Identification and validation of asteraceae mirnas by the expressed sequence tag analysis

Gene

Volumn 493, Issue 2, 2012, Pages 253-259

  Monavar Feshani, Aboozar ^a   Mohammadi, Saeed ^a   Frazier, Taylor P ^b   Abbasi, Abbas ^a   Abedini, Raha ^a   Karimi Farsad, Laleh ^a   Ehya, Farveh ^a   Hosseini Salekdeh, Ghasem ^a   Mardi, Mohsen ^a  

^a Agricultural Biotechnology Research Institute of Iran   (Iran)

^b VIRGINIA POLYTECHNIC INSTITUTE AND STATE UNIVERSITY   (United States)

Author keywords

Asteraceae; MicroRNA; QRT PCR; Safflower; Sunflower

Indexed keywords

MICRORNA;

ARTICLE; ASTERACEAE; CONTROLLED STUDY; COTYLEDON; CROP; EXPRESSED SEQUENCE TAG; GENE EXPRESSION; GENE EXPRESSION REGULATION; GENE IDENTIFICATION; GERMINATION; HELIANTHUS ANNUUS; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; QUANTITATIVE ANALYSIS; REAL TIME POLYMERASE CHAIN REACTION; SAFFLOWER; SEEDLING; VEGETATIVE STAGE;

ASTERACEAE; BASE SEQUENCE; CARTHAMUS TINCTORIUS; CONSERVED SEQUENCE; COTYLEDON; EXPRESSED SEQUENCE TAGS; GENE EXPRESSION REGULATION, PLANT; GERMINATION; HELIANTHUS; MICRORNAS; MOLECULAR SEQUENCE DATA; REAL-TIME POLYMERASE CHAIN REACTION; RNA, PLANT;

ASTERACEAE; CARTHAMUS TINCTORIUS; COTYLEDON (GENUS); HELIANTHUS; HELIANTHUS ANNUUS; MAGNOLIOPHYTA;

EID: 84855851052     PISSN: 03781119     EISSN: 18790038     Source Type: Journal    
DOI: 10.1016/j.gene.2011.11.024     Document Type: Article

References (48)

