Identification of novel soybean microRNAs involved in abiotic and biotic stresses

BMC Genomics

Volumn 12, Issue , 2011, Pages

  Kulcheski, Franceli R ^a   de Oliveira, Luiz F V ^a   Molina, Lorrayne G ^a   Almerão, Maurício P ^a   Rodrigues, Fabiana A ^b   Marcolino, Juliana ^b   Barbosa, Joice F ^b   Stolf Moreira, Renata ^b   Nepomuceno, Alexandre L ^b   Marcelino Guimarães, Francismar C ^b   Abdelnoor, Ricardo V ^b   Nascimento, Leandro C ^c   Carazzolle, Marcelo F ^c   Pereira, Gonçalo A G ^c   Margis, Rogério ^a  

^a FEDERAL UNIVERSITY OF RIO GRANDE DO SUL   (Brazil)

^b EMBRAPA CERRADOS   (Brazil)

^c UNIVERSITY OF CAMPINAS   (Brazil)

Author keywords

[No Author keywords available]

Indexed keywords

MICRORNA; PLANT RNA;

ABIOTIC STRESS; ARTICLE; BIOTIC STRESS; CONTROLLED STUDY; DOWN REGULATION; DROUGHT RESISTANCE; DROUGHT TOLERANCE; GENE CONSTRUCT; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENE FUNCTION; GENE IDENTIFICATION; GENE LIBRARY; GENETIC CONSERVATION; GENETIC DIFFERENCE; GENETIC SUSCEPTIBILITY; HIGH THROUGHPUT SEQUENCING; NONHUMAN; PROCESS DEVELOPMENT; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RNA ANALYSIS; RNA SEQUENCE; RUST (PLANT DISEASE); SEEDLING; SOYBEAN; UPREGULATION; VALIDATION PROCESS; GENETICS; METABOLISM; NUCLEOTIDE SEQUENCE; PHYSIOLOGICAL STRESS; PLANT LEAF; PLANT ROOT; POLYMERASE CHAIN REACTION; SEQUENCE ANALYSIS;

EUKARYOTA; FUNGI; GLYCINE MAX; MIMOSA;

BASE SEQUENCE; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, PLANT; MICRORNAS; PLANT LEAVES; PLANT ROOTS; POLYMERASE CHAIN REACTION; RNA, PLANT; SEQUENCE ANALYSIS, RNA; SOYBEANS; STRESS, PHYSIOLOGICAL;

EID: 79958123270     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-12-307     Document Type: Article

References (60)

