Research Article | Volume: 5, Issue: 2, March-April, 2017

Computational identification of miRNAs and their targets from Niger (Guizotia abyssinica)

K. Y. Prathiba S. Usha B. Suchithra M. N. Jyothi V. R. Devaraj R. Nageshbabu   

Open Access   

Published:  Mar 20, 2017

DOI: 10.7324/JABB.2017.50208

MicroRNAs play a pivotal role in regulating a broad range of biological processes, acting by cleaving mRNAs or by translational repression. A group of plant microRNAs are evolutionarily conserved; however, others are expressed in a species-specific manner. In this study we used homology-based analysis with available expressed sequence tag (EST) of Niger (Guizotia abyssinica) to predict conserved miRNAs. Two potent miRNAs targeting 49 genes were identified. The newly identified miRNAs belongs to miR2592 and miR396 family. Targets recognized were F-box proteins, leucine zipper, DEAD box RNA helicase, disease resistant proteins. Gene annotations revealed miRNAs were involved in growth and development and Encyclopaedia of Genes and Genomes (KEGG) pathway analyses showed miRNAs were involved in metabolic pathways.

Keyword:     EST GO analysis miRNA Transcription factors.


Prathiba KY, Usha S, Suchithra B, Jyothi MN, Devaraj VR, Nagesh babu R. Computational identification of miRNAs and their targets from Niger (Guizotia abyssinica). J App Biol Biotech. 2017; 5 (02): 053-058. DOI: 10.7324/JABB.2017.50208

Copyright: Author(s). This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial-ShareAlike license.

HTML Full Text

1. Chen X. Small RNAs and their roles in plant development. Annual review of cell and developmental biology 2009; 25:21-44.

2. Li YF, Zheng Y, Addo-Quaye C, Zhang L, Saini A, Jagadeeswaran G, et al. Transcriptome-wide identification of microRNA targets in rice. The Plant journal: for cell and molecular biology 2010; 62(5):742-59.

3. Martinez G, Forment J, Llave C, Pallas V, Gomez G. High-throughput sequencing, characterization and detection of new and conserved cucumber miRNAs. PloS one 2011; 6(5):e19523.

4. Carrington JC, Ambros V. Role of micro RNAs in plant and animal development. Science 2003; 301:336-338.

5. Sunkar R, Li YF, Jagadeeswaran G. Functions of micro RNAs in plant stress responses. Trends in Plant Science 2012; 17(4):196-203.

6. Zhang B, Pan X, Anderson TA. Identification of 188 conserved maize microRNAs and their targets. FEBS letters 2006; 580(15):3753-62.

7. Allen E, Xie Z, Gustafson AM, Sung GH, Spatafora JW, Carrington JC. Evolution of microRNA genes by inverted duplication of target gene sequences in Arabidopsis thaliana. Nature genetics 2004; 36(12):1282-90.

8. Fahlgren N, Howell MD, Kasschau KD, Chapman EJ, Sullivan CM, Cumbie JS, et al. High-throughput sequencing of Arabidopsis microRNAs: evidence for frequent birth and death of MIRNA genes. PloS one 2007; 2(2):e219.

9. Yong Huang, Quan Zou, Shun Ming Tang, Li Gang Wang, Xing JiaShen. Computational identification and characteristics of novel microRNAs from the silkworm (Bombyx mori L.). Molecular Biology Reports 2010; 37(7): 3171-3176.

10. Xi Hong, Ling Ping Zhao, Quan Zou, Zhan Bin Wang. Identification of MicroRNA Genes and their mRNA Targets in Festuca arundinacea. Applied Biochemistry and Biotechnology 2014; 172(8): 3875-3887.

11. Huang Y, Zou Q, Wang ZB. Computational identification of miRNA genes and their targets in mulberry. Russian Journal of Plant Physiology 2014; 61(4): 537-542.