1. Adai A., et al. Computational prediction of miRNAs in Arabidopsis thaliana. Genome Res. 2005, 15:78-91.
2. Bartel D.P. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 2004, 116:281-297.
3. Carrington J.C., Ambros V. Role of microRNAs in plant and animal development. Science 2003, 301:336-338.
4. Chen X. miRNA as a translational repressor of APETALA2 in Arabidopsis flower development. Science 2004, 303:2022-2025.
5. Chen C., et al. Real-time quantification of microRNAs by stem-loop RT-PCR. Nucleic Acids Res. 2005, 33(20):179.
6. Dai X., Zhuang Z., Zhao P.X. Computational analysis of miRNA targets in plants: current status and challenges. Brief. Bioinform. 2010, 12:115-121. http://bioinfo3.noble.org/psRNATarget.
7. Fattash I., Voss B., Reski R., Hess W.R., Frank W. Evidence for the rapid expansion of microRNA-mediated regulation in early land plant evolution. BMC Plant Biol. 2007, 7:13.
8. Frazier T.P., Zhang B.H. Identification of plant microRNAs using expressed sequence tag analysis. Methods Mol. Biol. 2011, 678:13-25.
9. Frazier T.P., Xie F., Freistaedter A., Burklew C.E., Zhang B. Identification and characterization of microRNAs and their target genes in tobacco (Nicotiana tabacum). Planta 2010, 232:1289-1308.
10. Frazier T.P., Sun G., Burklew C.E., Zhang B.H. Salt and drought stresses induce the aberrant expression of microRNA genes in tobacco. Mol. Biotechnol 2011, 10.1007/s12033-011-9387-5.
11. Funk V.A., et al. Everywhere but Antarctica: using a supertree to understand the diversity and distribution of the Compositae. Biol. Skr. 2005, 55:343-374.
12. Griffiths-Jones S., Saini H.K., van Dongen S., Enright A.J. miRBase: tools for microRNA genomics. Nucleic Acids Res. 2008, 36(Database Issue):D154-D158. http://www.mirbase.org.
13. Han Y., et al. Conserved miRNAs and their targets identified in lettuce (Lactuca) by EST analysis. Gene 2010, 463:1-7.
14. Jagadeeswaran G., Saini A., Sunkar R. Biotic and abiotic stress downregulate miR398 expression in Arabidopsis. Planta 2009, 229:1009-1014.
15. Jeffrey C. q Compositae. Mansfeld's encyclopedia of agricultural and horticultural crops 2001, vol. 4:2035-2145. Springer, Berlin-Heidelberg-New York.
16. Jones-Rhoades M.W., Bartel D.P. Computational identification of plant microRNAs and their targets, including a stress-induced miRNA. Mol. Cell 2004, 14:787-799.
17. 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.
18. Kim J.H., Choi D., Kende H. The AtGRF family of putative transcription factors is involved in leaf and cotyledon growth in Arabidopsis. Plant J. 2003, 36:94-104.
19. Kwak P.B., Wang Q.Q., Chen X.S., Qiu1 C.X., Yang Z.M. Enrichment of a set of microRNAs during the cotton fiber development. BMC Genomics 2009, 10:457.
20. Lewis R., Mendu V., McNear D., Tang G. Roles of microRNAs in plant abiotic stress. Molecular Techniques in Crop Improvement 2009, 357-372. Springer, Netherlands. 2nd edn. S. Mohan Jain, D.S. Brar (Eds.).
21. Li H., et al. Investigation of the microRNAs in safflower seed, leaf, and petal by high-throughput sequencing. Planta 2010, 233:611-619.
22. Liu P.P., Montgomery T.A., Fahlgren N., Kasschau K.D., Nonogaki H., Carrington J.C. Repression of AUXIN RESPONSE FACTOR10 by microRNA160 is critical for seed germination and post-germination stages. Plant J. 2007, 52:133-146.
23. Llave C., Xie Z., Kasschau K.D., Carrington J.C. Cleavage of Scarecrow-like mRNA targets directed by a class of Arabidopsis miRNA. Science 2002, 297:2053-2056.
24. Lu S., Sun Y.H., Chiang V.L. Stress-responsive microRNAs in Populus. Plant J. 2008, 55:131-151.
25. Markham N.R., Zuker M. DINAMelt web server for nucleic acid melting prediction. Nucleic Acids Res. 2005, 33:W577-W581.
26. Merchan F., Boualem A., Crespi M., Frugier F. Plant polycistronic precursors containing non-homologous microRNAs target transcripts encoding functionally related proteins. Genome Biol. 2009, 10:R136.
27. Meyers B.C., et al. Criteria for annotation of plant MicroRNAs. Plant Cell 2008, 20:3186-3190.
28. Mica E., et al. High throughput approaches reveal splicing of primary microRNA transcripts and tissue specific expression of mature microRNAs in Vitis vinifera. BMC Genomics 2009, 10:558.
29. Pfaffl M.W. A new mathematical model for relative quantification in real-time RT-PCR. Nucleic Acids Res. 2001, 29:2002-2007.
30. Phillips J.R., Dalmay T., Bartels D. The role of small RNAs in abiotic stress. FEBS Lett. 2007, 581:3592-3597.
31. Stevens P.F. Angiosperm Phylogeny Website. Version 9, 2011 http://www.mobot.org/MOBOT/research/APweb/.
32. Sunkar R., Jagadeeswaran G. In silico identification of conserved microRNAs in large number of diverse plant species. BMC Plant Biol. 2008, 8:37.
33. Sunkar R., Girke T., Jain P.K., Zhu J.K. Cloning and characterization of microRNAs from rice. Plant Cell 2005, 17:1397-1411.
34. Tyler D.M., et al. Functionally distinct regulatory RNAs generated by bidirectional transcription and processing of microRNA loci. Genes Dev. 2008, 22:26-36.
35. Unver T., Budak H. Conserved microRNAs and their targets in model grass species Brachypodium distachyon. Planta 2009, 230:659-669.
36. Unver T., Namuth-Covert D.M., Budak H. Review of current methodological approaches for characterizing MicroRNAs in plants. Int. J. Plant Genomics 2009, 2009:262463.
37. Varkonyi-Gasic E., Wu R., Wood M., Walton E.F., Hellens R.P. Protocol: a highly sensitive RT-PCR method for detection and quantification of microRNAs. Plant Methods 2007, 3:1-12.
38. Voinnet O. Origin, biogenesis, and activity of plant microRNAs. Cell 2009, 136:669-687.
39. Xie F., Frazier T.P., Zhang B. Identification, characterization and expression analysis of MicroRNAs and their targets in the potato (Solanum tuberosum). Gene 2010, 473:8-22.
40. Xie F., Frazier T.P., Zhang B.H. Identification and characterization of microRNAs and their targets in the bioenergy plant switchgrass (Panicum virgatum). Planta 2010, 232:417-434.
41. Xue X., Sun J., Zhang O., Wang Z., Huang Y., Pan W. Identification and characterization of novel MicroRNAs from Schistosoma japonicum. PLoS One 2008, 3(12):e4034.
42. Yang T., Xue L., An L. Functional diversity of miRNA in plants. Plant Sci. 2007, 172:423-432.
43. Yin Z., Li C., Han X., Shen F. Identification of conserved microRNAs and their target genes in tomato (Lycopersicon esculentum). Gene 2008, 414:60-66.
44. Zhang B.H., Pan X.P., Wang Q.L., Cobb G.P., Anderson T.A. Identification and characterization of new plant microRNAs using EST analysis. Cell Res. 2005, 15:336-360.
45. Zhang B.H., Pan X., Cobb G.P., Anderson T.A. Plant microRNA: a small regulatory molecule with big impact. Dev. Biol. 2006, 289:3-16.
46. Zhang B.H., Pan X., Cannon C.H., Cobb G.P., Anderson T.A. Conservation and divergence of plant microRNA genes. Plant J. 2006, 46:243-259.
47. Zhang B.H., Pan X.P., Cox S.B., Cobb G.P., Anderson T.A. Evidence that miRNAs are different from other RNAs. Cell. Mol. Life Sci. 2006, 63:246-254.
48. Zhang B.H., Pan X.P., Stellwag E.J. Identification of soybean microRNAs and their targets. Planta 2008, 229:161-182.