Number	5
e-ISSN	14387948
Language	English
Publisher	Springer Berlin Heidelberg
Publisher Date	2016-07-27
Publisher Place	Berlin, Heidelberg
Access Restriction	One Nation One Subscription (ONOS)
Subject Keyword	Tinospora Transcriptome Transcription factor Terpenes EST-SSR Cell Biology Plant Genetics & Genomics Microbial Genetics and Genomics Biochemistry Bioinformatics Animal Genetics and Genomics
Content Type	Text
Resource Type	Article
Subject	Genetics Medicine

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De novo transcriptome sequencing facilitates genomic resource generation in Tinospora cordifolia

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