Journal of Ginseng Research

The Korean Society of Ginseng (고려인삼학회)
권호 표지
DOI QR코드

DOI QR Code

Insilico profiling of microRNAs in Korean ginseng (Panax ginseng Meyer)

  • Mathiyalagan, Ramya (Korean Ginseng Center and Ginseng Resource Bank, Kyung Hee University) ;
  • Subramaniyam, Sathiyamoorthy (Korean Ginseng Center and Ginseng Resource Bank, Kyung Hee University) ;
  • Natarajan, Sathishkumar (Korean Ginseng Center and Ginseng Resource Bank, Kyung Hee University) ;
  • Kim, Yeon Ju (Korean Ginseng Center and Ginseng Resource Bank, Kyung Hee University) ;
  • Sun, Myung Suk (Korean Ginseng Center and Ginseng Resource Bank, Kyung Hee University) ;
  • Kim, Se Young (Korean Ginseng Center and Ginseng Resource Bank, Kyung Hee University) ;
  • Kim, Yu-Jin (Korean Ginseng Center and Ginseng Resource Bank, Kyung Hee University) ;
  • Yang, Deok Chun (Korean Ginseng Center and Ginseng Resource Bank, Kyung Hee University)
  • Received : 2012.10.08
  • Accepted : 2012.12.10
  • Published : 2013.04.15
Download PDF
⟨ Previous Next ⟩

Abstract

MicroRNAs (miRNAs) are a class of recently discovered non-coding small RNA molecules, on average approximately 21 nucleotides in length, which underlie numerous important biological roles in gene regulation in various organisms. The miRNA database (release 18) has 18,226 miRNAs, which have been deposited from different species. Although miRNAs have been identified and validated in many plant species, no studies have been reported on discovering miRNAs in Panax ginseng Meyer, which is a traditionally known medicinal plant in oriental medicine, also known as Korean ginseng. It has triterpene ginseng saponins called ginsenosides, which are responsible for its various pharmacological activities. Predicting conserved miRNAs by homology-based analysis with available expressed sequence tag (EST) sequences can be powerful, if the species lacks whole genome sequence information. In this study by using the EST based computational approach, 69 conserved miRNAs belonging to 44 miRNA families were identified in Korean ginseng. The digital gene expression patterns of predicted conserved miRNAs were analyzed by deep sequencing using small RNA sequences of flower buds, leaves, and lateral roots. We have found that many of the identified miRNAs showed tissue specific expressions. Using the insilico method, 346 potential targets were identified for the predicted 69 conserved miRNAs by searching the ginseng EST database, and the predicted targets were mainly involved in secondary metabolic processes, responses to biotic and abiotic stress, and transcription regulator activities, as well as a variety of other metabolic processes.

