CTDB: An Integrated Chickpea Transcriptome Database for Functional and Applied Genomics

PloS One
Mohit VermaMukesh Jain

Abstract

Chickpea is an important grain legume used as a rich source of protein in human diet. The narrow genetic diversity and limited availability of genomic resources are the major constraints in implementing breeding strategies and biotechnological interventions for genetic enhancement of chickpea. We developed an integrated Chickpea Transcriptome Database (CTDB), which provides the comprehensive web interface for visualization and easy retrieval of transcriptome data in chickpea. The database features many tools for similarity search, functional annotation (putative function, PFAM domain and gene ontology) search and comparative gene expression analysis. The current release of CTDB (v2.0) hosts transcriptome datasets with high quality functional annotation from cultivated (desi and kabuli types) and wild chickpea. A catalog of transcription factor families and their expression profiles in chickpea are available in the database. The gene expression data have been integrated to study the expression profiles of chickpea transcripts in major tissues/organs and various stages of flower development. The utilities, such as similarity search, ortholog identification and comparative gene expression have also been implemented in the database...Continue Reading

References

Dec 24, 2009·BMC Bioinformatics·Ji HeMichael K Udvardi
Apr 23, 2010·The Plant Journal : for Cell and Molecular Biology·Marc LibaultGary Stacey
Aug 7, 2010·BMC Plant Biology·Andrew J SeverinRandy C Shoemaker
Jan 11, 2011·DNA Research : an International Journal for Rapid Publication of Reports on Genes and Genomes·Rohini GargMukesh Jain
Nov 24, 2011·Nucleic Acids Research·Jun LiPatrick Xuechun Zhao
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Jun 8, 2012·Plant Biotechnology Journal·Shalu JhanwarMukesh Jain
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Jan 29, 2013·Nature Biotechnology·Rajeev K VarshneyDouglas R Cook
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Jun 24, 2014·BMC Bioinformatics·Dadakhalandar DoddamaniRajeev K Varshney

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Citations

Feb 10, 2018·Plant, Cell & Environment·Crystal SweetmanDavid A Day
Jul 28, 2018·Journal of Biomolecular Structure & Dynamics·Ameya D BendreSureshkumar Ramasamy
Aug 30, 2019·Molecular Biology Reports·Jagadale Mahesh VasantraoBidyut K Sarmah
Jan 21, 2019·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Runfeng WangRavindra N Chibbar

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Datasets Mentioned

BETA
JN412096.1

Methods Mentioned

BETA
PCR
genotyping

Software Mentioned

GEA Flower
SoySeq
Ortholog Search
BLAST
SoyPlex
LjGEA
Centos
Perl
MySQL
MtGEA

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