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In Silico Identification of Novel microRNAs and Targets Using EST Analysis in Allium cepa L.

  • Bahram Baghban Kohnehrouz
  • Meysam Bastami
  • Shahnoush Nayeri
Original Research Article
  • 161 Downloads

Abstract

microRNAs (miRNAs) are a newly discovered class of non-coding small RNAs roughly 22 nucleotides long. Increasing evidence has shown that miRNAs play multiple roles in biological processes, including development, cell proliferation, apoptosis and stress responses. The identification of miRNAs and their targets is an important need to understand their roles in the development and physiology of sweet onion (Allium cepa). In this research, several computational approaches were combined to make concise prediction of the potential miRNAs and their targets. We used previously known miRNAs from other plant species against Expressed Sequence Tags (EST) database to search for the potential miRNAs. As a result, nine potential miRNAs were identified in eight ESTs of A. cepa, belonging to eight families. We could further BLAST the mRNA database and found total 154 number of the potential targets in A. cepa based on these potential miRNAs. According to the mRNA target information provided by NCBI, most of the target mRNAs appeared to be involved in plant growth, signal transduction, development, and stress responses. Gene ontology (GO) analysis implicated these targets in 32 biological processes such as protein ubiquitination, plant hormone signalling pathways and heme biosynthesis.

Keywords

Allium cepa Comparative genomics EST analysis Gene ontology miRNAs targets 

Notes

Acknowledgements

This work was financially supported by Department of Plant Breeding and Biotechnology, University of Tabriz, Tabriz, Iran.

Compliance with Ethical Standards

Conflict of interest

The authors declare no conflict of interest.

Supplementary material

12539_2017_240_MOESM1_ESM.pdf (118 kb)
Supplementary material 1 (PDF 119 kb)

