Indian Journal of Plant Physiology

, Volume 23, Issue 1, pp 179–191 | Cite as

Computational identification and functional annotation of microRNAs and their targets in three species of kiwifruit (Actinidia spp.)

  • Karam Jayanandi Devi
  • Prasanta Saha
  • Sreejita Chakraborty
  • Ravi Rajwanshi
Short Communication


MicroRNAs (miRNAs) are a class of small non-coding RNA of approximately 22 nucleotides in length derived from one arm of hairpin stem-loop secondary precursors, that regulates gene expression at the transcriptional or post-transcriptional level either through cleavage or translation inhibition of the target mRNA. In the present study, an attempt was made to identify conserved miRNAs in Actinidia delicosa, Actinidia chinensis, and Actinidia eriantha expressed sequence tags (ESTs) through computational approach. To identify the novel miRNAs, 57757 ESTs of A. delicosa, 47384 ESTs of A. chinensis and 12650 EST sequences of A. eriantha were analysed. A total of 16 miRNAs from A. chinensis, 3 from A. eriantha and 1 from A. delicosa were predicted with their pre-miRNAs forming a stem-loop structure. psRNATarget server identified a total of 75 target genes including transcription factors, kinases, binding proteins, transporters that were involved in flower development, sucrose biosynthesis, stress responses. The results from the present study will shed more light on understanding the functions of miRNA in regulating the growth and development of Actinidia spp.


miRNA ESTs kiwifruit mfold psRNAtarget 



KJD, PS, SC, and RR acknowledge Assam University, Silchar, Assam, India for providing infrastructural facility to carry out the present study. KJD acknowledges University Grants Commission (India) for non-NET fellowship. RR acknowledges funding from Department of Science & Technology (DST), Science & Engineering Research Board (SERB), Government of India vide grant no. EEQ/2016/000501.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflicts of interest.

