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Chickpea Transcriptome Atlas II - Abiotic Stress

ABSTRACT: In this study, we aim to present a global view of transcriptome dynamics during various abiotic stresses in chickpea. We generated about 252 million high-quality reads from eight libraries (control, desiccation, salinity and cold stress samples for roots and shoots) using Illumina high-throughput sequencing GAII platform. We mapped the reads to the desi 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. We collected different tissue samples (root and shoot tissues of 10-day-old seedlings subjected to control (kept in water), desiccation (transferred on folds of tissue paper), salinity (transferred to beaker containing 150 mM NaCl solution) and cold (kept in water at 4 M-BM-1 1M-BM-0C) stress for 5 h. 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 abiotic stress conditions were identified.

ORGANISM(S): Cicer arietinum

SUBMITTER: Mukesh Jain

PROVIDER: E-GEOD-53711 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Chickpea Transcriptome Atlas II - Abiotic Stress

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Project description:In this study, we aim to present a global view of transcriptome dynamics during flower development in chickpea. We generated around 234 million high-quality reads for eight flower development stages (ranging from 16 to 40 million reads for each stage) and 91 million high-quality reads from three vegetative tissues using Illumina high-throughput sequencing GAII platform. Because of non-availability of reference genome sequence, we mapped the reads to chickpea transcriptome comprised of 34,760 transcripts for estimation of their transcriptional activity in different tissue samples. The transcriptome dynamics was studied by comparison of gene expression during flower development stages with vegetative tissues. We collected different tissue samples used in this study and total RNA isolated 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 34760 chickpea transcripts and reads per kilobase per million (RPKM) was calculated for each gene in all the sample to measure their gene expression. Differential expression analysis was performed using DESeq software. The genes preferentially expression during various stages of flower development as compared to vegetative stages and those with speciifc expression were identified.

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