References

  1. 1.
    Zhang BH, Pan XP, Wang QL, George PC, Anderson TA (2005) Identification and characterization of new plant microRNAs using EST analysis. Cell Res 15(5):336–360CrossRefGoogle Scholar
  2. 2.
    Zhou X, Ruan J, Wang G, Zhang W (2007) Characterization and identification of microRNA core promoters in four model species. PLoS Comput Biol 3(3):e37CrossRefGoogle Scholar
  3. 3.
    Bartel DP (2004) MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116(2):281–297CrossRefGoogle Scholar
  4. 4.
    Park MY, Wu G, Gonzalez-Sulser A, Vaucheret H, Poethig RS (2005) Nuclear processing and export of microRNAs in Arabidopsis. Proc Natl Acad Sci USA 102(10):3691–3696CrossRefGoogle Scholar
  5. 5.
    Taylor RS, Tarver JE, Hiscock SJ, Donoghue PC (2014) Evolutionary history of plant microRNAs. Trends Plant Sci 19(3):175–182CrossRefGoogle Scholar
  6. 6.
    Bagga S, Bracht J, Hunter S, Massirer K, Holtz J, Eachus R, Pasquinelli AE (2005) Regulation by let-7 and lin-4 miRNAs results in target mRNA degradation. Cell 122(4):553–563CrossRefGoogle Scholar
  7. 7.
    Xie F, Frazier TP, Zhang B (2011) Identification, characterization and expression analysis of MicroRNAs and their targets in the potato (Solanum tuberosum). Gene 473(1):8–22CrossRefGoogle Scholar
  8. 8.
    Wang X-J, Reyes JL, Chua N-H, Gaasterland T (2004) Prediction and identification of Arabidopsis thaliana microRNAs and their mRNA targets. Genome Biol 5(9):1Google Scholar
  9. 9.
    Adams MD, Kelley JM, Gocayne JD, Dubnick M, Polymeropoulos MH, Xiao H, Merril CR, Wu A, Olde B, Moreno RF (1991) Complementary DNA sequencing: expressed sequence tags and human genome project. Science 252(5013):1651–1656CrossRefGoogle Scholar
  10. 10.
    Bentwich I, Avniel A, Karov Y, Aharonov R, Gilad S, Barad O, Barzilai A, Einat P, Einav U, Meiri E (2005) Identification of hundreds of conserved and nonconserved human microRNAs. Nat Genet 37(7):766–770CrossRefGoogle Scholar
  11. 11.
    Lewis BP, Burge CB, Bartel DP (2005) Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell 120(1):15–20CrossRefGoogle Scholar
  12. 12.
    Wang X-J, Reyes JL, Chua N-H, Gaasterland T (2004) Prediction and identification of Arabidopsis thaliana microRNAs and their mRNA targets. Genome Biol 5(9):R65CrossRefGoogle Scholar
  13. 13.
    Zhang B, Pan X, Anderson TA (2006) Identification of 188 conserved maize microRNAs and their targets. FEBS Lett 580(15):3753–3762CrossRefGoogle Scholar
  14. 14.
    Zhang B, Pan X, Cannon CH, Cobb GP, Anderson TA (2006) Conservation and divergence of plant microRNA genes. Plant J 46(2):243–259CrossRefGoogle Scholar
  15. 15.
    Matukumalli LK, Grefenstette JJ, Sonstegard TS, Van Tassell CP (2004) EST-PAGE—managing and analyzing EST data. Bioinformatics 20(2):286–288CrossRefGoogle Scholar
  16. 16.
    Graham MA, Silverstein KA, Cannon SB, VandenBosch KA (2004) Computational identification and characterization of novel genes from legumes. Plant Physiol 135(3):1179–1197CrossRefGoogle Scholar
  17. 17.
    Jung J, Park H-W, Hahn Y, Hur C-G, In D, Chung H-J, Liu J, Choi D-W (2003) Discovery of genes for ginsenoside biosynthesis by analysis of ginseng expressed sequence tags. Plant Cell Rep 22(3):224–230CrossRefGoogle Scholar
  18. 18.
    Ohlrogge J, Benning C (2000) Unraveling plant metabolism by EST analysis. Curr Opin Plant Biol 3(3):224–228CrossRefGoogle Scholar
  19. 19.
    Xie FL, Huang SQ, Guo K, Xiang AL, Zhu YY, Nie L, Yang ZM (2007) Computational identification of novel microRNAs and targets in Brassica napus. FEBS Lett 581(7):1464–1474CrossRefGoogle Scholar
  20. 20.
    Zhang B, Pan X, Stellwag EJ (2008) Identification of soybean microRNAs and their targets. Planta 229(1):161–182CrossRefGoogle Scholar
  21. 21.
