About Data

Chickpea Transcriptome Database (CTDB) release 2.0 provides sequence, annotation and comprehensive expression profiling data for the chickpea transcriptome. The current release of database provides transcriptome sequence from cultivated (Cicer arietinum desi (ICC4958) and kabuli (ICCV2)) and wild (Cicer reticulatum, PI489777) chickpea genotypes.

The transcriptomes have been sequenced using next generation technologies for long read (Roche 454) and short read (Illumina platform) from various tissue samples of chickpea at a very high depth. The statistics of sequence data and assembly generated is as below.

Types	Sequence data		Number of Transcripts	Nomenclature
Types	Roche 454	Illumina	Number of Transcripts	Nomenclature
Desi	1,931,224	106,660,317	34,760	CaTC00001-CaTC34760
Kabuli	1,643,836	108,429,800	43,389	Cak00001-Cak43389
Wild	969,132	--	37,265	CrTC00001-CrTC37265

                      For detail on sequence data generated, assembly strategy and number of transcripts, please read our publicatios:
      desi (Garg et al, 2011, Plant Physiol.), kabuli (Agarwal et al, 2012, PLOS ONE), wild (Jhanwar et al, 2012, Plant Biotechnol. J.)

       The putative function has been assigned to the transcripts based on their homology to known proteins in various databases (TAIR, Uniref90, Uniref100, NR, PFAM and SMART etc.). GOSlim terms have been assigned to the transcripts based on their similarity with Arabidopsis proteins. Transcription factor encloding transcripts were identified using hidden Markov model profiles search using HMMER.

       Based on the transcriptome assemblies generated above, several genic functional molecular markers (microsatellites and single nucleotide polymorphisms) were identified among the different chickpea genotypes. The strategy for their identification has been reported in our previous articles (Agarwal et al, 2012, PLOS ONE; Jhanwar et al, 2012, Plant Biotechnol. J.).

       Two types of gene expression data are available in this database. One dataset provide expression information in the major tissue samples, including shoot, root, mature leaf, flower bud and young pod based on Roche 454 sequence data as reported in (Garg et al, 2011, Plant Physiol.). Other dataset (GEA: flower development) provide comprehensive gene expression information for the vegetative tissues (germinating seedling, young leaf and shoot apical meristem) and eight stages of flower development [(flower bud (4 mm; FB1), flower bud (6 mm; FB2), flower bud (8 mm; FB3), flower bud (8-10 mm; FB4), flower (unopened; FL1), flower (opened; FL2), flower (mature; FL3) and flower (drooped; FL4))] as reported (Singh et al, 2013, Plant Biotechnol. J.).

       We have also integrated a tool for Comparative genomic analysis with other legumes and Arabidopsis, which include BLAST search, ortholog search and gene expression search of orthologs in major tissues.

       We plan to integrate more transcriptome data on other chickpea genotypes and gene expression data in future as and when it is ready.