Supplementary material

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  1. Abdel-Ghany, S. E., & Pilon, M. (2008). MicroRNA mediated systemic down-regulation of copper protein expression in response to low copper availability in Arabidopsis. The Journal of Biology Chemistry, 283, 15932–15945.CrossRefGoogle Scholar
  2. Altschul, S. F., Gish, W., Miller, E. W., & Lipman, D. J. (1990). Basic local alignment search tool. Journal of Molecular Biology, 215, 403–410.CrossRefPubMedGoogle Scholar
  3. Aukerman, M. J., & Sakai, H. (2003). Regulation of flowering time and floral organ identity by a microRNA and its APETALA2-like target genes. The Plant Cell, 15, 2730–2741.CrossRefPubMedPubMedCentralGoogle Scholar
  4. Avsar, B., & Aliabadi, E. D. (2015). Putative microRNA analysis of the kiwifruit Actinidia chinensis through genomic data. International Journal of Life Sciences, Biotechnology and Pharmaceutical Research, 4(2), 96–99.Google Scholar
  5. Bartel, D. (2004). MicroRNAs: Genomics, biogenesis, mechanism and function. Cell, 116, 281–297.CrossRefPubMedGoogle Scholar
  6. Bologna, N. G., Mateos, J. L., Bresso, E. G., & Palatnik, J. F. (2009). A loop-to-base processing mechanism underlies the biogenesis of plant microRNAs miR319 and miR159. The EMBO Journal, 28, 3646–3656.CrossRefPubMedPubMedCentralGoogle Scholar
  7. Bologna, N. G., Schapire, A. L., Zhai, J., Chorostecki, U., Boisbouvier, J., Meyers, B. C., et al. (2013). Multiple RNA recognition patterns during microRNA biogenesis in plants. Genome Research, 23, 1675–1689.CrossRefPubMedPubMedCentralGoogle Scholar
  8. Bonnet, E., Wuyts, J., Rouze, P., & Van de Peer, Y. (2004). Evidence that microRNA precursors, unlike other non-coding RNAs, have lower folding free energies than random sequences. Bioinformatics, 20(17), 2911–2917.CrossRefPubMedGoogle Scholar
  9. Borazai, M. Y. K., Baloch, I. A., & Din, M. (2011). Computational identification of microRNAs and their targets in two species of evergreen spruce tree (Picea). World Academy of Science, Engineering and Technology, 5, 3.Google Scholar
  10. Chakraborty, S., Devi, K.J., Deb, B., Rajwanshi, R. (2016). Identification and characterization of novel microRNAs and their targets in Cucumis melo L.: An insilico approach. Focus on Science, 2(1), 1–11.CrossRefGoogle Scholar
  11. Chaves, S. S., Fernandes-Brum, C. N., Silva, G. F. F., Ferrara-Barbosa, B. C., Paiva, L. V., Nogueira, F. T. S., et al. (2015). New Insights on Coffea miRNAs: Features and Evolutionary Conservation. Applied Biochemistry and Biotechnology, 177, 879–908.CrossRefPubMedGoogle Scholar
  12. Dai, X., & Zhao, P. X. (2011). psRNATarget: A plant small RNA target analysis server. Nucleic Acids Research, 39, W155–W159.CrossRefPubMedPubMedCentralGoogle Scholar
  13. Das, A., Chaudhury, S., Kalita, M. C., & Mondal, T. K. (2015). In silico identification, characterization and expression analysis of miRNAs in Cannabis sativa L. Plant Gene, 2, 17–24.CrossRefGoogle Scholar
  14. Das, A., Das, P., Kalita, M. C., & Mondal, T. K. (2016). Computational identification, target prediction, and validation of conserved miRNAs in insulin plant (Costus pictus D. Don). Applied Biochemistry and Biotechnology, 178, 513–526.CrossRefPubMedGoogle Scholar
  15. Devi, K. J., Chakraborty, S., Deb, B., & Rajwanshi, R. (2016). Computational identification and functional annotation of microRNAs and their targets from expressed sequence tags (ESTs) and genome survey sequences (GSSs) of coffee (Coffea arabica L.). Plant Gene, 6, 30–42.CrossRefGoogle Scholar
  16. Fuliang, X., Taylor, P. F., & Zhang, B. (2010). Identification and characterization of microRNAs and their targets in the bioenergy plant switchgrass (Panicum virgatum). Planta, 232, 417–434.CrossRefGoogle Scholar
  17. Huang, H. W., & Ferguson, A. R. (2007). Genetic resources of kiwifruit: Domestication and breeding. Horticultural Reviews, 33, 1–121.Google Scholar