    Jin W, Li N, Zhang B, Wu F, Li W, Guo A, Deng Z (2008) Identification and verification of microRNA in wheat (Triticum aestivum). J Plant Res 121(3):351–355CrossRefGoogle Scholar
  22. 22.
    Frazier TP, Xie F, Freistaedter A, Burklew CE, Zhang B (2010) Identification and characterization of microRNAs and their target genes in tobacco (Nicotiana tabacum). Planta 232(6):1289–1308CrossRefGoogle Scholar
  23. 23.
    Xie F, Frazier TP, Zhang B (2010) Identification and characterization of microRNAs and their targets in the bioenergy plant switchgrass (Panicum virgatum). Planta 232(2):417–434CrossRefGoogle Scholar
  24. 24.
    Pilcher RLR, Moxon S, Pakseresht N, Moulton V, Manning K, Seymour G, Dalmay T (2007) Identification of novel small RNAs in tomato (Solanum lycopersicum). Planta 226(3):709–717CrossRefGoogle Scholar
  25. 25.
    Wang J, Yang X, Xu H, Chi X, Zhang M, Hou X (2012) Identification and characterization of microRNAs and their target genes in Brassica oleracea. Gene 505(2):300–308CrossRefGoogle Scholar
  26. 26.
    Usha S, Jyothi M, Suchithra B, Dixit R, Rai D (2017) Computational identification of MicroRNAs and their targets from finger millet (Eleusinecoracana). Interdiscip Sci Comput Life Sci 9(1):72–79CrossRefGoogle Scholar
  27. 27.
    Tilman D, Balzer C, Hill J, Befort BL (2011) Global food demand and the sustainable intensification of agriculture. Proc Natl Acad Sci 108(50):20260–20264CrossRefGoogle Scholar
  28. 28.
    Mathews DH, Sabina J, Zuker M, Turner DH (1999) Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. J Mol Biol 288(5):911–940CrossRefGoogle Scholar
  29. 29.
    Zuker M (2003) Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res 31(13):3406–3415CrossRefGoogle Scholar
  30. 30.
    Du H, Zhang L, Liu L, Tang X-F, Yang W-J, Wu Y-M, Huang Y-B, Tang Y-X (2009) Biochemical and molecular characterization of plant MYB transcription factor family. Biochemistry (Moscow) 74(1):1–11CrossRefGoogle Scholar
  31. 31.
    Dsouza M, Larsen N, Overbeek R (1997) Searching for patterns in genomic data. Trends Genet 13(12):497–498CrossRefGoogle Scholar
  32. 32.
    Llave C, Xie Z, Kasschau KD, Carrington JC (2002) Cleavage of Scarecrow-like mRNA targets directed by a class of Arabidopsis miRNA. Science 297(5589):2053–2056CrossRefGoogle Scholar
  33. 33.
    Sunkar R, Zhu J-K (2004) Novel and stress-regulated microRNAs and other small RNAs from Arabidopsis. Plant Cell 16(8):2001–2019CrossRefGoogle Scholar
  34. 34.
    Schwab R, Palatnik JF, Riester M, Schommer C, Schmid M, Weigel D (2005) Specific effects of microRNAs on the plant transcriptome. Dev Cell 8(4):517–527CrossRefGoogle Scholar
  35. 35.
    Rhoades MW, Reinhart BJ, Lim LP, Burge CB, Bartel B, Bartel DP (2002) Prediction of plant microRNA targets. Cell 110(4):513–520CrossRefGoogle Scholar
  36. 36.
    Lan Y, Su N, Shen Y, Zhang R, Wu F, Cheng Z, Wang J, Zhang X, Guo X, Lei C (2012) Identification of novel MiRNAs and MiRNA expression profiling during grain development in indica rice. BMC Genom 13(1):1CrossRefGoogle Scholar
  37. 37.
    Zhang Y (2005) miRU: an automated plant miRNA target prediction server. Nucleic Acids Res 33(suppl 2):W701–W704CrossRefGoogle Scholar
  38. 38.
    Ding H, Gao J, Luo M, Peng H, Lin H, Yuan G, Shen Y, Zhao M, Pan G, Zhang Z (2013) Identification and functional analysis of miRNAs in developing kernels of a viviparous mutant in maize. Crop J 1(2):115–126CrossRefGoogle Scholar
  39. 39.
    Zhu J-K (2008) Reconstituting plant miRNA biogenesis. Proc Natl Acad Sci 105(29):9851–9852CrossRefGoogle Scholar
  40. 40.
    Lelandais-Brière C, Naya L, Sallet E, Calenge F, Frugier F, Hartmann C, Gouzy J, Crespi M (2009) Genome-wide Medicago truncatula small RNA analysis revealed novel microRNAs and isoforms differentially regulated in roots and nodules. Plant Cell 21(9):2780–2796CrossRefGoogle Scholar
