메뉴 건너뛰기




Volumn 7, Issue 10, 2012, Pages

Identification of Novel Oryza sativa miRNAs in Deep Sequencing-Based Small RNA Libraries of Rice Infected with Rice Stripe Virus

Author keywords

[No Author keywords available]

Indexed keywords

MICRORNA; RNA PRECURSOR; SMALL INTERFERING RNA; VIRUS RNA;

EID: 84867391567     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0046443     Document Type: Article
Times cited : (54)

References (52)
  • 1
    • 60149086351 scopus 로고    scopus 로고
    • Origin, biogenesis, and activity of plant microRNAs
    • Voinnet O, (2009) Origin, biogenesis, and activity of plant microRNAs. Cell 136: 669-687.
    • (2009) Cell , vol.136 , pp. 669-687
    • Voinnet, O.1
  • 2
    • 0038299558 scopus 로고    scopus 로고
    • Role of microRNAs in plant and animal development
    • Carrington JC, Ambros V, (2003) Role of microRNAs in plant and animal development. Science 301: 336-338.
    • (2003) Science , vol.301 , pp. 336-338
    • Carrington, J.C.1    Ambros, V.2
  • 3
    • 0037144457 scopus 로고    scopus 로고
    • Cleavage of Scarecrow-like mRNA targets directed by a class of Arabidopsis miRNA
    • Llave C, Xie Z, Kasschau KD, Carrington JC, (2002) Cleavage of Scarecrow-like mRNA targets directed by a class of Arabidopsis miRNA. Science 297: 2053-2056.
    • (2002) Science , vol.297 , pp. 2053-2056
    • Llave, C.1    Xie, Z.2    Kasschau, K.D.3    Carrington, J.C.4
  • 5
    • 0347444723 scopus 로고    scopus 로고
    • MicroRNAs: genomics, biogenesis, mechanism, and function
    • Bartel DP, (2004) MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116: 281-297.
    • (2004) Cell , vol.116 , pp. 281-297
    • Bartel, D.P.1
  • 6
    • 0142165224 scopus 로고    scopus 로고
    • Functional siRNAs and miRNAs exhibit strand bias
    • Khvorova A, Reynolds A, Jayasena SD, (2003) Functional siRNAs and miRNAs exhibit strand bias. Cell 115: 209-216.
    • (2003) Cell , vol.115 , pp. 209-216
    • Khvorova, A.1    Reynolds, A.2    Jayasena, S.D.3
  • 7
    • 27744596243 scopus 로고    scopus 로고
    • Control of root cap formation by MicroRNA-targeted auxin response factors in Arabidopsis
    • Wang JW, Wang LJ, Mao YB, Cai WJ, Xue HW, et al. (2005) Control of root cap formation by MicroRNA-targeted auxin response factors in Arabidopsis. Plant Cell 17: 2204-2216.
    • (2005) Plant Cell , vol.17 , pp. 2204-2216
    • Wang, J.W.1    Wang, L.J.2    Mao, Y.B.3    Cai, W.J.4    Xue, H.W.5
  • 11
    • 24944510549 scopus 로고    scopus 로고
    • MicroRNA directs mRNA cleavage of the transcription factor NAC1 to downregulate auxin signals for arabidopsis lateral root development
    • Guo HS, Xie Q, Fei JF, Chua NH, (2005) MicroRNA directs mRNA cleavage of the transcription factor NAC1 to downregulate auxin signals for arabidopsis lateral root development. Plant Cell 17: 1376-1386.
    • (2005) Plant Cell , vol.17 , pp. 1376-1386
    • Guo, H.S.1    Xie, Q.2    Fei, J.F.3    Chua, N.H.4
  • 12
    • 1642366133 scopus 로고    scopus 로고
    • A microRNA as a translational repressor of APETALA2 in Arabidopsis flower development
    • Chen X, (2004) A microRNA as a translational repressor of APETALA2 in Arabidopsis flower development. Science 303: 2022-2025.