  18. Huber, S. C., & Huber, J. L. (1996). Role and regulation of sucrose-phosphate synthase in higher plants. Annual Review on Plant Physiology and Plant Molecular Biology, 47, 431–444.CrossRefGoogle Scholar
  19. Huijser, P., & Schmid, P. (2011). The control of developmental phase transitions in plants. Development, 138, 4117–4129.CrossRefPubMedGoogle Scholar
  20. Iwasawa, H., Morita, E., Yui, S., & Yamazaki, M. (2011). Antioxidant effects of kiwi fruit in vitro and in vivo. Biological and Pharmaceutical Bulletin, 34(1), 128–134.CrossRefPubMedGoogle Scholar
  21. Kim, S., Soltis, P. S., Wall, K., & Soltis, D. E. (2006). Phylogeney and domain evolution in the APETALA2-like gene family. Molecular Biology and Evolution, 23, 107–120.CrossRefPubMedGoogle Scholar
  22. Kimura, M. (1980). A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotides sequences. Journal of Molecular Evolution, 16(2), 111–120.CrossRefPubMedGoogle Scholar
  23. Langenkamper, G., McHale, R., Gardner, R. C., & MacRae, E. (1998). Sucrose-phosphate synthase steady-state mRNA increases in ripening kiwifruit. Plant Molecular Biology, 36(6), 857–869.CrossRefPubMedGoogle Scholar
  24. Ma, C., Burd, S., & Lers, A. (2015). miR408 is involved in abiotic stress responses in Arabidopsis. The Plant Journal, 84, 169–187.CrossRefPubMedGoogle Scholar
  25. Pandey, B., Gupta, O. P., Pandey, D. M., Sharma, I., & Sharma, P. (2013). Identification of new stress-induced microRNAs and their targets in wheat using computational approach. Plant Signaling & Behaviour, 8(5), e23932.CrossRefGoogle Scholar
  26. Park, W., Li, J., Song, R., Messing, J., & Chen, X. (2002). CARPEL FACTORY, a dicer homolog, and Hen1 a novel protein, act in microRNA metabolism in Arabidiopsis thaliana. Current Biology, 12, 1484–1495.CrossRefPubMedPubMedCentralGoogle Scholar
  27. Rajwanshi, R., Chakraborty, S., Jayanandi, K., & Deb, B. (2014). Orthologous plant miRNAs: Microregulators with great potential for improving stress tolerance in plants. Theoretical and Applied Genetics, 127, 2525–2543.CrossRefPubMedGoogle Scholar
  28. Reinhart, B. J., Weinstein, E. G., Rhoades, M. W., Bartel, B., & Bartel, D. P. (2002). MicroRNAs in plants. Genes & Development, 16(13), 1616–1626.CrossRefGoogle Scholar
  29. Rubio-Somoza, I.,  & Weigel, D. (2011). MicroRNA networks and developmental plasticity in plants. Trends in Plant Science, 16(5), 258–264.CrossRefPubMedGoogle Scholar
  30. Sunkar, R., & Jagadeeshwaran, G. (2008). In silico identification of conserved microRNAs in large number of diverse plant species. BMC Plant Biology, 8, 37.CrossRefPubMedPubMedCentralGoogle Scholar
  31. Tamura, K., Stetcher, G., Peterson, D., Flilipski, A., & Kumar, S. (2013). MEGA6: Molecular evolutionary genetics analysis version 6.0. Molecular Biology and Evolution, 30(12), 2725–2729.CrossRefPubMedPubMedCentralGoogle Scholar
  32. Tavarini, S., Degl’Innocenti, E., Remorini, D., Massai, R., & Guidi, L. (2008). Antioxidant capacity, ascorbic acid, total phenols and carotenoids changes during harvest and after storage of Hayward kiwifruit. Food Chemistry, 107(1), 282–288.CrossRefGoogle Scholar
  33. Testolin, R., & Ferguson, A. R. (2009). Kiwifruit (Actinidia spp.) production and marketing in Italy. New Zealand Journal of Crop Horticultural Science, 37(1), 1–32.CrossRefGoogle Scholar
  34. Varkonyi-Gasic, E., Lough, R. H., Moss, S. M. A., Wu, R., & Hellens, R. P. (2012). Kiwifruit floral gene APETALA2 is alternatively spliced and accumulates in aberrant indeterminate flowers in the absence of miR172. Plant Molecular Biology, 78, 417–429.CrossRefPubMedGoogle Scholar
  35. Voinnet, O. (2009). Origin, biogenesis, and activity of plant MicroRNAs. Cell, 136, 669–687.CrossRefPubMedGoogle Scholar
  36. Wan, L. C., Zhang, H., Lu, S., Zhang, L., Qiu, Z., Zhao, Y., et al. (2012). Trancriptome-wide identification and characterization of miRNAs from Pinus densata. BMC Genomics, 13, 132.CrossRefPubMedPubMedCentralGoogle Scholar
