High throughput sequencing of small RNA component of leaves and inflorescence revealed conserved and novel miRNAs as well as phasiRNA loci in chickpea

Srivastava, S and Zheng, Y and Kudapa, H and Jagadeeswaran, G and Hivrale, V and Varshney, R K and Sunkar, R (2015) High throughput sequencing of small RNA component of leaves and inflorescence revealed conserved and novel miRNAs as well as phasiRNA loci in chickpea. Plant Science, 235. pp. 46-57. ISSN 0168-9452

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Abstract

Among legumes, chickpea (Cicer arietinum L.) is the second most important crop after soybean. MicroRNAs (miRNAs) play important roles by regulating target gene expression important for plant development and tolerance to stress conditions. Additionally, recently discovered phased siRNAs (phasiRNAs), a new class of small RNAs, are abundantly produced in legumes. Nevertheless, little is known about these regulatory molecules in chickpea. The small RNA population was sequenced from leaves and flowers of chickpea to identify conserved and novel miRNAs as well as phasiRNAs/phasiRNA loci. Bioinformatics analysis revealed 157 miRNA loci for the 96 highly conserved and known miRNA homologs belonging to 38 miRNA families in chickpea. Furthermore, 20 novel miRNAs belonging to 17 miRNA families were identified. Sequence analysis revealed approximately 60 phasiRNA loci. Potential target genes likely to be regulated by these miRNAs were predicted and some were confirmed by modified 5′ RACE assay. Predicted targets are mostly transcription factors that might be important for developmental processes, and others include superoxide dismutases, plantacyanin, laccases and F-box proteins that could participate in stress responses and protein degradation. Overall, this study provides an inventory of miRNA–target gene interactions for chickpea, useful for the comparative analysis of small RNAs among legumes.

Item Type:	Article
Divisions:	RP-Grain Legumes
CRP:	CGIAR Research Program on Grain Legumes
Uncontrolled Keywords:	Chickpea, MicroRNAs, PhasiRNAs, Posttranscriptional gene regulation
Subjects:	Mandate crops > Chickpea
Depositing User:	Mr B K Murthy
Date Deposited:	22 Jul 2015 05:26
Last Modified:	21 Oct 2016 06:41
URI:	http://oar.icrisat.org/id/eprint/8669
Official URL:	http://dx.doi.org/10.1016/j.plantsci.2015.03.002
Projects:	UNSPECIFIED
Funders:	UNSPECIFIED
Acknowledgement:	UNSPECIFIED
Links:	Google Scholar

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