    • (2004) Science , vol.303 , pp. 2022-2025
    • Chen, X.1
  • 13
    • 33144478111 scopus 로고    scopus 로고
    • MicroRNA-guided processing impairs Plum pox virus replication, but the virus readily evolves to escape this silencing mechanism
    • Simon-Mateo C, Garcia JA, (2006) MicroRNA-guided processing impairs Plum pox virus replication, but the virus readily evolves to escape this silencing mechanism. J Virol 80: 2429-2436.
    • (2006) J Virol , vol.80 , pp. 2429-2436
    • Simon-Mateo, C.1    Garcia, J.A.2
  • 15
    • 68149141334 scopus 로고    scopus 로고
    • Host small RNAs are big contributors to plant innate immunity
    • Padmanabhan C, Zhang X, Jin H, (2009) Host small RNAs are big contributors to plant innate immunity. Curr Opin Plant Biol 12: 465-472.
    • (2009) Curr Opin Plant Biol , vol.12 , pp. 465-472
    • Padmanabhan, C.1    Zhang, X.2    Jin, H.3
  • 16
    • 51749111395 scopus 로고    scopus 로고
    • Roles of microRNA in plant defense and virus offense interaction
    • Lu YD, Gan QH, Chi XY, Qin S, (2008) Roles of microRNA in plant defense and virus offense interaction. Plant Cell Rep 27: 1571-1579.
    • (2008) Plant Cell Rep , vol.27 , pp. 1571-1579
    • Lu, Y.D.1    Gan, Q.H.2    Chi, X.Y.3    Qin, S.4
  • 17
    • 33645967758 scopus 로고    scopus 로고
    • A plant miRNA contributes to antibacterial resistance by repressing auxin signaling
    • Navarro L, Dunoyer P, Jay F, Arnold B, Dharmasiri N, et al. (2006) A plant miRNA contributes to antibacterial resistance by repressing auxin signaling. Science 312: 436-439.
    • (2006) Science , vol.312 , pp. 436-439
    • Navarro, L.1    Dunoyer, P.2    Jay, F.3    Arnold, B.4    Dharmasiri, N.5
  • 18
    • 78651293534 scopus 로고    scopus 로고
    • miRBase: integrating microRNA annotation and deep-sequencing data
    • Kozomara A, Griffiths-Jones S, (2011) miRBase: integrating microRNA annotation and deep-sequencing data. Nucleic Acids Res 39: D152-157.
    • (2011) Nucleic Acids Res , vol.39
    • Kozomara, A.1    Griffiths-Jones, S.2
  • 19
    • 34547115664 scopus 로고    scopus 로고
    • High-throughput sequencing of Arabidopsis microRNAs: evidence for frequent birth and death of MIRNA genes
    • Fahlgren N, Howell MD, Kasschau KD, Chapman EJ, Sullivan CM, et al. (2007) High-throughput sequencing of Arabidopsis microRNAs: evidence for frequent birth and death of MIRNA genes. PLoS One 2: e219.
    • (2007) PLoS One , vol.2
    • Fahlgren, N.1    Howell, M.D.2    Kasschau, K.D.3    Chapman, E.J.4    Sullivan, C.M.5
  • 20
    • 27744471144 scopus 로고    scopus 로고
    • Novel and mechanical stress-responsive MicroRNAs in Populus trichocarpa that are absent from Arabidopsis
    • Lu S, Sun YH, Shi R, Clark C, Li L, et al. (2005) Novel and mechanical stress-responsive MicroRNAs in Populus trichocarpa that are absent from Arabidopsis. Plant Cell 17: 2186-2203.
    • (2005) Plant Cell , vol.17 , pp. 2186-2203
    • Lu, S.1    Sun, Y.H.2    Shi, R.3    Clark, C.4    Li, L.5
  • 21
    • 33845688601 scopus 로고    scopus 로고
    • A diverse and evolutionarily fluid set of microRNAs in Arabidopsis thaliana
    • Rajagopalan R, Vaucheret H, Trejo J, Bartel DP, (2006) A diverse and evolutionarily fluid set of microRNAs in Arabidopsis thaliana. Genes Dev 20: 3407-3425.