  37. Wang, X., Zhang, J., Li, F., Gu, J., He, T., Zhang, X., et al. (2005). MicroRNA identification based on sequence and structure alignment. Bioinformatics, 21, 3610–3614.CrossRefPubMedGoogle Scholar
  38. Wu, B., Wang, M., Ma, Y., Yuan, L., & Lu, S. (2012). High-throughput sequencing and characterization of the small RNA transcriptome reveal features of novel and conserved microRNAs in Panax ginseng. PLoS ONE, 7, e44385.CrossRefPubMedPubMedCentralGoogle Scholar
  39. Xie, F., Frazier, T. P., & Zhang, B. (2011). Identification, characterization and expression analysis of MicroRNAs and their targets in the potato (Solanum tuberosum). Gene, 473, 8–22.CrossRefPubMedGoogle Scholar
  40. Xie, F. L., Huang, S. Q., Guo, K., Xiang, A. L., Zhu, Y. Y., Nie, L., et al. (2007). Computational identification of novel microRNAs and targets in Brassica napus. FEBS Letter, 581, 1464–1474.CrossRefGoogle Scholar
  41. Xie, K., Shen, J., Hou, X., Yao, J., Li, X., Xiao, J., et al. (2012). Gradual increase of miR156 regulates temporal expression changes of numerous genes during leaf development in rice. Plant Physiology, 158(3), 1382–1394.CrossRefPubMedPubMedCentralGoogle Scholar
  42. Xu, M. Y., Dong, Y., Zhang, Q. X., Zhang, L., Luo, Y. Z., Sun, J., et al. (2012). Identification of miRNAs and their targets from Brassica napus by high-throughput sequencing and degradome analysis. BMC Genomics, 13, 421.CrossRefPubMedPubMedCentralGoogle Scholar
  43. Zhai, J., Jeong, D. H., Paoli, E. D., Park, S., Rosen, B. D., Li, Y., et al. (2011). MicroRNAs as master regulators of the plant NB-LRR defense gene family via the production of phased, trans-acting siRNAs. Genes & Development, 25, 2540–2553.CrossRefGoogle Scholar
  44. Zhai, L., Xu, L., Wang, Y., Zhu, X., Feng, H., Li, C., et al. (2016). Transcriptional identification and characterization of differentially expressed genes associated with embryogenesis in radish (Raphanus sativus L.). Science Reporter, 6, 21652.CrossRefGoogle Scholar
  45. Zhang, B.H., Pan, X.P., Wang, Q.L., Cobb, G.P. & Anderson, T.A., (2005). Identification and characterization of new plant microRNAs using EST analysis. Cell Research, 15(5), 336–360.CrossRefPubMedGoogle Scholar
  46. Zhang, L., Chia, J.-M., Kumari, S., Stein, J. C., Liu, Z., Narechania, A., et al. (2009a). A Genome-Wide Characterization of MicroRNA Genes in Maize. PLoS Genetics, 5, e1000716.CrossRefPubMedPubMedCentralGoogle Scholar
  47. Zhang, W., Luo, Y., Gong, X., Zeng, W., & Li, S. (2009b). Computational identification of 48 potato microRNAs and their targets. Computational Biology and Chemistry, 33, 84–93.CrossRefPubMedGoogle Scholar
  48. Zhang, B. H., Pan, X., Cannon, C. H., Cobb, G. P., & Anderson, T. A. (2006a). Conservation and divergence of plant microRNA genes. The Plant Journal, 46(2), 243–259.CrossRefPubMedGoogle Scholar
  49. Zhang, B. H., Pan, X. P., Wang, Q. L., Cobb, G. P., & Anderson, T. A. (2006b). Computational identification of microRNAs and their targets. Gene, 397, 26–37.CrossRefGoogle Scholar
  50. Zhang, B., Wang, Q., & Pan, X. (2007). MicroRNAs and their regulatory roles in animals and plants. Journal of Cellular Physiology, 210(2), 279–289.CrossRefPubMedGoogle Scholar
  51. Zhang, N., Yang, J., Wang, Z., Wen, Y., He, W., Liu, B., et al. (2014). Identification of novel and conserved microRNAs related to drought stress in potato by deep sequencing. PLoS ONE, 9(4), e95489.CrossRefPubMedPubMedCentralGoogle Scholar
  52. Zhu, Q. H., Upadhyaya, N. M., Gubler, F., & Helliwell, C. A. (2009). Over-expression of miR172 causes loss of spikelet determinacy and floral organ abnormalities in rice (Oryza sativa). BMC Plant Biology, 17(9), 149.CrossRefGoogle Scholar
  53. Zuker, M. (2003). Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Research, 31, 3406–3415.CrossRefPubMedPubMedCentralGoogle Scholar

Copyright information

© Indian Society for Plant Physiology 2018

Authors and Affiliations

  1. 1.Department of BiotechnologyAssam UniversitySilcharIndia

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