Genome-wide profiling and analysis of Festuca arundinacea miRNAs and transcriptomes in response to foliar glyphosate application

Molecular Genetics and Genomics

Volumn 283, Issue 4, 2010, Pages 397-413

  Unver, Turgay ^a   Bakar, Mine ^a   Shearman, Robert C ^b   Budak, Hikmet ^a  

^a SABANCI UNIVERSITY   (Turkey)

^b UNIVERSITY OF NEBRASKA LINCOLN   (United States)

Author keywords

Affymetrix; Festuca arundinecea; GeneChip wheat genome array; Glyphosate; MiRNA; Transcriptome analyses

Indexed keywords

GLYPHOSATE; MICRORNA; RIBOSOME PROTEIN; TRANSCRIPTOME; DRUG DERIVATIVE; GLYCINE;

ARTICLE; CONTROLLED STUDY; DOWN REGULATION; FUNCTIONAL GENOMICS; GENE EXPRESSION PROFILING; GENOME ANALYSIS; HERBICIDE TOLERANCE; MICROARRAY ANALYSIS; NONHUMAN; NUCLEOTIDE SEQUENCE; PLANT GENOME; PRIORITY JOURNAL; PROTEIN SECONDARY STRUCTURE; REAL TIME POLYMERASE CHAIN REACTION; TALL FESCUE; UPREGULATION; CHEMICAL STRUCTURE; CHEMISTRY; CONFORMATION; DRUG EFFECT; FESCUE; GENE EXPRESSION REGULATION; GENETIC ASSOCIATION; GENETIC TRANSCRIPTION; GENETICS;

FALCONIDAE; FESTUCA; FESTUCA ARUNDINACEA; OSA; POACEAE; TRITICUM AESTIVUM;

BASE SEQUENCE; FESTUCA; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, PLANT; GENOME-WIDE ASSOCIATION STUDY; GLYCINE; MICRORNAS; MODELS, MOLECULAR; NUCLEIC ACID CONFORMATION; TRANSCRIPTION, GENETIC;

EID: 77949885564     PISSN: 16174615     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00438-010-0526-7     Document Type: Article

References (46)