    • (2006) Genes Dev , vol.20 , pp. 3407-3425
    • Rajagopalan, R.1    Vaucheret, H.2    Trejo, J.3    Bartel, D.P.4
  • 22
    • 84862907762 scopus 로고    scopus 로고
    • Identification of conserved and novel microRNAs that are responsive to heat stress in Brassica rapa
    • Yu X, Wang H, Lu Y, de Ruiter M, Cariaso M, et al. (2011) Identification of conserved and novel microRNAs that are responsive to heat stress in Brassica rapa. J Exp Bot 63: 1025-1038.
    • (2011) J Exp Bot , vol.63 , pp. 1025-1038
    • Yu, X.1    Wang, H.2    Lu, Y.3    de Ruiter, M.4    Cariaso, M.5
  • 23
    • 84861338860 scopus 로고    scopus 로고
    • Identification and characterization of microRNAs in Phaseolus vulgaris by high-throughput sequencing
    • Pelaez P, Trejo MS, Iniguez LP, Estrada-Navarrete G, Covarrubias AA, et al. (2012) Identification and characterization of microRNAs in Phaseolus vulgaris by high-throughput sequencing. BMC Genomics 13: 83.
    • (2012) BMC Genomics , vol.13 , pp. 83
    • Pelaez, P.1    Trejo, M.S.2    Iniguez, L.P.3    Estrada-Navarrete, G.4    Covarrubias, A.A.5
  • 24
    • 77950484612 scopus 로고    scopus 로고
    • Deep sequencing identifies novel and conserved microRNAs in peanuts (Arachis hypogaea L.)
    • Zhao CZ, Xia H, Frazier TP, Yao YY, Bi YP, et al. (2010) Deep sequencing identifies novel and conserved microRNAs in peanuts (Arachis hypogaea L.). BMC Plant Biol 10: 3.
    • (2010) BMC Plant Biol , vol.10 , pp. 3
    • Zhao, C.Z.1    Xia, H.2    Frazier, T.P.3    Yao, Y.Y.4    Bi, Y.P.5
  • 25
    • 84864352611 scopus 로고    scopus 로고
    • Genome-wide analysis of microRNAs in rubber tree (Hevea brasiliensis L.) using high-throughput sequencing
    • Lertpanyasampatha M, Gao L, Kongsawadworakul P, Viboonjun U, Chrestin H, et al. (2012) Genome-wide analysis of microRNAs in rubber tree (Hevea brasiliensis L.) using high-throughput sequencing. Planta.
    • (2012) Planta
    • Lertpanyasampatha, M.1    Gao, L.2    Kongsawadworakul, P.3    Viboonjun, U.4    Chrestin, H.5
  • 26
    • 77953489252 scopus 로고    scopus 로고
    • Identification of grapevine microRNAs and their targets using high-throughput sequencing and degradome analysis
    • Pantaleo V, Szittya G, Moxon S, Miozzi L, Moulton V, et al. (2010) Identification of grapevine microRNAs and their targets using high-throughput sequencing and degradome analysis. Plant J 62: 960-976.
    • (2010) Plant J , vol.62 , pp. 960-976
    • Pantaleo, V.1    Szittya, G.2    Moxon, S.3    Miozzi, L.4    Moulton, V.5
  • 27
    • 42149157716 scopus 로고    scopus 로고
    • Identification of novel and candidate miRNAs in rice by high throughput sequencing
    • Sunkar R, Zhou X, Zheng Y, Zhang W, Zhu JK, (2008) Identification of novel and candidate miRNAs in rice by high throughput sequencing. BMC Plant Biol 8: 25.
    • (2008) BMC Plant Biol , vol.8 , pp. 25
    • Sunkar, R.1    Zhou, X.2    Zheng, Y.3    Zhang, W.4    Zhu, J.K.5
  • 28
    • 70350438585 scopus 로고    scopus 로고
    • Deep sequencing of Brachypodium small RNAs at the global genome level identifies microRNAs involved in cold stress response
    • 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: 449.
