Biotechnology Letters

, Volume 34, Issue 4, pp 737–745 | Cite as

Mining of miRNAs and potential targets from gene oriented clusters of transcripts sequences of the anti-malarial plant, Artemisia annua

  • Álvaro L. Pérez-Quintero
  • Gaurav SablokEmail author
  • Tatiana V. Tatarinova
  • Ana Conesa
  • Jimmy Kuo
  • Camilo López
Original Research Paper


miRNAs involved in the biosynthesis of artemisinin, an anti-malarial compound form the plant Artemisia annua, have been identified using computational approaches to find conserved pre-miRNAs in available A. annua UniGene collections. Eleven pre-miRNAs were found from nine families. Targets predicted for these miRNAs were mainly transcription factors for conserved miRNAs. No target genes involved in artemisinin biosynthesis were found. However, miR390 was predicted to target a gene involved in the trichome development, which is the site of synthesis of artemisinin and could be a candidate for genetic transformation aiming to increase the content of artemisinin. Phylogenetic analyses were carried out to determinate the relation between A. annua and other plant pre-miRNAs: the pre-miRNA-based phylogenetic trees failed to correspond to known phylogenies, suggesting that pre-miRNA primary sequences may be too variable to accurately predict phylogenetic relations.


Anti-malarial plant Artemisia annua miRNAs 



Gaurav Sablok thanks Key Laboratory of Horticultural Plant Biology (MOE), Huazhong Agricultural University. Tatiana Tatarinova would like to thank the University of Glamorgan’s Research Investment Scheme for supporting this project and Dr Owain Kerton for editing. Financial support for Camilo López and Alvaro Perez comes from Dirección de Investigaciones sede Bogota (Universidad Nacional), Colciencias, and Ministerio de Agricultura de Colombia. This work has been partially funded by Spanish MICINN grant BIO2009-10799.


