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Pradhan S, Bandhiwal N, Shah N, et al. Global transcriptome analysis of developing chickpea (Cicer arietinum L.) seeds. Front Plant Sci. 2014;5:698doi: 10.3389/fpls.2014.00698.
Pradhan, S., Bandhiwal, N., Shah, N., Kant, C., Gaur, R., & Bhatia, S. (2014). Global transcriptome analysis of developing chickpea (Cicer arietinum L.) seeds. Frontiers in plant science, 5698. https://doi.org/10.3389/fpls.2014.00698
Pradhan, Seema, et al. "Global transcriptome analysis of developing chickpea (Cicer arietinum L.) seeds." Frontiers in plant science vol. 5 (2014): 698. doi: https://doi.org/10.3389/fpls.2014.00698
Pradhan S, Bandhiwal N, Shah N, Kant C, Gaur R, Bhatia S. Global transcriptome analysis of developing chickpea (Cicer arietinum L.) seeds. Front Plant Sci. 2014 Dec 16;5:698. doi: 10.3389/fpls.2014.00698. eCollection 2014. PMID: 25566273; PMCID: PMC4267183.
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Front Plant Sci. 2014 Dec 16;5:698. doi: 10.3389/fpls.2014.00698. eCollection 2014.

Global transcriptome analysis of developing chickpea (Cicer arietinum L.) seeds.

Frontiers in plant science

Seema Pradhan, Nitesh Bandhiwal, Niraj Shah, Chandra Kant, Rashmi Gaur, Sabhyata Bhatia

Affiliations

  1. National Institute of Plant Genome Research New Delhi, India.

PMID: 25566273 PMCID: PMC4267183 DOI: 10.3389/fpls.2014.00698

Abstract

Understanding developmental processes, especially in non-model crop plants, is extremely important in order to unravel unique mechanisms regulating development. Chickpea (C. arietinum L.) seeds are especially valued for their high carbohydrate and protein content. Therefore, in order to elucidate the mechanisms underlying seed development in chickpea, deep sequencing of transcriptomes from four developmental stages was undertaken. In this study, next generation sequencing platform was utilized to sequence the transcriptome of four distinct stages of seed development in chickpea. About 1.3 million reads were generated which were assembled into 51,099 unigenes by merging the de novo and reference assemblies. Functional annotation of the unigenes was carried out using the Uniprot, COG and KEGG databases. RPKM based digital expression analysis revealed specific gene activities at different stages of development which was validated using Real time PCR analysis. More than 90% of the unigenes were found to be expressed in at least one of the four seed tissues. DEGseq was used to determine differentially expressing genes which revealed that only 6.75% of the unigenes were differentially expressed at various stages. Homology based comparison revealed 17.5% of the unigenes to be putatively seed specific. Transcription factors were predicted based on HMM profiles built using TF sequences from five legume plants and analyzed for their differential expression during progression of seed development. Expression analysis of genes involved in biosynthesis of important secondary metabolites suggested that chickpea seeds can serve as a good source of antioxidants. Since transcriptomes are a valuable source of molecular markers like simple sequence repeats (SSRs), about 12,000 SSRs were mined in chickpea seed transcriptome and few of them were validated. In conclusion, this study will serve as a valuable resource for improved chickpea breeding.

Keywords: Transcriptome; annotation; assembly; chickpea; differential expression; next generation sequencing; seed

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