    • (2009) BMC Genomics , vol.10 , pp. 449
    • Zhang, J.1    Xu, Y.2    Huan, Q.3    Chong, K.4
  • 29
    • 39549115890 scopus 로고    scopus 로고
    • Cloning and characterization of microRNAs from wheat (Triticum aestivum L.)
    • Yao Y, Guo G, Ni Z, Sunkar R, Du J, et al. (2007) Cloning and characterization of microRNAs from wheat (Triticum aestivum L.). Genome Biol 8: R96.
    • (2007) Genome Biol , vol.8
    • Yao, Y.1    Guo, G.2    Ni, Z.3    Sunkar, R.4    Du, J.5
  • 30
    • 76949103466 scopus 로고    scopus 로고
    • High throughput approaches reveal splicing of primary microRNA transcripts and tissue specific expression of mature microRNAs in Vitis vinifera
    • Mica E, Piccolo V, Delledonne M, Ferrarini A, Pezzotti M, et al. (2009) High throughput approaches reveal splicing of primary microRNA transcripts and tissue specific expression of mature microRNAs in Vitis vinifera. BMC Genomics 10: 558.
    • (2009) BMC Genomics , vol.10 , pp. 558
    • Mica, E.1    Piccolo, V.2    Delledonne, M.3    Ferrarini, A.4    Pezzotti, M.5
  • 32
    • 78650971549 scopus 로고    scopus 로고
    • Identification of miRNAs and their target genes in developing soybean seeds by deep sequencing
    • Song QX, Liu YF, Hu XY, Zhang WK, Ma B, et al. (2011) Identification of miRNAs and their target genes in developing soybean seeds by deep sequencing. BMC Plant Biol 11: 5.
    • (2011) BMC Plant Biol , vol.11 , pp. 5
    • Song, Q.X.1    Liu, Y.F.2    Hu, X.Y.3    Zhang, W.K.4    Ma, B.5
  • 33
    • 79956144553 scopus 로고    scopus 로고
    • Genome-wide discovery and analysis of microRNAs and other small RNAs from rice embryogenic callus
    • Chen CJ, liu Q, Zhang YC, Qu LH, Chen YQ, et al. (2011) Genome-wide discovery and analysis of microRNAs and other small RNAs from rice embryogenic callus. RNA Biol 8: 538-547.
    • (2011) RNA Biol , vol.8 , pp. 538-547
    • Chen, C.J.1    Liu, Q.2    Zhang, Y.C.3    Qu, L.H.4    Chen, Y.Q.5
  • 34
    • 79954606171 scopus 로고    scopus 로고
    • Identification and analysis of seven HO-responsive miRNAs and 32 new miRNAs in the seedlings of rice (Oryza sativa L. ssp. indica)
    • Li T, Li H, Zhang YX, Liu JY, (2011) Identification and analysis of seven HO-responsive miRNAs and 32 new miRNAs in the seedlings of rice (Oryza sativa L. ssp. indica). Nucleic Acids Res 39: 2821-2833.
    • (2011) Nucleic Acids Res , vol.39 , pp. 2821-2833
    • Li, T.1    Li, H.2    Zhang, Y.X.3    Liu, J.Y.4
  • 35
    • 80054096606 scopus 로고    scopus 로고
    • Differential expression of the microRNAs in superior and inferior spikelets in rice (Oryza sativa)
    • Peng T, Lv Q, Zhang J, Li J, Du Y, et al. (2011) Differential expression of the microRNAs in superior and inferior spikelets in rice (Oryza sativa). J Exp Bot 62: 4943-4954.
    • (2011) J Exp Bot , vol.62 , pp. 4943-4954
    • Peng, T.1    Lv, Q.2    Zhang, J.3    Li, J.4    Du, Y.5
  • 36
    • 79959262495 scopus 로고    scopus 로고
    • Deep sequencing on genome-wide scale reveals the unique composition and expression patterns of microRNAs in developing pollen of Oryza sativa
    • Wei LQ, Yan LF, Wang T, (2011) Deep sequencing on genome-wide scale reveals the unique composition and expression patterns of microRNAs in developing pollen of Oryza sativa. Genome Biol 12: R53.