12. LIU Yong-xin, CHANG Wei, HAN Ying-peng, ZOU Quan, GUO Mao-zu3 and LI Wen-bin. In silico Detection of Novel MicroRNAs Genes in Soybean Genome. Agricultural Sciences in China 2011; 10(9): 1336-1345

13. Usha S, Jyothi MN, Suchithra B, Rekha Dixit, Rai DV, Nagesh Babu R. Computational identification of micro RNAs and their targets from Finger millet (Eleusine coracana). Interdisciplinary Sciences Computational Life Sciences. 2015; doi: 10.1007/s12539-015-0130-y.

14. Huang X, Madan A. CAP3: A DNA sequence assembly program. Genome Res. 1999; 9:868-877

15. Zuker M. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res. 2003; 31:3406-3415.

16. Leyi Wei, Minghong Liao, Yue Gao, Rongrong Ji, Zengyou He, Quan Zou. Improved and Promising Identification of Human MicroRNAs by Incorporating a High-quality Negative Set. IEEE/ACM Transactions on Computational Biology and Bioinformatics 2013; [Epub ahead of print].

17. Xinbin Dai, Patrick X Zhao. psRNATarget: A Plant Small RNA Target Analysis Server. Nuc. Aci. Res. 2011; 39:W155-W159.

18. Ye J, Fang L, et al. Nucleic Acids Res. 2006; 34(Web service issue), 293-297.

19. Ambros V, Bartel B, Bartel DP. A uniform system for microRNA annotation. RNA 2003; 9:277-279.

20. Chi X, Yang Q, Chen X, Wang J et al. Identification and characterization of microRNAs from peanut (Arachis hypogaea L.) by high throughput sequencing. PLoS One 2011; 1 6: e27530.

21. Xu L, Wang Y, Xu Y, Wang L, Zhai L et al. Identification and characterization of novel and conserved microRNAs in radish (Raphanus sativus L.) using high-throughput sequencing. Plant Science 2013; 201-202: 108-114.

22. Han Y, Luan F, Zhu H, Shao Y, Chen A, Lu C, Luo Y, Zhu B. Computational identification of microRNAs and their targets in Wheat (Triticum aestivum L.). Science in China Series C-Life Sciences 2009; 52:1091-1100.

23. Ikeda Y, Kinoshita Y, Susaki D, Ikeda Y, Iwano M, Takayama S, Higashiyama T, Kakutani T, Kinoshita T. HMG domain containing SSRP1 is required for DNA demethylation and genomic imprinting in Arabidopsis. Dev Cell. 2011; 21(3):589-96.

24. Roy A, Dutta A, Roy D, Ganguly P, Ghosh R, Kar RK, Bhunia A, Mukhobadhyay J, Chaudhuri S. Deciphering the role of the AT-rich interaction domain and the HMG-box domain of ARID-HMG proteins of Arabidopsis thaliana. Plant Mol Biol. 2016; 92(3):371-88.

25. Stefanowicz K, Lannoo N, Zhao Y, Eggermont L, Van Hove J, Al Atalah B, Van Damme EJ. Glycan-binding F-box protein from Arabidopsis thaliana protects plants from Pseudomonas syringae infection. BMC Plant Biol. 2016; 16(1):213.

26. He Y, Wang C, Higgins JD, Yu J, Zong J, Lu P, Zhang D, Liang W. MEIOTIC F-BOX Is Essential for Male Meiotic DNA Double-Strand Break Repair in Rice. Plant Cell 2016; 28(8):1879-93.

27. Liu Y, Tabata D, Imai R. A Cold-Inducible DEAD-Box RNA Helicase from Arabidopsis thaliana Regulates Plant Growth and Development under Low Temperature. PLoS One 2016; 11(4):e0154040.

28. Martin GB, Bogdanove AJ, Sessa G. Understanding the functions of plant disease resistance proteins. Annu Rev Plant Biol. 2003; 54:23-61.

29. Djebbi S, Bouktila D, Makni H, Makni M, Mezghani-Khemakhem M. Identification and characterization of novel NBS-LRR resistance gene analogues from the pea. Genet Mol Res. 2015; 14(2):6419-28.

30. Lei X, Yao Q, Xu X, Liu Y. Isolation and characterization of NBS-LRR resistance gene analogues from mango. Biotechnol Biotechnol Equip. 2014; 28(3):417-424.

Article Metrics
71 Views 62 Downloads 133 Total



Related Search

By author names