Keywords

References

  1. Bartel DP. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 2004;116:281-297. https://doi.org/10.1016/S0092-8674(04)00045-5
  2. Zhou X, Ruan J, Wang G, Zhang W. Characterization and identification of microRNA core promoters in four model species. PLoS Comput Biol 2007;3:e37. https://doi.org/10.1371/journal.pcbi.0030037
  3. Jones-Rhoades MW, Bartel DP, Bartel B. MicroRNAS and their regulatory roles in plants. Annu Rev Plant Biol 2006;57:19-53. https://doi.org/10.1146/annurev.arplant.57.032905.105218
  4. Lu Y, Yang X. Computational identification of novel microRNAs and their targets in Vigna unguiculata. Comp Funct Genomics 2010;pii: 128297.
  5. Sunkar R, Zhu JK. Novel and stress-regulated microRNAs and other small RNAs from Arabidopsis. Plant Cell 2004;16:2001-2019. https://doi.org/10.1105/tpc.104.022830
  6. Zhang B, Pan X, Anderson TA. Identification of 188 conserved maize microRNAs and their targets. FEBS Lett 2006;580:3753-3762. https://doi.org/10.1016/j.febslet.2006.05.063
  7. Ambros V. The functions of animal microRNAs. Nature 2004;431:350-355. https://doi.org/10.1038/nature02871
  8. Jagadeeswaran G, Zheng Y, Li YF, Shukla LI, Matts J, Hoyt P, Macmil SL, Wiley GB, Roe BA, Zhang W et al. Cloning and characterization of small RNAs from Medicago truncatula reveals four novel legume-specific microRNA families. New Phytol 2009;184:85-98. https://doi.org/10.1111/j.1469-8137.2009.02915.x
  9. Pantaleo V, Szittya G, Moxon S, Miozzi L, Moulton V, Dalmay T, Burgyan J. Identification of grapevine microRNAs and their targets using high-throughput sequencing and degradome analysis. Plant J 2010;62:960-976.
  10. Song C, Wang C, Zhang C, Korir NK, Yu H, Ma Z, Fang J. Deep sequencing discovery of novel and conserved microRNAs in trifoliate orange (Citrus trifoliata). BMC Genomics 2010;11:431. https://doi.org/10.1186/1471-2164-11-431
  11. Xie F, Frazier TP, Zhang B. Identification, characterization and expression analysis of microRNAs and their targets in the potato (Solanum tuberosum). Gene 2011;473:8-22. https://doi.org/10.1016/j.gene.2010.09.007
  12. Song C, Fang J, Li X, Liu H, Thomas Chao C. Identification and characterization of 27 conserved microRNAs in citrus. Planta 2009;230:671-685. https://doi.org/10.1007/s00425-009-0971-x
  13. Xie F, Frazier TP, Zhang B. Identification and characterization of microRNAs and their targets in the bioenergy plant switchgrass (Panicum virgatum). Planta 2010;232:417-434. https://doi.org/10.1007/s00425-010-1182-1
  14. Han Y, Zhu B, Luan F, Zhu H, Shao Y, Chen A, Lu C, Luo Y. Conserved miRNAs and their targets identified in lettuce (Lactuca) by EST analysis. Gene 2010;463:1-7. https://doi.org/10.1016/j.gene.2010.04.012
  15. Frazier TP, Xie F, Freistaedter A, Burklew CE, Zhang B. Identification and characterization of microRNAs and their target genes in tobacco (Nicotiana tabacum). Planta 2010;232:1289-1308. https://doi.org/10.1007/s00425-010-1255-1
  16. Zhao CZ, Xia H, Frazier TP, Yao YY, Bi YP, Li AQ, Li MJ, Li CS, Zhang BH, Wang XJ. Deep sequencing identifies novel and conserved microRNAs in peanuts (Arachis hypogaea L.). BMC Plant Biol 2010;10:3. https://doi.org/10.1186/1471-2229-10-3
  17. Mohorianu I, Schwach F, Jing R, Lopez-Gomollon S, Moxon S, Szittya G, Sorefan K, Moulton V, Dalmay T. Profiling of short RNAs during fleshy fruit development reveals stage-specific sRNAome expression patterns. Plant J 2011;67:232-246. https://doi.org/10.1111/j.1365-313X.2011.04586.x
  18. Wang C, Wang X, Kibet NK, Song C, Zhang C, Li X, Han J, Fang J. Deep sequencing of grapevine flower and berry short RNA library for discovery of novel microRNAs and validation of precise sequences of grapevine microRNAs deposited in miRBase. Physiol Plant 2011;143:64-81. https://doi.org/10.1111/j.1399-3054.2011.01481.x
