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

S. Srivastava; Y. Zheng; H. Kudapa; G. Jagadeeswaran; V. Hivrale; R.K. Varshney; R. Sunkar

doi:10.1016/j.plantsci.2015.03.002

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

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

S. Srivastava, Y. Zheng, H. Kudapa, G. Jagadeeswaran, V. Hivrale, R.K. Varshney and R. Sunkar

Plant Science, Vol.235, pp.46-57

2015

DOI: https://doi.org/10.1016/j.plantsci.2015.03.002

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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.

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Title: High throughput sequencing of small RNA component of leaves and inflorescence revealed conserved and novel miRNAs as well as phasiRNA loci in chickpea
Authors/Creators: S. Srivastava (Author/Creator) - Oklahoma State University
Y. Zheng (Author/Creator) - Kunming University of Science and Technology
H. Kudapa (Author/Creator) - International Crops Research Institute for the Semi-Arid Tropics
G. Jagadeeswaran (Author/Creator) - Oklahoma State University
V. Hivrale (Author/Creator) - Oklahoma State University
R.K. Varshney (Author/Creator) - International Crops Research Institute for the Semi-Arid Tropics
R. Sunkar (Author/Creator) - Oklahoma State University
Publication Details: Plant Science, Vol.235, pp.46-57
Publisher: Elsevier
Identifiers: 991005542396007891
Copyright: © 2015 The Authors.
Murdoch Affiliation: Murdoch University
Language: English
Resource Type: Journal article

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Collaboration types: Domestic collaboration; International collaboration
Citation topics: 3 Agriculture, Environment & Ecology; 3.4 Crop Science; 3.4.159 Arabidopsis
Web Of Science research areas: Biochemistry & Molecular Biology; Plant Sciences
ESI research areas: Plant & Animal Science