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

Journal of Ginseng Research

Volumn 37, Issue 2, 2013, Pages 227-247

  Mathiyalagan, Ramya ^a   Subramaniyam, Sathiyamoorthy ^a   Natarajan, Sathishkumar ^a   Kim, Yeon Ju ^a   Sun, Myung Suk ^a   Kim, Se Young ^a   Kim, Yu Jin ^a   Yang, Deok Chun ^a  

^a Kyung Hee University   (South Korea)

Author keywords

Deep sequencing; Expressed sequence tag; MicroRNA; Panax ginseng

Indexed keywords

PANAX GINSENG;

EID: 84876031003     PISSN: 12268453     EISSN: None     Source Type: Journal    
DOI: 10.5142/jgr.2013.37.227     Document Type: Article

References (50)

1. Bartel DP. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 2004;116:281-297.
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.
3. Jones-Rhoades MW, Bartel DP, Bartel B. MicroRNAS and their regulatory roles in plants. Annu Rev Plant Biol 2006;57:19-53.
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 microR-- NAs and other small RNAs from Arabidopsis. Plant Cell 2004;16:2001-2019.
6. Zhang B, Pan X, Anderson TA. Identification of 188 conserved maize microRNAs and their targets. FEBS Lett 2006;580:3753-3762.
7. Ambros V. The functions of animal microRNAs. Nature 2004;431:350-355.
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.
9. Pantaleo V, Szittya G, Moxon S, Miozzi L, Moulton V, Dalmay T, Burgyan J. Identification of grapevine microR--NAs 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.
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.
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.
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.
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.
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.
16. Zhao CZ, Xia H, Frazier TP, Yao YY, Bi YP, Li AQ, Li MJ, Li CS, Zhang B., Wang XJ. Deep sequencing identifies novel and conserved microRNAs in peanuts (Arachis hypogaea L.). BMC Plant Biol 2010;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.
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.
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.
20. Choi KT. Botanical characteristics, pharmacological effects and medicinal components of Korean Panax ginseng C A Meyer. Acta Pharmacol Sin 2008;29:1109-1118.
21. Kim SK, Park JH. Trends in ginseng research in 2010. J Ginseng Res 2011;35:389-398.
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.
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.
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.
25. Meng Y, Ma X, Chen D, Wu P, Chen M. MicroRNAmediated signaling involved in plant root development. Biochem Biophys Res Commun 2010;393:345-349.
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.
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.
28. Jones-Rhoades MW. Prediction of plant miRNA genes. Methods Mol Biol 2010;592:19-30.
29. Zhang B, Pan X, Cannon CH, Cobb GP, Anderson TA. Conservation and divergence of plant microRNA genes. Plant J 2006;46:243-259.
30. Zhang B, Pan X, Stellwag EJ. Identification of soybean microRNAs and their targets. Planta 2008;229:161-182.
31. Sunkar R, Jagadeeswaran G. Insilico identification of conserved microRNAs in large number of diverse plant species. BMC Plant Biol 2008;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.
33. Kozomara A, Griffiths-Jones S. miRBase:integrating microRNA annotation and deep-sequencing data. Nucleic Acids Res 2011;39(Database issue):D152-D157.
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.
35. Guleria P, Yadav SK. Identification of miR414 and expression analysis of conserved miRNAs from Stevia rebaudiana. Genomics Proteomics Bioinformatics 2011;9:211-217.
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.
37. Luo Y., 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.
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.
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.
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.
42. Kantar M, Unver T, Budak H. Regulation of barley miR-- NAs upon dehydration stress correlated with target gene expression. Funct Integr Genomics 2010;10:493-507.
43. Smalheiser NR, Torvik VI. Mammalian microRNAs derived from genomic repeats. Trends Genet 2005;21:322-326.
44. Zhang B., Pan XP, Cox SB, Cobb GP, Anderson TA. Evidence that miRNAs are different from other RNAs. Cell Mol Life Sci 2006;63:246-254.
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.
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.
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.
48. Wu G, Poethig RS. Temporal regulation of shoot development in Arabidopsis thaliana by miR156 and its target SPL3. Development 2006;133:3539-3547.
49. Palatnik J., Allen E, Wu X, Schommer C, Schwab R, Carrington JC, Weigel D. Control of leaf morphogenesis by microRNAs. Nature 2003;425:257-263.
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.