Kompelli, S.K. and Kompelli, V.S.P. and Enjala, C. and Suravajhala, P. (2015) Genome-wide identification of miRNAs in pigeonpea (Cajanus cajan L.). Australian Journal of Crop Science, 9 (3). pp. 215-222.
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Abstract
MicroRNAs (miRNA) are endogenous small RNAs that play essential roles in plant growth, development and response to biotic and abiotic stress. With the availability of draft genome sequence of pigeonpea, understanding miRNA repertoire of several crops has begun to be facilitated. In the present study, we have attempted to find miRNA sequences in pigeonpea using genome-wide computational approaches. Further whole genome sequence (WGS) based comparative studies using homology and secondary structure analysis was done. A total of 142 potential conserved miRNAs belonging to 48 families were identified and considered for this study. The size of these 48 miRNA families ranged from one to ten members while the length of miRNAs ranged from 19 nt to 24 nt. Furthermore pigeonpea pre-miRNA sequences were identified which varied from 62 to 203 nt while these sequences were found to have high negative minimal folding free energy (MFE), adjusted MFE (AMFE) and MFE index (MFEI) which is in agreement with the published data from crop sequences. Furthermore, this criterion distinguishes miRNAs from other coding and non-coding RNAs. Among the miRNAs, Uracil was found to be dominant nucleotide base in the first position at the 5’ end of the mature miRNAs. A total of 423 potential miRNA targets were identified for newly identified pigeonpea miRNAs using psRNATarget tool. These target genes include a number of transcription factors that control plant growth and development, linked to metabolic enzymes involved in stress response. We believe these identified miRNA target genes would help us to know more about the important roles of miRNAs, suggesting that genome-wide computational analysis is a good alternative strategy for identifying new miRNAs and their targets.
| Item Type: | Article |
|---|---|
| Uncontrolled Keywords: | miRNAs, Target validation, Stress related genes, Plant growth. |
| Author Affiliation: | Bioclues.org, Kukatpally 500072, Hyderabad, India |
| Subjects: | Crop Improvement |
| Divisions: | Pigeonpea |
| Depositing User: | Mr B Krishnamurthy |
| Date Deposited: | 04 Sep 2015 10:19 |
| Last Modified: | 04 Sep 2015 10:19 |
| URI: | http://eprints.icrisat.ac.in/id/eprint/13813 |
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