title: High throughput sequencing of small RNA component of leaves and inflorescence revealed conserved and novel miRNAs as well as phasiRNA loci in chickpea.
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.
authors.affiliation: Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK 74078 USA.
authors.forename: Sangeeta
authors.initials: S
authors.lastname: Srivastava
authors.affiliation: Faculty of Life Science and Technology, Kunming University of Science and Technology, 727, South Jingming Road, Kunming, Yunnan 650500, China.
authors.forename: Yun
authors.initials: Y
authors.lastname: Zheng
authors.affiliation: International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad 502324, India.
authors.forename: Himabindu
authors.initials: H
authors.lastname: Kudapa
authors.affiliation: Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK 74078 USA.
authors.forename: Guru
authors.initials: G
authors.lastname: Jagadeeswaran
authors.affiliation: Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK 74078 USA.
authors.forename: Vandana
authors.initials: V
authors.lastname: Hivrale
authors.affiliation: International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad 502324, India; School of Plant Biology and Institute of Agriculture, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia. Electronic address: R.K.Varshney@CGIAR.ORG.
authors.forename: Rajeev K
authors.initials: RK
authors.lastname: Varshney
authors.affiliation: Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK 74078 USA. Electronic address: ramanjulu.sunkar@okstate.edu.
authors.forename: Ramanjulu
authors.initials: R
authors.lastname: Sunkar
mesh_terms: D001483:Base Sequence; D029863:Cicer / Q000235:genetics*; D019295:Computational Biology; D017124:Conserved Sequence; D044783:F-Box Proteins / Q000235:genetics; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods; D056626:Inflorescence; D035683:MicroRNAs; D008969:Molecular Sequence Data; D010088:Oxidoreductases / Q000235:genetics; D018515:Plant Leaves; D010940:Plant Proteins / Q000235:genetics; D018749:RNA, Plant; D034741:RNA, Small Interfering; D013312:Stress, Physiological / Q000235:genetics; D014157:Transcription Factors / Q000235:genetics
chemical_list: D044783:F-Box Proteins; D035683:MicroRNAs; D010940:Plant Proteins; D018749:RNA, Plant; D034741:RNA, Small Interfering; D014157:Transcription Factors; D010088:Oxidoreductases
keywords: Chickpea; MicroRNAs; PhasiRNAs; Posttranscriptional gene regulation