  1. Adenot X, Elmayan T, Lauressergues D, Boutet S, Bouché N, Gasciolli V, Vaucheret H (2006) DRB4-dependent TAS3 trans-acting siRNAs control leaf morphology through AGO7. Current Biol 16:927–932CrossRefGoogle Scholar
  2. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403–410PubMedGoogle Scholar
  3. Ambros V, Bartel B, Bartel DP, Burge CB, Carrington JC, Chen X, Dreyfuss G, Eddy SR, Griffiths-Jones S, Marshall M, Matzke M, Ruvkun G, Tuschl T (2003) A uniform system for microRNA annotation. RNA 9:277–279PubMedCrossRefGoogle Scholar
  4. Axtell MJ, Snyder JA, Bartel DP (2007) Common functions for diverse small RNAs of land plants. Plant Cell 19:1750–1769PubMedCrossRefGoogle Scholar
  5. Bartel DP (2004) MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116:281–297PubMedCrossRefGoogle Scholar
  6. Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Wheeler DL (2007) GenBank. Nucleic Acids Res 35:D21–D25PubMedCrossRefGoogle Scholar
  7. Bouwmeester HJ, Wallaart TE, Janssen MH, Van LB, Jansen BJ, Posthumus MA, Schmidt CO, De Kraker JW, König WA, Franssen MC (1999) Amorpha-4, 11-diene synthase catalyses the first probable step in artemisinin biosynthesis. Phytochemistry 52:843–854PubMedCrossRefGoogle Scholar
  8. Chuang JC, Jones PA (2007) Epigenetics and microRNAs. Pediatr Res 61:24R–29RPubMedCrossRefGoogle Scholar
  9. Conesa A, Götz S (2008) Blast2GO: A comprehensive suite for functional analysis in plant genomics. Int J Plant Genomics 2008:619832PubMedGoogle Scholar
  10. Conesa A, Gotz S, Garcia-Gomez JM, Terol J, Talon M, Robles M (2005) Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 21:3674–3676PubMedCrossRefGoogle Scholar
  11. Cuperus JT, Fahlgren N, Carrington JC (2011) Evolution and Functional Diversification of MIRNA Genes. Plant Cell 23:431–442PubMedCrossRefGoogle Scholar
  12. Enright AJ, John B, Gaul U, Tuschl T, Sander C, Marks DS (2003) MicroRNA targets in Drosophila. Genome Biol 5:R1PubMedCrossRefGoogle Scholar
  13. Freyhult E, Prusis P, Lapinsh M, Wikberg JE, Moulton V, Gustafsson MG (2005) Unbiased descriptor and parameter selection confirms the potential of proteochemometric modelling. BMC Bioinformatics 6:50PubMedCrossRefGoogle Scholar
  14. Gandikota M, Birkenbihl RP, Höhmann S, Cardon GH, Saedler H, Huijser P (2007) The miRNA156/157 recognition element in the 3′ UTR of the Arabidopsis SBP box gene SPL3 prevents early flowering by translational inhibition in seedlings. Plant J 49:683–693PubMedCrossRefGoogle Scholar
  15. Garcia D (2008) A miRacle in plant development: role of microRNAs in cell differentiation and patterning. Semin Cell Dev Biol 19:586–595PubMedCrossRefGoogle Scholar
  16. Götz S, García-Gómez JM, Terol J, Williams TD, Nagaraj SH, Nueda MJ, Robles M, Talón M, Dopazo J, Conesa A (2008) High-throughput functional annotation with the Blast2GO suite. Nucleic Acids Res 36:3420–3435PubMedCrossRefGoogle Scholar
  17. Graham IA, Besser K, Blumer S, Branigan CA, Czechowski T, Elias L, Guterman I, Harvey D et al. (2010) The genetic map of Artemisia annua L. identifies loci affecting yield of the antimalarial drug Artemisinin. Science 327:328–331PubMedCrossRefGoogle Scholar
  18. Griffiths-Jones S, Saini HK, Van Dongen S, Enright AJ (2008) miRBase: tools for microRNA genomics. Nucleic Acids Res 36:D154–D158PubMedCrossRefGoogle Scholar
  19. Gupta PK, Rustgi S (2004) Molecular markers from the transcribed/expressed region of the genome in higher plants. Funct Integr Genomics 4:139–162PubMedCrossRefGoogle Scholar
  20. Jiang M, Anderson J, Gillespie J, Mayne M (2008) uShuffle: a useful tool for shuffling biological sequences while preserving the k-let counts. BMC Bioinformatics 9:192PubMedCrossRefGoogle Scholar
  21. Jones-Rhoades MW, Bartel DP (2004) Computational identification of plant microRNAs and their targets, including a stress-induced miRNA. Mol Cell. 14:787–799PubMedCrossRefGoogle Scholar
  22. Jones-Rhoades MW, Bartel DP, Bartel B (2006) MicroRNAS and their regulatory roles in plants. Annu Rev Plant Biol 57:19–53PubMedCrossRefGoogle Scholar
  23. Kidner CA, Martienssen RA (2005) The developmental role of microRNA in plants. Curr Opin Plant Biol 8:38–44PubMedCrossRefGoogle Scholar
  24. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ, Higgins DG (2007) Clustal W and Clustal X version 2.0. Bioinformatics 23:2947–2948PubMedCrossRefGoogle Scholar
  25. Lin X, Zhou Y, Zhang J, Lu X, Zhang F, Shen Q, Wu S, Chen Y, Wang T, Tang K (2011) Enhancement of artemisinin content in tetraploid Artemisia annua plants by modulating the expression of genes in artemisinin biosynthetic pathway. Biotechnol Appl Biochem 58:50–57PubMedCrossRefGoogle Scholar
