LegumeIP V3: From Models to Crops - An Integrative Gene Discovery Platform for Translational Genomics in Legumes

  • [C. arietinum (transcript)]
  • Detail of Experiment mapped on Cicer arietinum ICC 4958 CaV2


Nameglobal view of transcriptome dynamics during salinity stress in different chickpea genotypes
DescriptionIn this study, we aim to present a global view of transcriptome dynamics during salinity stress in different chickpea genotypes. We generated about 600 million high-quality reads from 16 libraries (control and stress samples for two chickpea genotypes for salinity stress at two developmental stages) using Illumina high-throughput sequencing platform. We mapped the reads to the kabuli chickpea genome for estimation of their transcript abundance in different tissue samples. The transcriptome dynamics was studied by differential gene expression analyses between stress treatment and control sample for each genotype. Overall design: We collected roots of chickpea genotypes from vegetative and reproductive stage plants subjected to control (water) and salinity (irrigated with 80 mM NaCl solution) stress. Total RNA isolated from these tissue samples was subjected to Illumina sequencing. The sequenced data was further filtered using NGS QC Toolkit to obtain high-quality reads. The filtered reads were mapped to annotated chickpea genome using TopHat and fragments per exon kilobase per million (FPKM) was calculated using Cufflinks software for each gene in all the sample to measure their gene expression. Differential expression analysis was performed using Cuffdiff software. The differentially expressed genes during various stress conditions were identified.
ContactNational Institute of Plant Genome Research (NIPGR)
SpeciesCicer arietinum
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Mapped Genomes CaV2    
Expression Analysis Expression Profile /  Differential Expression /  Co-expression


Name Genotype Mutation Stage Tissue Treatment Level Time Samples Xref Download alignments
reproductive_ICCV2_80mMNaCl ICCV2 Reproductive plants 80 mM NaCl solution
  • reproductive_ICCV2_80mMNaCl_1
  • reproductive_ICCV2_80mMNaCl_2
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reproductive_ICCV2_water ICCV2 Reproductive plants water
  • reproductive_ICCV2_water_1
  • reproductive_ICCV2_water_2
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reproductive_JG62_80mMNaCl JG62 Reproductive plants 80 mM NaCl solution
  • reproductive_JG62_80mMNaCl_1
  • reproductive_JG62_80mMNaCl_2
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reproductive_JG62_water JG62 Reproductive plants water
  • reproductive_JG62_water_1
  • reproductive_JG62_water_2
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vegetative_ICCV2_80mMNaCl ICCV2 Vegetative plants 80 mM NaCl solution
  • vegetative_ICCV2_80mMNaCl_1
  • vegetative_ICCV2_80mMNaCl_2
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vegetative_ICCV2_water ICCV2 Vegetative plants water
  • vegetative_ICCV2_water_1
  • vegetative_ICCV2_water_2
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vegetative_JG62_80mMNaCl JG62 Vegetative plants 80 mM NaCl solution
  • vegetative_JG62_80mMNaCl_1
  • vegetative_JG62_80mMNaCl_2
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vegetative_JG62_water JG62 Vegetative plants water
  • vegetative_JG62_water_1
  • vegetative_JG62_water_2
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