    • (2011) Genome Biol , vol.12
    • Wei, L.Q.1    Yan, L.F.2    Wang, T.3
  • 37
    • 49449118941 scopus 로고    scopus 로고
    • Recent Rice stripe virus Epidemics in Zhejiang Province, China, and Experiments on Sowing Date, Disease-Yield Loss Relationships, and Seedling Susceptibility
    • Wang HD, Chen JP, Zhang HM, Sun XL, Zhu JL, et al. (2008) Recent Rice stripe virus Epidemics in Zhejiang Province, China, and Experiments on Sowing Date, Disease-Yield Loss Relationships, and Seedling Susceptibility. Plant Dis 92: 1190-1196.
    • (2008) Plant Dis , vol.92 , pp. 1190-1196
    • Wang, H.D.1    Chen, J.P.2    Zhang, H.M.3    Sun, X.L.4    Zhu, J.L.5
  • 38
    • 80052339278 scopus 로고    scopus 로고
    • Viral infection induces expression of novel phased microRNAs from conserved cellular microRNA precursors
    • Du P, Wu J, Zhang J, Zhao S, Zheng H, et al. (2011) Viral infection induces expression of novel phased microRNAs from conserved cellular microRNA precursors. PLoS Pathog 7: e1002176.
    • (2011) PLoS Pathog , vol.7
    • Du, P.1    Wu, J.2    Zhang, J.3    Zhao, S.4    Zheng, H.5
  • 39
    • 77953324674 scopus 로고    scopus 로고
    • Characterization of siRNAs derived from rice stripe virus in infected rice plants by deep sequencing
    • Yan F, Zhang H, Adams MJ, Yang J, Peng J, et al. (2010) Characterization of siRNAs derived from rice stripe virus in infected rice plants by deep sequencing. Arch Virol 155: 935-940.
    • (2010) Arch Virol , vol.155 , pp. 935-940
    • Yan, F.1    Zhang, H.2    Adams, M.J.3    Yang, J.4    Peng, J.5
  • 40
    • 34848851665 scopus 로고    scopus 로고
    • Genomic analysis of rice stripe virus Zhejiang isolate shows the presence of an OTU-like domain in the RNA1 protein and a novel sequence motif conserved within the intergenic regions of ambisense segments of tenuiviruses
    • Zhang HM, Yang J, Sun HR, Xin X, Wang HD, et al. (2007) Genomic analysis of rice stripe virus Zhejiang isolate shows the presence of an OTU-like domain in the RNA1 protein and a novel sequence motif conserved within the intergenic regions of ambisense segments of tenuiviruses. Arch Virol 152: 1917-1923.
    • (2007) Arch Virol , vol.152 , pp. 1917-1923
    • Zhang, H.M.1    Yang, J.2    Sun, H.R.3    Xin, X.4    Wang, H.D.5
  • 42
    • 79959967431 scopus 로고    scopus 로고
    • psRNATarget: a plant small RNA target analysis server
    • Dai X, Zhao PX, (2011) psRNATarget: a plant small RNA target analysis server. Nucleic Acids Res 39: W155-159.
    • (2011) Nucleic Acids Res , vol.39
    • Dai, X.1    Zhao, P.X.2
  • 43
    • 77955422438 scopus 로고    scopus 로고
    • Global expression analysis of miRNA gene cluster and family based on isomiRs from deep sequencing data
    • Guo L, Lu Z, (2010) Global expression analysis of miRNA gene cluster and family based on isomiRs from deep sequencing data. Comput Biol Chem 34: 165-171.
    • (2010) Comput Biol Chem , vol.34 , pp. 165-171
    • Guo, L.1    Lu, Z.2
  • 44
    • 78650053705 scopus 로고    scopus 로고
    • Naturally occurring variations in sequence length creates microRNA isoforms that differ in argonaute effector complex specificity
    • Ebhardt HA, Fedynak A, Fahlman RP, (2010) Naturally occurring variations in sequence length creates microRNA isoforms that differ in argonaute effector complex specificity. Silence 1: 12.
