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

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Title Global transcriptome analysis of developing chickpea (Cicer arietinum L.) seeds
 
Creator Pradhan, Seema
Bandhiwal, Nitesh
Shah, Niraj
Kant, Chandra
Gaur, Rashmi
Bhatia, Sabhyata
 
Subject Transcriptome
Chickpea
seed
assembly
next generation sequencing
annotation
differential expression
 
Description Accepted date: 24 November 2014
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.
This work was funded by the Department of Biotechnology,
Government of India, under the Next Generation Challenge
Programme on Chickpea Genomics (grant number
BT/PR12919/AGR/02/676/2009). SP acknowledges the award of
research fellowship from the Department of Biotechnology. CK
acknowledges the award of research fellowship from the Council
of Scientific and Industrial Reasearch. Authors acknowledge
Kamlesh Sahu for his help.
 
Date 2015-12-22T06:34:01Z
2015-12-22T06:34:01Z
2014
 
Type Article
 
Identifier Front. Plant Sc., 5: 698
1664-462X
http://172.16.0.77:8080/jspui/handle/123456789/441
http://journal.frontiersin.org/article/10.3389/fpls.2014.00698/abstract
10.3389/fpls.2014.00698
 
Language en_US
 
Publisher Frontiers Media S.A.