Computational identification of microRNAs and their targets in two species of evergreen spruce tree (Picea)

World Academy of Science, Engineering and Technology

Volumn 75, Issue , 2011, Pages 413-418

  Barozai, Muhammad Y K ^a   Baloch, Ifthikhar A ^a   Din, M ^a  

^a University of Baluchistan   (Iran)

Author keywords

BLast; Comparative genomics; Micro RNAs; Spruce

Indexed keywords

ARABIDOPSIS; BELONG TO; BLAST; COMPARATIVE GENOMICS; COMPUTATIONAL IDENTIFICATION; HYPOTHETICAL PROTEIN; MICRO-RNAS; MINIMUM FREE ENERGIES; ORTHOLOGUES; PICEA GLAUCA; SPRUCE; SPRUCE TREES; STEM-LOOP STRUCTURES;

FREE ENERGY; TRANSCRIPTION FACTORS; RNA;

NUCLEIC ACIDS; FORESTRY;

FREE ENERGY; GENETIC ENGINEERING; GENOTYPES; NUCLEIC ACIDS; PICEA GLAUCA; PICEA SITCHENSIS; PROTEINS;

EID: 79953664746     PISSN: 2010376X     EISSN: 20103778     Source Type: Journal    
DOI: None     Document Type: Article

References (36)

1. Sunset Western Garden Book, (1995): 606-607.
2. Sigurgeirsson, A. and Szmidt, A. E. Phylogenetic and biogeographic implications of chloroplast DNA variation in Picea. Nordic Journal of Botany 13(3): (1993) 233-246.
3. Mica E., Gianfranceschi L. and Pe M. E., Characterization of five microRNA families in maize. J. Expl. Bot. 57(11): (2006) 2601-2612.
4. Bonnet E., Wuyts J., Rouze P. and Van-de-Peer Y. Detection of 91 potential conserved plant microRNAs in Arabidopsis thaliana and Oryza sativa identifies important target genes. PNAS USA. 101: (2004) 11511-11516.
5. Weber M.J. New human and mouse microRNA genes found by homology search. FEBS J.272: (2005) 59-73.
6. Bartel D. P. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell.116: (2004) 281-297.
7. Carrington J.C. and Ambros V. Role of microRNAs in plant and animal development. Sci. 301: (2003) 336-338.
8. Hammond S. C., Bernstein E., Beach D and Hannon G.J. An RNAdirected nuclease mediatesposttranscriptional gene silencing in Drosophila cells. Nat. 404: (2000) 293-296.
9. Kurihara Y. and Watanabe Y. Arabidopsis micro-RNA biogenesis through Dicer-like 1protein functions. PNAS USA.101: (2004) 12753-12758.
10. Aukerman M. J. and Sakai H. Regulation of flowering time and floral organ identity by a microRNA and its APETALA2-Like target genes. Plant Cell.15: (2003) 2730-2741.
11. Tang G., Reinhart B. J., Bartel D. P. and Zamore P.D. A biochemical framework for RNA silencing in plants. Genes Dev. 17: (2003) 49-63.
12. Novina C. D. and Sharp P.A. The RNAi revolution. Nat. 430: (2004) 161-164.
13. Kidner C. A and Martienssen R. A. The developmental role of microRNA in plants.Curr Opin Plant Biol.8: (2005) 38-44.
14. Chen X. A microRNA as a translational repressor of APETALA2 in Arabidopsis flower development. Sci. 303: (2003) 2022-2025.
15. Allen E., Xie Z., Gustafson A. M., and Carrington J. C., MicroRNAdirected phasing during transacting siRNA biogenesis in plants. Cell. 121: (2005) 207-221.
16. Yoshikawa M., Peragine A., Park M. Y. and Poethig R. S., A pathway for the biogenesis of trans-acting siRNAs in Arabidopsis. Genes & Dev. 19: (2005) 2164-2175.
17. Lu S., Sun Y. H., Shi R., Clark C., Li L. and Chiang V. L. Novel and mechanical stress responsive microRNAs in Populus trichocarpa that are absent from Arabidopsis. The PlantCell.17: (2005) 2186-2203.
18. Sunkar R. and Zhu J. K. Novel and stress-regulated microRNAs and other small RNAs from Arabidopsis. The Plant Cell.16: (2004) 2001-2019.
19. Johnson S. M., Grosshansm H., Shingara J., Byrom M., Jarvis R., Cheng A., Labourier E., Reinert K. L., Brown D. and Slack F.J. RAS is regulated by the let-7 microRNA family. Cell.120(5): (2005) 635-647.
20. Bennasser Y., Le S.Y., Yeung M. L. and Jeang K. T., HIV-1 encoded candidate micro-RNAs and their cellular targets. Retro viro.1(1):(2004) 43.
21. Reinhart B. J., Weinstein E. G., Rhoades M. W., Bartel B. and Bartel D. P. MicroRNAs in plants. Genes Dev. 16: (2002) 1616-1626.
22. Mario A.V., Juan C.P. and Jean-Philippe V.C. A Family of MicroRNAs Present in Plants and Animals. Plant Cell.18: (2006) 3355-3369.
23. Barozai M.Y.K., Irfan M., Yousaf R., Ali I., Qaisar U., Maqbool A., Zahoor M., Rashid B., Hussnain T., and Riazuddin S. Identification of micro-RNAs in cotton. Plant Physiol and Biochem. 46 (8-9): (2008) 739-51.
24. Zhang B., Pan X., Cannon C. H., Cobb G. P. and Anderson T.A., Conservation and divergence ofplant microRNA genes. The Plant J. 46: (2006) 243-259.
25. Griffiths-Jones S. The microRNA Registry. Nucleic Acids Res. 32D: (2004) 109-111.
26. Altschul S. F. Gish W., Miller W., Myers E.W and Lipman D. J. Basic local alignment search tool. J. Mol. Biol. 215: (1990) 403-410.
27. Stephen F. A., Madden T. L., Schäffer A. A., Zhang J., Zhang Z., Miller W. and Lipman D. J. Gapped BLAST and PSI-BLAST, A new generation of protein database search programs. Nucleic Acids Res. 25: (1997) 3389-3402.
28. Zuker M. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res. 31: (2003) 3406-3415.
29. Li S. C., Pan C.U. and Lin W.C. Bioinformatic discovery of microRNA precursors from human ESTs and introns. BMC Gen. 7: (2006) 164.
30. Crooks G.E., Hon G., Chandonia J. M., Brenner S.E. WebLogo: A sequence logo generator, Gen. Res. 14: (2004)1188-1190.
31. Kruger J and Rehmsmeier M. RNA hybrid: microRNA target prediction easy, fast and flexible Nucl. Acids. Res., 34(2): (2006) 451-454.
32. Zhang B. H., Pan X. P., Wang Q. L., Cobb G. P., Todd A. A. Identification and characterization of new plant microRNAs using EST analysis. Cell Research, 15(5): (2005) 336-360.
33. Yakovlev I. A., Fossdal C. G., Johnsen O. MicroRNAs, the epigenetic memory and climatic adaptation in Norway spruce. New Phytol. 187: (2010) 1154-1169.
34. Ambros V., Bartel B. and Bartel D. P. A uniform system for microRNA annotation. RNA. 9: (2003) 277-279.
35. Meyers B. C., Axtell M. J., Bartel B., et al. Criteria for Annotation of Plant MicroRNAs. The Plant Cell. 20: (2008) 3186-3190.
36. Aili L., and Long M. Evolution of plant microRNA gene families Cell Research 17: (2007) 212-218.