  41. 41.
    Borges F, Pereira PA, Slotkin RK, Martienssen RA, Becker JD (2011) MicroRNA activity in the Arabidopsis male germline. J Exp Bot 62(5):1611–1620CrossRefGoogle Scholar
  42. 42.
    Sunkar R, Zhou X, Zheng Y, Zhang W, Zhu J-K (2008) Identification of novel and candidate miRNAs in rice by high throughput sequencing. BMC Plant Biol 8(1):1CrossRefGoogle Scholar
  43. 43.
    Fattash I, Voß B, Reski R, Hess WR, Frank W (2007) Evidence for the rapid expansion of microRNA-mediated regulation in early land plant evolution. BMC Plant Biol 7(1):1CrossRefGoogle Scholar
  44. 44.
    Zhang B, Pan X, Cox S, Cobb G, Anderson T (2006) Evidence that miRNAs are different from other RNAs. Cell Mol Life Sci CMLS 63(2):246–254CrossRefGoogle Scholar
  45. 45.
    Feshani AM, Mohammadi S, Frazier TP, Abbasi A, Abedini R, Farsad LK, Ehya F, Salekdeh GH, Mardi M (2012) Identification and validation of Asteraceae miRNAs by the expressed sequence tag analysis. Gene 493(2):253–259CrossRefGoogle Scholar
  46. 46.
    Meyers BC, Axtell MJ, Bartel B, Bartel DP, Baulcombe D, Bowman JL, Cao X, Carrington JC, Chen X, Green PJ (2008) Criteria for annotation of plant microRNAs. Plant Cell 20(12):3186–3190CrossRefGoogle Scholar
  47. 47.
    Jones-Rhoades MW, Bartel DP (2004) Computational identification of plant microRNAs and their targets, including a stress-induced miRNA. Mol Cell 14(6):787–799CrossRefGoogle Scholar
  48. 48.
    Czemmel S, Heppel SC, Bogs J (2012) R2R3 MYB transcription factors: key regulators of the flavonoid biosynthetic pathway in grapevine. Protoplasma 249(2):109–118CrossRefGoogle Scholar
  49. 49.
    Feller A, Machemer K, Braun EL, Grotewold E (2011) Evolutionary and comparative analysis of MYB and bHLH plant transcription factors. Plant J 66(1):94–116CrossRefGoogle Scholar
  50. 50.
    Ma Q, Dai X, Xu Y, Guo J, Liu Y, Chen N, Xiao J, Zhang D, Xu Z, Zhang X (2009) Enhanced tolerance to chilling stress in OsMYB3R-2 transgenic rice is mediated by alteration in cell cycle and ectopic expression of stress genes. Plant Physiol 150(1):244–256CrossRefGoogle Scholar
  51. 51.
    Chen J, Xia X, Yin W (2009) Expression profiling and functional characterization of a DREB2-type gene from Populus euphratica. Biochem Biophys Res Commun 378(3):483–487CrossRefGoogle Scholar
  52. 52.
    Chen M, Wang Q-Y, Cheng X-G, Xu Z-S, Li L-C, Ye X-G, Xia L-Q, Ma Y-Z (2007) GmDREB2, a soybean DRE-binding transcription factor, conferred drought and high-salt tolerance in transgenic plants. Biochem Biophys Res Commun 353(2):299–305CrossRefGoogle Scholar
  53. 53.
    Cler E, Papai G, Schultz P, Davidson I (2009) Recent advances in understanding the structure and function of general transcription factor TFIID. Cell Mol Life Sci 66(13):2123–2134CrossRefGoogle Scholar
  54. 54.
    Unver T, Budak H (2009) Conserved microRNAs and their targets in model grass species Brachypodium distachyon. Planta 230(4):659–669CrossRefGoogle Scholar
  55. 55.
    Dye BT, Schulman BA (2007) Structural mechanisms underlying posttranslational modification by ubiquitin-like proteins. Annu Rev Biophys Biomol Struct 36:131–150CrossRefGoogle Scholar
  56. 56.
    Lechner E, Achard P, Vansiri A, Potuschak T, Genschik P (2006) F-box proteins everywhere. Curr Opin Plant Biol 9(6):631–638CrossRefGoogle Scholar
  57. 57.
    Qiao H, Chang KN, Yazaki J, Ecker JR (2009) Interplay between ethylene, ETP1/ETP2 F-box proteins, and degradation of EIN2 triggers ethylene responses in Arabidopsis. Genes Dev 23(4):512–521CrossRefGoogle Scholar
  58. 58.
    Solano R, Stepanova A, Chao Q, Ecker JR (1998) Nuclear events in ethylene signaling: a transcriptional cascade mediated by ETHYLENE-INSENSITIVE3 and ETHYLENE-RESPONSE-FACTOR1. Genes Dev 12(23):3703–3714CrossRefGoogle Scholar