  19. Vogler BK, Pittler MH, Ernst E. The efficacy of ginseng. A systematic review of randomised clinical trials. Eur J Clin Pharmacol 1999;55:567-575. https://doi.org/10.1007/s002280050674
  20. Choi KT. Botanical characteristics, pharmacological effects and medicinal components of Korean Panax ginseng C A Meyer. Acta Pharmacol Sin 2008;29:1109-1118. https://doi.org/10.1111/j.1745-7254.2008.00869.x
  21. Kim SK, Park JH. Trends in ginseng research in 2010. J Ginseng Res 2011;35:389-398. https://doi.org/10.5142/jgr.2011.35.4.389
  22. Yang Y, Chen X, Chen J, Xu H, Li J, Zhang Z. Differential miRNA expression in Rehmannia glutinosa plants subjected to continuous cropping. BMC Plant Biol 2011;11:53. https://doi.org/10.1186/1471-2229-11-53
  23. Pani A, Mahapatra RK, Behera N, Naik PK. Computational identification of sweet wormwood (Artemisia annua) microRNA and their mRNA targets. Genomics Proteomics Bioinformatics 2011;9:200-210. https://doi.org/10.1016/S1672-0229(11)60023-5
  24. Xu Q, Liu Y, Zhu A, Wu X, Ye J, Yu K, Guo W, Deng X. Discovery and comparative profiling of microRNAs in a sweet orange red-flesh mutant and its wild type. BMC Genomics 2010;11:246. https://doi.org/10.1186/1471-2164-11-246
  25. Meng Y, Ma X, Chen D, Wu P, Chen M. MicroRNA-mediated signaling involved in plant root development. Biochem Biophys Res Commun 2010;393:345-349. https://doi.org/10.1016/j.bbrc.2010.01.129
  26. Griffiths-Jones S, Saini HK, van Dongen S, Enright AJ. miRBase: tools for microRNA genomics. Nucleic Acids Res 2008;36(Database issue):D154-D158. https://doi.org/10.1093/nar/gkn221
  27. Sathiyamoorthy S, In JG, Lee BS, Kwon WS, Yang DU, Kim JH, Yang DC. Insilico analysis for expressed sequence tags from embryogenic callus and flower buds of Panax ginseng C. A. Meyer. J Ginseng Res 2011;35:21-30. https://doi.org/10.5142/jgr.2011.35.1.021
  28. Jones-Rhoades MW. Prediction of plant miRNA genes. Methods Mol Biol 2010;592:19-30. https://doi.org/10.1007/978-1-60327-005-2_2
  29. Zhang B, Pan X, Cannon CH, Cobb GP, Anderson TA. Conservation and divergence of plant microRNA genes. Plant J 2006;46:243-259. https://doi.org/10.1111/j.1365-313X.2006.02697.x
  30. Zhang B, Pan X, Stellwag EJ. Identification of soybean microRNAs and their targets. Planta 2008;229:161-182. https://doi.org/10.1007/s00425-008-0818-x
  31. Sunkar R, Jagadeeswaran G. Insilico identification of conserved microRNAs in large number of diverse plant species. BMC Plant Biol 2008;8:37. https://doi.org/10.1186/1471-2229-8-37
  32. Dhandapani V, Ramchiary N, Paul P, Kim J, Choi SH, Lee J, Hur Y, Lim YP. Identification of potential microRNAs and their targets in Brassica rapa L. Mol Cells 2011;32:21-37. https://doi.org/10.1007/s10059-011-2313-7
  33. Kozomara A, Griffiths-Jones S. miRBase: integrating microRNA annotation and deep-sequencing data. Nucleic Acids Res 2011;39(Database issue):D152-D157. https://doi.org/10.1093/nar/gkq1027
  34. Sunkar R, Zhou X, Zheng Y, Zhang W, Zhu JK. Identification of novel and candidate miRNAs in rice by high throughput sequencing. BMC Plant Biol 2008;8:25. https://doi.org/10.1186/1471-2229-8-25
  35. Guleria P, Yadav SK. Identification of miR414 and expression analysis of conserved miRNAs from Stevia rebaudiana. Genomics Proteomics Bioinformatics 2011;9:211-217. https://doi.org/10.1016/S1672-0229(11)60024-7
  36. Unver T, Parmaksiz I, Dundar E. Identification of conserved micro-RNAs and their target transcripts in opium poppy (Papaver somniferum L.). Plant Cell Rep 2010;29:757-769. https://doi.org/10.1007/s00299-010-0862-4
  37. Luo YC, Zhou H, Li Y, Chen JY, Yang JH, Chen YQ, Qu LH. Rice embryogenic calli express a unique set of microRNAs, suggesting regulatory roles of microRNAs in plant post-embryogenic development. FEBS Lett 2006;580:5111-5116. https://doi.org/10.1016/j.febslet.2006.08.046