1. Mallory AC, Vaucheret H. Functions of microRNAs and related small RNAs in plants. Nat Genet 2006, 38(Suppl):S31-36.
2. Chen X. MicroRNA biogenesis and function in plants. FEBS Lett 2005, 579(26):5923-5931. 10.1016/j.febslet.2005.07.071, 16144699.
3. Lu YD, Gan QH, Chi XY, Qin S. Roles of microRNA in plant defense and virus offense interaction. Plant Cell Rep 2008, 27(10):1571-1579. 10.1007/s00299-008-0584-z, 18626646.
4. Shukla LI, Chinnusamy V, Sunkar R. The role of microRNAs and other endogenous small RNAs in plant stress responses. Biochim Biophys Acta 2008, 1779(11):743-748.
5. Bartel B, Bartel DP. MicroRNAs: at the root of plant development?. Plant Physiol 2003, 132(2):709-717. 10.1104/pp.103.023630, 523861, 12805599.
6. Bartel DP. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 2004, 116(2):281-297. 10.1016/S0092-8674(04)00045-5, 14744438.
7. Ambros V, Lee RC, Lavanway A, Williams PT, Jewell D. MicroRNAs and other tiny endogenous RNAs in C. elegans. Curr Biol 2003, 13(10):807-818. 10.1016/S0960-9822(03)00287-2, 12747828.
8. Voinnet O. Origin, biogenesis, and activity of plant microRNAs. Cell 2009, 136(4):669-687. 10.1016/j.cell.2009.01.046, 19239888.
9. Bartel DP. MicroRNAs: target recognition and regulatory functions. Cell 2009, 136(2):215-233. 10.1016/j.cell.2009.01.002, 19167326.
10. Guo L, Lu Z. Global expression analysis of miRNA gene cluster and family based on isomiRs from deep sequencing data. Comput Biol Chem 34(3):165-171.
11. Ebhardt HA, Fedynak A, Fahlman RP. Naturally occurring variations in sequence length creates microRNA isoforms that differ in argonaute effector complex specificity. Silence 2010, 1(12).
12. Naya L, Khan GA, Sorin C, Hartmann C, Crespi M, Lelandais-Briere C. Cleavage of a non-conserved target by a specific miR156 isoform in root apexes of Medicago truncatula. Plant Signal Behav 5(3):328-331.
13. Park W, Li J, Song R, Messing J, Chen X. CARPEL FACTORY, a Dicer homolog, and HEN1, a novel protein, act in microRNA metabolism in Arabidopsis thaliana. Curr Biol 2002, 12(17):1484-1495. 10.1016/S0960-9822(02)01017-5, 12225663.
14. Reinhart BJ, Bartel DP. Small RNAs correspond to centromere heterochromatic repeats. Science 2002, 297(5588):1831. 10.1126/science.1077183, 12193644.
15. Griffiths-Jones S. The microRNA Registry. Nucleic Acids Res 2004, (32 Database):D109-111.
16. Griffiths-Jones S. miRBase: the microRNA sequence database. Methods Mol Biol 2006, 342:129-138.
17. Griffiths-Jones S, Grocock RJ, van Dongen S, Bateman A, Enright AJ. miRBase: microRNA sequences, targets and gene nomenclature. Nucleic Acids Res 2006, (34 Database):D140-144.
18. Griffiths-Jones S, Saini HK, van Dongen S, Enright AJ. miRBase: tools for microRNA genomics. Nucleic Acids Res 2008, (36 Database):D154-158.
19. Yang T, Xue L, An L. Functional diversity of miRNA in plants. Plant Science 2007, 172:423-432.
20. Lelandais-Briere C, Sorin C, Declerck M, Benslimane A, Crespi M, Hartmann C. Small RNA diversity in plants and its impact in development. Curr Genomics 11(1):14-23.
21. Liu Q, Chen Y-Q. Insights into the mechanism of plant development: interactions of miRNAs pathway with phytormone response. Biochem Biophys Res Commun 2009, 384:1-5. 10.1016/j.bbrc.2009.04.028, 19366618.
22. Chuck G, Candela H, Hake S. Big impacts by small RNAs in plant development. Curr Opin Plant Biol 2009, 12(1):81-86. 10.1016/j.pbi.2008.09.008, 18980858.
23. Katiyar-Agarwal S, Jin H. Role of small RNAs in host-microbe interactions. Annu Rev Phytopathol 2010, 48:225-246. 10.1146/annurev-phyto-073009-114457, 20687832.
24. Lu XY, Huang XL. Plant miRNAs and abiotic stress responses. Biochem Biophys Res Commun 2008, 368(3):458-462. 10.1016/j.bbrc.2008.02.007, 18267107.