  26. Meyers BC, Axtell MJ, Bartel B, Bartel DP, Baulcombe D, Bowman JL, Cao X, Carrington JC et al (2008) Criteria for annotation of plant MicroRNAs. Plant Cell. 20:3186–3190PubMedCrossRefGoogle Scholar
  27. Notredame C (2010) Computing Multiple Sequence/Structure Alignments with the T-Coffee Package. Curr Protoc Bioinformatics Chapter 3: pp 1–25Google Scholar
  28. Olofsson L, Engström A, Lundgren A, Brodelius PE (2011) Relative expression of genes of terpene metabolism in different tissues of Artemisia annua L. BMC Plant Biol 11:45PubMedCrossRefGoogle Scholar
  29. Parida SK, Anand Raj Kumar K, Dalal V, Singh NK, Mohapatra T (2006) UniGene derived microsatellite markers for the cereal genomes. Theor Appl Genet 112:808–817PubMedCrossRefGoogle Scholar
  30. Pérez-Quintero AL, Neme R, Zapata A, López C (2010) Plant microRNAs and their role in defense against viruses: a bioinformatics approach. BMC Plant Biol 10:138PubMedCrossRefGoogle Scholar
  31. Robert-Seilaniantz A, Bari R, Jones JDG (2010) A biotic or abiotic stress? In: Pareek A, Sopory SK, Bohnert HJ, Govindjee (eds) Abiotic stress adaptation in plants: physiological. Molecular and Genomic Foundation, Springer, Dordrecht, pp 113–116Google Scholar
  32. Ruegger M, Dewey E, Gray WM, Hobbie L, Turner J, Estelle M (1998) The TIR1 protein of Arabidopsis functions in auxin response and is related to human SKP2 and yeast grr1p. Genes Dev 12:198–207PubMedCrossRefGoogle Scholar
  33. Rydén AM, Ruyter-Spira C, Litjens R, Takahashi S, Quax W, Osada H, Bouwmeester H, Kayser O (2010) Molecular cloning and characterization of a broad substrate terpenoidoxidoreductase from Artemisia annua. Plant Cell Physiol 51:1219–1228PubMedCrossRefGoogle Scholar
  34. Schwab R, Palatnik JF, Riester M, Schommer C, Schmid M, Weigel D (2005) Specific effects of microRNAs on the plant transcriptome. Dev Cell 8:517–527PubMedCrossRefGoogle Scholar
  35. Wang W, Wang Y, Zhang Q, Qi Y, Guo D (2009) Global characterization of Artemisia annua glandular trichome transcriptome using 454 pyrosequencing. BMC Genomics 10:465PubMedCrossRefGoogle Scholar
  36. Xie FL, Huang SQ, Guo K, Xiang AL, Zhu YY, Nie L, Yang ZM (2007) Computational identification of novel microRNAs and targets in Brassicanapus. FEBS Lett 581:1464–1474PubMedCrossRefGoogle Scholar
  37. Yamasaki H, Hayashi M, Fukazawa M, Kobayashi Y, Shikanai T (2009) SQUAMOSA Promoter Binding Protein-Like7 Is a Central Regulator for Copper Homeostasis in Arabidopsis. Plant Cell 1:347–361CrossRefGoogle Scholar
  38. Yoon EK, Yang JH, Lim J, Kim SH, Kim SK, Lee WS (2010) Auxin regulation of the microRNA390-dependent transacting small interfering RNA pathway in Arabidopsis lateral root development. Nucleic Acid Res 38:1382–1391PubMedCrossRefGoogle Scholar
  39. Zhang B, Pan X, Cannon CH, Cobb GP, Anderson TA (2006a) Conservation and divergence of plant microRNA genes. Plant J 46:243–259PubMedCrossRefGoogle Scholar
  40. Zhang B, Pan X, Wang Q, Cobb GP, Anderson TA (2006b) Computational identification of microRNAs and their targets. Comput Biol Chem 30:395–407PubMedCrossRefGoogle Scholar
  41. Zhang J, Xu Y, Huan Q, Chong K (2009) Deep sequencing of Brachypodium small RNAs at the global genome level identifies microRNAs involved in cold stress response. BMC Genomics 10:449PubMedCrossRefGoogle Scholar
  42. Zhang Z, Yu J, Li D, Zhang Z, Liu F, Zhou X, Wang T, Ling Y, Su Z (2010) PMRD: plant microRNA database. Nucleic Acids Res 38:D806–D813PubMedCrossRefGoogle Scholar
  43. Zuker M (2003) Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res 31:3406–3415PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media B.V. 2011

Authors and Affiliations

  • Álvaro L. Pérez-Quintero
    • 1
  • Gaurav Sablok
    • 2
    Email author
  • Tatiana V. Tatarinova
    • 3
  • Ana Conesa
    • 4
  • Jimmy Kuo
    • 5
  • Camilo López
    • 1
  1. 1.Departamento de BiologíaUniversidad Nacional de Colombia, BogotáBogota, DCColombia
  2. 2.Key Laboratory of Horticultural Plant Biology (MOE)Huazhong Agricultural UniversityWuhanChina
  3. 3.Division of Mathematics and StatisticsUniversity of GlamorganPontypriddUK
  4. 4.Bioinformatics and Genomics DepartmentCentro de Investigación Príncipe FelipeAvdaValenciaSpain
  5. 5.Department of Planning and ResearchNational Museum of Marine Biology and AquariumPingtungTaiwan

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