  38. Schommer C, Bresso EG, Spinelli S, Palatnik J. Role of microRNA miR319 in plant development. In: Sunkar R, ed. MicroRNAs in plant development and stress responses. Berlin: Springer, 2012. p.29-47.
  39. Thiebaut F, Rojas CA, Almeida KL, Grativol C, Domiciano GC, Lamb CR, Engler Jde A, Hemerly AS, Ferreira PC. Regulation of miR319 during cold stress in sugarcane. Plant Cell Environ 2012;35:502-512. https://doi.org/10.1111/j.1365-3040.2011.02430.x
  40. Rajagopalan R, Vaucheret H, Trejo J, Bartel DP. A diverse and evolutionarily fluid set of microRNAs in Arabidopsis thaliana. Genes Dev 2006;20:3407-3425. https://doi.org/10.1101/gad.1476406
  41. Fahlgren N, Jogdeo S, Kasschau KD, Sullivan CM, Chapman EJ, Laubinger S, Smith LM, Dasenko M, Givan SA, Weigel D et al. MicroRNA gene evolution in Arabidopsis lyrata and Arabidopsis thaliana. Plant Cell 2010;22:1074-1089. https://doi.org/10.1105/tpc.110.073999
  42. Kantar M, Unver T, Budak H. Regulation of barley miRNAs upon dehydration stress correlated with target gene expression. Funct Integr Genomics 2010;10:493-507. https://doi.org/10.1007/s10142-010-0181-4
  43. Smalheiser NR, Torvik VI. Mammalian microRNAs derived from genomic repeats. Trends Genet 2005;21:322-326. https://doi.org/10.1016/j.tig.2005.04.008
  44. Zhang BH, Pan XP, Cox SB, Cobb GP, Anderson TA. Evidence that miRNAs are different from other RNAs. Cell Mol Life Sci 2006;63:246-254. https://doi.org/10.1007/s00018-005-5467-7
  45. Moxon S, Jing R, Szittya G, Schwach F, Rusholme Pilcher RL, Moulton V, Dalmay T. Deep sequencing of tomato short RNAs identifies microRNAs targeting genes involved in fruit ripening. Genome Res 2008;18:1602-1609. https://doi.org/10.1101/gr.080127.108
  46. Jones-Rhoades MW, Bartel DP. Computational identification of plant microRNAs and their targets, including a stress-induced miRNA. Mol Cell 2004;14:787-799. https://doi.org/10.1016/j.molcel.2004.05.027
  47. Lewis BP, Burge CB, Bartel DP. Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell 2005;120:15-20. https://doi.org/10.1016/j.cell.2004.12.035
  48. Wu G, Poethig RS. Temporal regulation of shoot development in Arabidopsis thaliana by miR156 and its target SPL3. Development 2006;133:3539-3547. https://doi.org/10.1242/dev.02521
  49. Palatnik JF, Allen E, Wu X, Schommer C, Schwab R, Carrington JC, Weigel D. Control of leaf morphogenesis by microRNAs. Nature 2003;425:257-263. https://doi.org/10.1038/nature01958
  50. Shim JS, Lee OR, Kim YJ, Lee JH, Kim JH, Jung DY, In JG, Lee BS, Yang DC. Overexpression of PgSQS1 increases ginsenoside production and negatively affects ginseng growth rate in Panax ginseng. J Ginseng Res 2010;34:98-103. https://doi.org/10.5142/jgr.2010.34.2.098

Cited by

  1. Comprehensive characterization of a time-course transcriptional response induced by autotoxins in Panax ginseng using RNA-Seq vol.16, pp.1, 2015, https://doi.org/10.1186/s12864-015-2151-7
  2. Time-Course Transcriptome Analysis Reveals Resistance Genes of Panax ginseng Induced by Cylindrocarpon destructans Infection Using RNA-Seq vol.11, pp.2, 2016, https://doi.org/10.1371/journal.pone.0149408
  3. The mRNA and miRNA transcriptomic landscape of Panax ginseng under the high ambient temperature vol.12, pp.S2, 2018, https://doi.org/10.1186/s12918-018-0548-z
  4. vol.16, pp.11, 2018, https://doi.org/10.1111/pbi.12926
  5. MicroRNA‐Based Biotechnology for Plant Improvement vol.230, pp.1, 2015, https://doi.org/10.1002/jcp.24685
  6. Validation of Suitable Reference Genes for Assessing Gene Expression of MicroRNAs in Lonicera japonica vol.7, pp.None, 2013, https://doi.org/10.3389/fpls.2016.01101
  7. Till 2018: a survey of biomolecular sequences in genus Panax vol.44, pp.1, 2013, https://doi.org/10.1016/j.jgr.2019.06.004