1. Altschul SF, Madden TL, Schaffer AA, Zhang JH, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSIBLAST: a new generation of protein database search programs. Nucl Acids Res 25:3389-3402. doi:10.1093/nar/25.17.3389
2. Antony C, Cibert C, Géraud G, Santa Maria A, Maro B, Mayau V, Goud B (1992) The small GTP-binding protein rab6p is distributed from medial Golgi to the trans-Golgi network as determined by a confocal microscopic approach. J Cell Sci 103:785-796
3. Bartel DP (2004) MicroRNAs: genomics, biogenesis, mechanism, and function, Cell 116:281-197. doi:10.1016/S0092-8674(04)00045-5
4. Bartel B, Bartel DP (2003) MicroRNAs: at the root of plant development? Plant Physiol 132:709-717. doi:10.1104/pp.103. 023630
5. Baylis AD (2000) Why glyphosate is a global herbicide: strengths, weaknesses and prospects. Pest Manag Sci 56:299-308. doi: 10.1002/(SICI)1526- 4998(200004)56:4\299:AID-PS144[3.3.CO;2-B
6. Bonnet E, Wuyts J, Rouze P, Van de Peer Y (2004) Detection of 91 potential conserved plant microRNAs in Arabidopsis thaliana and Oryza sativa identifies important target genes. Proc Natl Acad Sci USA 101:11511-11516. doi:10.1073/pnas.0404025101
7. Budak H, Shearman RC, Parmaksiz I, Dweikat I (2004a) Comparative analysis of seeded and vegetative biotype buffalograsses based on phylogenetic relationship using ISSRs, SSRs, RAPDs, and SRAPs. Theor Appl Genet 109:280-288. doi:10.1007/s00122-004-1630-z
8. Budak H, Shearman RC, Parmaksiz I, Gaussoin RE, Riordan TP, Dweikat I (2004b) Molecular characterization of Buffalograss germplasm using sequence-related amplified polymorphism markers. Theor Appl Genet 108:328-334. doi:10.1007/s00122-003-1428-4
9. Budak H, Shearman RC, Gulsen O, Dweikat I (2005) Understanding ploidy complex and geographic origin of Buchloe dactyloides genome using cytoplasmic and nuclear marker systems. Theor Appl Genet 111:1545-1552. doi:10.1007/s00122- 005-0083-3
10. Budak H, Kasap Z, Shearman RC, Dweikat I, Sezerman U, Mahmood A (2006a) Molecular characterization of cDNA encoding resistance gene-like sequences in Buchloe dactyolides. Mol Biotechnol 34:293-301. doi:10.1385/MB:34:3:293
11. Budak H, Su S, Ergen N (2006b) Revealing constitutively expressed resistance genes in Agrostis species using PCR-based motif directed RNA fingerprinting. Genet Res 88:165-175. doi: 10.1017/S0016672307008518
12. Cebeci O, Budak H (2009) Global expression patterns of three Festuca species exposed to different doses of glyphosate using the Affymetrix GeneChip Wheat Genome Array. Comp Funct Genomics 2009:1-10. doi:10.1155/2009/505701
13. Cebeci O, Kokturk B, Ergen N, Ozturk L, Cakmak I, Budak H (2008) Differential expression of wheat transcriptomes in response to varying cadmium concentrations. Biol Plant 52:703-708. doi: 10.1007/s10535-008-0135-z
14. Devoto A, Muskett PR, Shirasu K (2003) Role of ubiquitination in the regulation of plant defense against pathogens. Curr Opin Plant Biol 6:307-311. doi:10.1016/S1369-5266(03)00060-8
15. Dinler G, Budak H (2008) Analysis of expressed sequence tags (ESTs) from Agrostis species obtained using sequence related amplified polymorphism. Biochem Genet 46:663-676. doi: 10.1007/s10528-008-9181-7
16. Eisen MB, Spellman PT, Brown PO, Botstein D (1998) Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci USA 95:14863-14868. doi:10.1073/pnas.95.25. 14863
17. Ergen NZ, Budak H (2009) Sequencing over 13 000 expressed sequence tags from six subtractive cDNA libraries of wild and modern wheats following slow drought stress. Plant Cell Environ 32:220-236. doi:10.1111/j.1365-3040.2008. 01915.x
18. Ergen ZN, Dinler G, Shearman R, Budak H (2007) Identifying, cloning and structural analysis of differentially expressed genes upon Puccinia infection of Festuca rubra var. rubra. Gene 393:145-152. doi:10.1016/j.gene.2007.02.005
19. Ergen NZ, Thimmapuram J, Bohnert HJ, Budak H (2009) Transcriptome pathways unique to dehydration tolerant relatives of modern wheat. Funct Integr Genomics 9:377-396. doi:10.1007/ s10142-009-0123-1
20. Ganesan G, Sankararamasubramanian HM, Narayanan JM, Sivaprakash KR, Parida A (2008) Transcript level characterization of a cDNA encoding stress regulated NAC transcription factor in the mangrove plant Avicennia marina. Plant Physiol Biochem 46:928-934. doi:10.1016/j.plaphy.2008.05.002
21. Geiger DR, Kapitan SW, Tucci MA (1986) Glyphosate inhibits photosynthesis and allocation of carbon to starch in sugar beet leaves. Plant Physiol 82:468-472. doi:10.1104/pp.82.2.468
22. Goud B, Zahraoui A, Tavitian A, Saraste J (1990) Small GTP-binding protein associated with Golgi cisternae. Nature 7:553-556. doi: 10.1038/345553a0