  59. 59.
    Bu Q, Li H, Zhao Q, Jiang H, Zhai Q, Zhang J, Wu X, Sun J, Xie Q, Wang D (2009) The Arabidopsis RING finger E3 ligase RHA2a is a novel positive regulator of abscisic acid signaling during seed germination and early seedling development. Plant Physiol 150(1):463–481CrossRefGoogle Scholar
  60. 60.
    Huang Y, Li CY, Pattison DL, Gray WM, Park S, Gibson SI (2010) SUGAR-INSENSITIVE3, a RING E3 ligase, is a new player in plant sugar response. Plant Physiol 152(4):1889–1900CrossRefGoogle Scholar
  61. 61.
    Peng M, Hannam C, Gu H, Bi YM, Rothstein SJ (2007) A mutation in NLA, which encodes a RING-type ubiquitin ligase, disrupts the adaptability of Arabidopsis to nitrogen limitation. Plant J 50(2):320–337CrossRefGoogle Scholar
  62. 62.
    Santner A, Estelle M (2009) Recent advances and emerging trends in plant hormone signalling. Nature 459(7250):1071–1078CrossRefGoogle Scholar
  63. 63.
    Stone SL, Williams LA, Farmer LM, Vierstra RD, Callis J (2006) KEEP ON GOING, a RING E3 ligase essential for Arabidopsis growth and development, is involved in abscisic acid signaling. Plant Cell 18(12):3415–3428CrossRefGoogle Scholar
  64. 64.
    Craig A, Ewan R, Mesmar J, Gudipati V, Sadanandom A (2009) E3 ubiquitin ligases and plant innate immunity. J Exp Bot 60(4):1123–1132CrossRefGoogle Scholar
  65. 65.
    Fujita Y, Fujita M, Shinozaki K, Yamaguchi-Shinozaki K (2011) ABA-mediated transcriptional regulation in response to osmotic stress in plants. J Plant Res 124(4):509–525CrossRefGoogle Scholar
  66. 66.
    Smirnova O, Stepanenko I, Shumnyi V (2011) The role of the COP1, SPA, and PIF proteins in plant photomorphogenesis. Biol Bull Rev 1(4):314–324CrossRefGoogle Scholar
  67. 67.
    Yan J, Wang J, Li Q, Hwang JR, Patterson C, Zhang H (2003) AtCHIP, a U-box-containing E3 ubiquitin ligase, plays a critical role in temperature stress tolerance in Arabidopsis. Plant Physiol 132(2):861–869CrossRefGoogle Scholar
  68. 68.
    Hématy K, Höfte H (2008) Novel receptor kinases involved in growth regulation. Curr Opin Plant Biol 11(3):321–328CrossRefGoogle Scholar
  69. 69.
    Nibau C, Cheung A (2011) New insights into the functional roles of CrRLKs in the control of plant cell growth and development. Plant Signal Behav 6(5):655–659CrossRefGoogle Scholar
  70. 70.
    Ederli L, Madeo L, Calderini O, Gehring C, Moretti C, Buonaurio R, Paolocci F, Pasqualini S (2011) The Arabidopsis thaliana cysteine-rich receptor-like kinase CRK20 modulates host responses to Pseudomonas syringae pv. tomato DC3000 infection. J Plant Physiol 168(15):1784–1794CrossRefGoogle Scholar
  71. 71.
    Yang X, Deng F, Ramonell KM (2012) Receptor-like kinases and receptor-like proteins: keys to pathogen recognition and defense signaling in plant innate immunity. Front Biol 7(2):155–166CrossRefGoogle Scholar
  72. 72.
    Haswell ES, Phillips R, Rees DC (2011) Mechanosensitive channels: what can they do and how do they do it? Structure 19(10):1356–1369CrossRefGoogle Scholar
  73. 73.
    Ortiz-Lopez A, Chang H-C, Bush D (2000) Amino acid transporters in plants. Biochim et Biophys (BBA) Biomembr 1465(1):275–280CrossRefGoogle Scholar

Copyright information

© Springer-Verlag 2017

Authors and Affiliations

  • Bahram Baghban Kohnehrouz
    • 1
  • Meysam Bastami
    • 2
  • Shahnoush Nayeri
    • 3
  1. 1.Department of Plant Breeding and BiotechnologyUniversity of TabrizTabrizIran
  2. 2.Department of Agricultural Biotechnology, Faculty of EngineeringImam Khomeini International UniversityQazvinIran
  3. 3.Department of Biotechnology, Faculty of New Technologies and Energy EngineeringShahid Beheshti UniversityTehranIran

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