    • (2010) Silence , vol.1 , pp. 12
    • Ebhardt, H.A.1    Fedynak, A.2    Fahlman, R.P.3
  • 46
    • 84862811570 scopus 로고    scopus 로고
    • The Rice stripe virus pc4 functions in movement and foliar necrosis expression in Nicotiana benthamiana
    • Zhang C, Pei X, Wang Z, Jia S, Guo S, et al. (2012) The Rice stripe virus pc4 functions in movement and foliar necrosis expression in Nicotiana benthamiana. Virology 425: 113-121.
    • (2012) Virology , vol.425 , pp. 113-121
    • Zhang, C.1    Pei, X.2    Wang, Z.3    Jia, S.4    Guo, S.5
  • 47
    • 83755172985 scopus 로고    scopus 로고
    • Repetitive prime-and-realign mechanism converts short capped RNA leaders into longer ones that may be more suitable for elongation during rice stripe virus transcription initiation
    • Yao M, Zhang T, Zhou T, Zhou Y, Zhou X, et al. (2012) Repetitive prime-and-realign mechanism converts short capped RNA leaders into longer ones that may be more suitable for elongation during rice stripe virus transcription initiation. J Gen Virol 93: 194-202.
    • (2012) J Gen Virol , vol.93 , pp. 194-202
    • Yao, M.1    Zhang, T.2    Zhou, T.3    Zhou, Y.4    Zhou, X.5
  • 48
    • 79957618532 scopus 로고    scopus 로고
    • The early secretory pathway and an actin-myosin VIII motility system are required for plasmodesmatal localization of the NSvc4 protein of Rice stripe virus
    • Yuan Z, Chen H, Chen Q, Omura T, Xie L, et al. (2011) The early secretory pathway and an actin-myosin VIII motility system are required for plasmodesmatal localization of the NSvc4 protein of Rice stripe virus. Virus Res 159: 62-68.
    • (2011) Virus Res , vol.159 , pp. 62-68
    • Yuan, Z.1    Chen, H.2    Chen, Q.3    Omura, T.4    Xie, L.5
  • 49
    • 80052417279 scopus 로고    scopus 로고
    • p2 of rice stripe virus (RSV) interacts with OsSGS3 and is a silencing suppressor
    • Du Z, Xiao D, Wu J, Jia D, Yuan Z, et al. (2011) p2 of rice stripe virus (RSV) interacts with OsSGS3 and is a silencing suppressor. Mol Plant Pathol 12: 808-814.
    • (2011) Mol Plant Pathol , vol.12 , pp. 808-814
    • Du, Z.1    Xiao, D.2    Wu, J.3    Jia, D.4    Yuan, Z.5
  • 50
    • 65549144244 scopus 로고    scopus 로고
    • Genetic diversity and population structure of rice stripe virus in China
    • Wei TY, Yang JG, Liao FL, Gao FL, Lu LM, et al. (2009) Genetic diversity and population structure of rice stripe virus in China. J Gen Virol 90: 1025-1034.
    • (2009) J Gen Virol , vol.90 , pp. 1025-1034
    • Wei, T.Y.1    Yang, J.G.2    Liao, F.L.3    Gao, F.L.4    Lu, L.M.5
  • 51
    • 57349168102 scopus 로고    scopus 로고
    • Identification of a movement protein of the tenuivirus rice stripe virus
    • Xiong R, Wu J, Zhou Y, Zhou X, (2008) Identification of a movement protein of the tenuivirus rice stripe virus. J Virol 82: 12304-12311.
    • (2008) J Virol , vol.82 , pp. 12304-12311
    • Xiong, R.1    Wu, J.2    Zhou, Y.3    Zhou, X.4
  • 52
    • 63749087829 scopus 로고    scopus 로고
    • Characterization and subcellular localization of an RNA silencing suppressor encoded by Rice stripe tenuivirus
    • Xiong R, Wu J, Zhou Y, Zhou X, (2009) Characterization and subcellular localization of an RNA silencing suppressor encoded by Rice stripe tenuivirus. Virology 387: 29-40.
    • (2009) Virology , vol.387 , pp. 29-40
    • Xiong, R.1    Wu, J.2    Zhou, Y.3    Zhou, X.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.