25. Sunkar R, Zhu JK. Novel and stress-regulated microRNAs and other small RNAs from Arabidopsis. Plant Cell 2004, 16(8):2001-2019. 10.1105/tpc.104.022830, 519194, 15258262.
26. Subramanian S, Fu Y, Sunkar R, Barbazuk WB, Zhu JK, Yu O. Novel and nodulation-regulated microRNAs in soybean roots. BMC Genomics 2008, 9:160. 10.1186/1471-2164-9-160, 2335117, 18402695.
27. Zhang B, Pan X, Stellwag EJ. Identification of soybean microRNAs and their targets. Planta 2008, 229(1):161-182. 10.1007/s00425-008-0818-x, 18815805.
28. Wang Y, Li P, Cao X, Wang X, Zhang A, Li X. Identification and expression analysis of miRNAs from nitrogen-fixing soybean nodules. Biochem Biophys Res Commun 2009, 378(4):799-803. 10.1016/j.bbrc.2008.11.140, 19084500.
29. Chen R, Hu Z, Zhang H. Identification of microRNAs in wild soybean (Glycine soja). J Integr Plant Biol 2009, 51(12):1071-1079. 10.1111/j.1744-7909.2009.00887.x, 20021554.
30. Joshi T, Yan Z, Libault M, Jeong DH, Park S, Green PJ, Sherrier DJ, Farmer A, May G, Meyers BC, Xu D, Stacey G. Prediction of novel miRNAs and associated target genes in Glycine max. BMC Bioinformatics 2010, 11(Suppl 1):S14. 10.1186/1471-2105-11-S1-S14, 3024872, 21172049.
31. Song QX, Liu YF, Hu XY, Zhang WK, Ma B, Chen SY, Zhang JS. Identification of miRNAs and their target genes in developing soybean seeds by deep sequencing. BMC Plant Biol 2011, 11:5. 10.1186/1471-2229-11-5, 3023735, 21219599.
32. Desclaux D, Roumet P. Impact of srought stress on the phenology of two soybean cultivars. Field and Crops Research 1996, 46(1-3):61-70.
33. Desclaux D, Huynh TT, Roumet P. Identification of soybean plant characteristics that indicate the timing of drought stress. Crop Science 2000, 40:716-722.
34. Van de Mortel M, Recknor JC, Graham MA, Nettleton D, Dittman JD, Nelson RT, Godoy CV, Abdelnoor RV, Almeida AMR, Baum TJ, Whitham SA. Distinct biphasic mRNA changes in response to Asian soybean rust infection. MPMI 2007, 20(8):887-899. 10.1094/MPMI-20-8-0887, 17722693.
35. Sinclair JB, Hartman GL. Soybean rust. Compendium of soybean diseases 1999, 25-26. St. Paul: American Phytopathological Society, Hartman ea, 4.
36. Yorinori JT, Paiva WM, Frederick RD, Costa Milan LM, Bertagnolli PF, Hartman GL, Godoy CV, Nunes Junior J. Epidemics of soybean rust (Phakopsora pachyrhizi) in Brazil and Paraguay from 2001 to 2003. Plant Dis 2005, 89:675-677.
37. Oya T, Nepomuceno AL, Neumaier N, Farias JRB, Tobita S, Ito O. Drought Tolerance Characteristics of Brazilian soybean cultivars - Evaluation and characterization of drought tolerance of various Brazilian soybean cultivars in the field. Plant Prod Sci 2004, 7(2):129-137.
38. Fehr WR, Caviness CE. Stages of soybean development. Special Report 80. 1977, Ames, USA: Iowa State University of Science and Technology, Iowa Agriculture and Home Economics Experiment Station.
39. Martins PK, Jordão BQ, Yamanaka N, Farias JRB, Beneventi MA, Binneck E, Fuganti R, Stolf R, Nepomuceno AL. Differential gene expression and mitotic cell analysis of the drought tolerant soybean (Glycine max L. Merrill Fabales, Fabaceae) cultivar MG/BR46 (Conquista) under two water deficit induction systems. Genet Mol Biol 2008, 31:512-521.
40. Silva DCG, Yamanaka N, Brogin RL, Arias CAA, Nepomuceno AL, Di Mauro AO, Pereira SS, Nogueira LM, Passianotto ALL, Abdelnoor RV. Molecular mapping of two loci that confer resistance to Asian Rust in soybean. Theor Appl Genet 2008, 117:57-63. 10.1007/s00122-008-0752-0, 18392802.
41. Li R, Li Y, Kristiansen K, Wang J. SOAP: short oligonucleotide alignment program. Bioinformatics 2008, 24(5):713-714. 10.1093/bioinformatics/btn025, 18227114.
42. Smith TF, Waterman MS. Identification of common molecular subsequences. J Mol Biol 1981, 147(1):195-197. 10.1016/0022-2836(81)90087-5, 7265238.