23. Haizel T, Thomas M, Franziska T, Ferenc N (1995) Characterization of membrane-bound small CTP-binding proteins from Nicotiana tabacum. Plant Physiol 108:59-67. doi:10.1104/pp.108.1.59
24. Hammond SM, Bernstein E, Beach D, Hannon GJ (2000) An RNAdirected nuclease mediates post-transcriptional gene silencing in Drosophila cells. Nature 404:293-296. doi:10.1038/35005107
25. Jones-Rhoades MW, Bartel DP (2004) Computational identification of plant micro-RNAs and their targets, including a stress-induced miRNA. Mol. Cell 14:787-799. doi:10.1016/j.molcel.2004.05.027
26. Jurca ME, Bottka S, Fehér A (2008) Characterization of a family of Arabidopsis receptor-like cytoplasmic kinases (RLCK class VI). Plant Cell Rep 4:739-748. doi:10.1007/s00299-007-0494-5
27. Kim HS, Delaney TP (2002) Arabidopsis SON1 is an F-box protein that regulates a novel induced defense response independent of both salicylic acid and systemic acquired resistance. Plant Cell 14:1469-1482. doi:10.1105/tpc. 001867
28. Kim KY, Park SW, Chung YS, Chung CH, Kim JI, Lee JH (2004) Molecular cloning of low-temperature-inducible ribosomal proteins from soybean. J Exp Bot 55:1153-1155. doi:10.1093/jxb/erh125
29. Kitchen LM, Witt WW, Rieck CE (1981) Inhibition of deltaaminolevulinic acid synthesis by glyphosate. Weed Sci 29:571-577
30. Llave C, Xie Z, Kasschau KD, Carrington JC (2002) Cleavage of Scarecrow-like mRNA targets directed by a class of Arabidopsis miRNA. Science 297:2056. doi:10.1126/science.1076311
31. Mallory AC, Reinhart BJ, Jones-Rhoades MW, Tang G, Zamore PD, Barton MK, Bartel DP (2004) MicroRNA control of PHABULOSA in leaf development: importance of pairing to the microRNA 50 region. EMBO J 23:3356-3364. doi:10.1038/sj.emboj. 7600340
32. Mette MF, Aufsatz W, Kanno T, Daxinger L, Rovina P, Matzke M, Matzke AJ (2005) Analysis of double-stranded RNA and small RNAs involved in RNA-mediated transcriptional gene silencing. Methods Mol Biol 309:61-82
33. Palme K, Diefenthal T, Moore I (1993) Theypt gene family from maize and Arabidopsis: structural and functional analysis. J Exp Bot 44:183-195
34. Raman S, Greb T, Peaucelle A, Blein T, Laufs P, Theres K (2008) Interplay of miR164, CUP-SHAPED COTYLEDON genes and LATERAL SUPPRESSOR controls axillary meristem formation in Arabidopsis thaliana. Plant J. 55:65-76. doi:10.1111/j.1365-313X.2008.03483.x
35. Reichman JR, Watrud LS, Lee EH, Burdick CA, Bollman MA, Storm MJ, King GA, Mallory-Smith C (2006) Establishment of transgenic herbicide-resistant creeping bentgrass (Agrostis stolonifera L.) in nonagronomic habitats. Mol Ecol 15:4243-4255. doi:10.1111/j.1365-294X.2006.03072.x
36. Reinhart BJ, Weinstein EG, Rhoades MW, Bartel B, Bartel DP (2002) MicroRNAs in plants. Genes Dev 16:1616-1626. doi:10.1101/ gad.1004402
37. Rodriguez-Concepcion M, Fores O, Martinez-Garcia JF, Gonzalez V, Philips MA, Ferrer A, Boronot A (2004) Distinct light mediated pathways regulated the biosynthesis and exchange of isoprenoid precursors during Arabidopsis seedling development. Plant Cell 16:144-156. doi:10.1105/tpc.016204
38. Sergiev IG, Alexieva VS, Ivanov SV, Moskova II, Karanov EN (2006) The phenylurea cytokinin 4PU-30 protects maize plants against glyphosate action. Pestic Biochem Physiol 85:139-146. doi:10.1016/j.pestbp.2006.01.001
39. Servaites JC, Tucci MA, Geiger DR (1987) Glyphosate effects on carbon assimilation, ribulose bisphosphate carboxylase activity, and metabolite levels in sugar beet leaves. Plant Physiol 85:370-374. doi:10.1104/pp.85.2.370
40. Su YS, Ozturk L, Cakmak I, Budak H (2009) Turfgrass species response exposed to increasing rates of glyphosate application. Eur J Agron 31:120-125. doi:10.1016/j.eja.2009.05.011
41. Unver T, Budak H (2009) Conserved microRNAs and their targets in model grass species Brachypodium distachyon. Planta 4:659-669. doi:10.1007/s00425-009- 0974-7
42. Unver T, Bozkurt O, Akkaya MS (2008) Identification of differentially expressed transcripts from leaves of the boron tolerant plant Gypsophila perfoliata L. Plant Cell Rep 27:1411-1422. doi:10.1007/s00299-008-0560-7
43. Unver T, Namuth-Covert DM, Budak H (2009) Review of current methodological approaches for characterizing microRNAs in plants. Int J Plant Genomics 262463. doi:10.1155/2009/262463
44. Varkonyi-Gasic E, Wu R, Wood M, Walton EF, Hellens RP (2007) Protocol: a highly sensitive RT-PCR method for detection and quantification of microRNAs. Plant Methods 3:1-12. doi: 10.1186/1746-4811-3-12
45. Zhang BH, Pan XP, Wang QL, Cobb GP, Anderson TA (2005) Identification and characterization of new plant microRNAs using EST analysis. Cell Res. 15:336-360. doi:10.1038/sj.cr.7290302
46. Zhang BH, Pan XP, Cannon CH, Cobb GP, Anderson TA (2006) Conservation and divergence of plant microRNA genes. Plant J. 46:243-259. doi:10.1111/j.1365- 313X.2006.02697.x