43. Meyers BC, Axtell MJ, Bartel B, Bartel DP, Baulcombe D, Bowman JL, Cao X, Carrington JC, Chen X, Green PJ, Griffiths-Jones S, Jacobsen SE, Mallory AC, Martienssen RA, Poethig RS, Qi Y, Vaucheret H, Voinnet O, Watanabe Y, Weigel D, Zhu JK. Criteria for annotation of plant MicroRNAs. Plant Cell 2008, 20(12):3186-3190. 10.1105/tpc.108.064311, 2630443, 19074682.
44. Zuker M. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res 2003, 31(13):3406-3415. 10.1093/nar/gkg595, 169194, 12824337.
45. Chen C, Ridzon DA, Broomer AJ, Zhou Z, Lee DH, Nguyen JT, Barbisin M, Xu NL, Mahuvakar VR, Andersen MR, Lao KQ, Livak KJ, Guegler KJ. Real-time quantification of microRNAs by stem-loop RT-PCR. Nucleic Acids Res 2005, 33(20):e179. 10.1093/nar/gni178, 1292995, 16314309.
46. Kulcheski FR, Marcelino-Guimaraes FC, Nepomuceno AL, Abdelnoor RV, Margis R. The use of microRNAs as reference genes for quantitative polymerase chain reaction in soybean. Anal Biochem 2010, 406(2):185-192. 10.1016/j.ab.2010.07.020, 20670612.
47. Zhang Y. miRU: an automated plant miRNA target prediction server. Nucleic Acids Res 2005, (33 Web Server):W701-704.
48. Du Z, Zhou X, Ling Y, Zhang Z, Su Z. agriGO: a GO analysis toolkit for the agricultural community. Nucleic Acids Res 2010, (38 Web Server):W64-70.
49. Jones-Rhoades MW, Bartel DP. Computational identification of plant microRNAs and their targets, including a stress-induced miRNA. Mol Cell 2004, 14(6):787-799. 10.1016/j.molcel.2004.05.027, 15200956.
50. Zhou L, Liu Y, Liu Z, Kong D, Duan M, Luo L. Genome-wide identification and analysis of drought-responsive microRNAs in Oryza sativa. J Exp Bot 2010, 61(15):4157-4168. 10.1093/jxb/erq237, 20729483.
51. Kantar M, Unver T, Budak H. Regulation of barley miRNAs upon dehydration stress correlated with target gene expression. Funct Integr Genomics 2010, 10(4):493-507. 10.1007/s10142-010-0181-4, 20676715.
52. Lu Y, Yang X. Computational Identification of Novel MicroRNAs and Their Targets in Vigna unguiculata. Comp Funct Genomics 2010,
53. Zang YX, Kim HU, Kim JA, Lim MH, Jin M, Lee SC, Kwon SJ, Lee SI, Hong JK, Park TH, Mun JH, Seol YJ, Hong SB, Park BS. Genome-wide identification of glucosinolate synthesis genes in Brassica rapa. FEBS J 2009, 276(13):3559-3574. 10.1111/j.1742-4658.2009.07076.x, 19456863.
54. Ramanjulu S, Bartels D. Drought- and desiccation-induced modulation of gene expression in plants. Plant Cell Environ 2002, 25(2):141-151. 10.1046/j.0016-8025.2001.00764.x, 11841659.
55. Axtell MJ, Snyder JA, Bartel DP. Common functions for diverse small RNAs of land plants. Plant Cell 2007, 19(6):1750-1769. 10.1105/tpc.107.051706, 1955733, 17601824.
56. Rajagopalan R, Vaucheret H, Trejo J, Bartel DP. A diverse and evolutionarily fluid set of microRNAs in Arabidopsis thaliana. Genes Dev 2006, 20(24):3407-3425. 10.1101/gad.1476406, 1698448, 17182867.
57. Choi JJ, Alkharouf NW, Schneider KT, Matthews BF, Frederick RD. Expression patterns in soybean resistant to Phakopsora pachyrhizi reveal the importance of peroxidases and lipoxygenases. Funct Integr Genomics 2008, 8(4):341-359. 10.1007/s10142-008-0080-0, 18414911.
58. Konishi H, Yamane H, Maeshima M, Komatsu S. Characterization of fructose-bisphosphate aldolase regulated by gibberellin in roots of rice seedling. Plant Mol Biol 2004, 56(6):839-848. 10.1007/s11103-004-5920-2, 15821984.
59. Belkhadir Y, Subramaniam R, Dangl JL. Plant disease resistance protein signaling: NBS-LRR proteins and their partners. Curr Opin Plant Biol 2004, 7(4):391-399. 10.1016/j.pbi.2004.05.009, 15231261.
60. Moffett P, Farnham G, Peart J, Baulcombe DC. Interaction between domains of a plant NBS-LRR protein in disease resistance-related cell death. EMBO J 2002, 21(17):4511-4519. 10.1093/emboj/cdf453, 126192, 12198153.