메뉴 건너뛰기




Volumn 7, Issue 8, 2012, Pages

Deep Sequencing and Microarray Hybridization Identify Conserved and Species-Specific MicroRNAs during Somatic Embryogenesis in Hybrid Yellow Poplar

Author keywords

[No Author keywords available]

Indexed keywords

MICRORNA; PLANT RNA;

EID: 84865587989     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0043451     Document Type: Article
Times cited : (65)

References (65)
  • 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
  • 4
    • 34547668337 scopus 로고    scopus 로고
    • Common functions for diverse small RNAs of land plants
    • Axtell MJ, Snyder JA, Bartell DP, (2007) Common functions for diverse small RNAs of land plants. Plant Cell 19: 1750-1769.
    • (2007) Plant Cell , vol.19 , pp. 1750-1769
    • Axtell, M.J.1    Snyder, J.A.2    Bartell, D.P.3
  • 5
    • 44649126240 scopus 로고    scopus 로고
    • Evidence for stage-specific modulation of specific microRNAs (miRNAs) and miRNA processing components in zygotic embryo and female gametophyte of loblolly pine (Pinus taeda)
    • Oh TJ, Wartell RM, Cairney J, Pullman GS, (2008) Evidence for stage-specific modulation of specific microRNAs (miRNAs) and miRNA processing components in zygotic embryo and female gametophyte of loblolly pine (Pinus taeda). New Phytologist 179: 67-80.
    • (2008) New Phytologist , vol.179 , pp. 67-80
    • Oh, T.J.1    Wartell, R.M.2    Cairney, J.3    Pullman, G.S.4
  • 6
    • 79951958197 scopus 로고    scopus 로고
    • Stage and tissue-specific modulation of ten conserved miRNAs and their targets during somatic embryogenesis of Valencia sweet orange
    • Wu X-M, Liu M-Y, Ge X-X, Xu Q, Guo W-W, (2011) Stage and tissue-specific modulation of ten conserved miRNAs and their targets during somatic embryogenesis of Valencia sweet orange. Planta 233: 495-505.
    • (2011) Planta , vol.233 , pp. 495-505
    • Wu, X.-M.1    Liu, M.-Y.2    Ge, X.-X.3    Xu, Q.4    Guo, W.-W.5
  • 7
    • 78649806773 scopus 로고    scopus 로고
    • MicroRNAs prevent precocious gene expression and enable pattern formation during plant embryogenesis
    • Nodine MD, Bartel DP, (2010) MicroRNAs prevent precocious gene expression and enable pattern formation during plant embryogenesis. Genes & Development 24: 2678-2692.
    • (2010) Genes & Development , vol.24 , pp. 2678-2692
    • Nodine, M.D.1    Bartel, D.P.2
  • 8
  • 9
    • 23844474230 scopus 로고    scopus 로고
    • Potential tree species for use in the restoration of unsanitary landfills
    • Kim KD, Lee EJ, (2005) Potential tree species for use in the restoration of unsanitary landfills. Environmental Management 36: 1-14.
    • (2005) Environmental Management , vol.36 , pp. 1-14
    • Kim, K.D.1    Lee, E.J.2
  • 10
  • 12
    • 34250888064 scopus 로고
    • Pollen ultrastructure of Liriodendron and its systematic significance
    • Wei ZX, Wu ZY, (1993) Pollen ultrastructure of Liriodendron and its systematic significance. Acta Bot Yunnanica 15: 163-166.
    • (1993) Acta Bot Yunnanica , vol.15 , pp. 163-166
    • Wei, Z.X.1    Wu, Z.Y.2
  • 14
    • 80052758396 scopus 로고    scopus 로고
    • Generation of a large-scale genomic resource for functional and comparative genomics in Liriodendron tulipifera L
    • Liang H, Ayyampalayam S, Wickett N, Barakat A, Xu Y, et al. (2011) Generation of a large-scale genomic resource for functional and comparative genomics in Liriodendron tulipifera L. Tree Genetics & Genomes 7: 941-954.
    • (2011) Tree Genetics & Genomes , vol.7 , pp. 941-954
    • Liang, H.1    Ayyampalayam, S.2    Wickett, N.3    Barakat, A.4    Xu, Y.5
  • 16
    • 0001705547 scopus 로고
    • Molecular biology of somatic embryogenesis
    • In: Thorpe T, editor, Dordrecht: Kluwer Academic
    • Dudits D, Györgyey J, Bögre L, Bakó L (1995) Molecular biology of somatic embryogenesis. In: Thorpe T, editor. In vitro embryogenesis in plant. Dordrecht: Kluwer Academic. pp. 267-308.
    • (1995) In vitro embryogenesis in plant , pp. 267-308
    • Dudits, D.1    Györgyey, J.2    Bögre, L.3    Bakó, L.4
  • 17
    • 22144457368 scopus 로고    scopus 로고
    • Antiquity of microRNAs and their targets in land plants
    • Axtell MJ, Bartel DP, (2005) Antiquity of microRNAs and their targets in land plants. Plant Cell 17: 1658-1673.
    • (2005) Plant Cell , vol.17 , pp. 1658-1673
    • Axtell, M.J.1    Bartel, D.P.2
  • 18
    • 39649117755 scopus 로고    scopus 로고
    • The impact of next-generation sequencing technology on genetics
    • Mardis ER, (2008) The impact of next-generation sequencing technology on genetics. Trends in Genetics 24: 133-141.
    • (2008) Trends in Genetics , vol.24 , pp. 133-141
    • Mardis, E.R.1
  • 19
    • 62549095240 scopus 로고    scopus 로고
    • High throughput sequencing technology reveals that the taxoid elicitor methyl jasmonate regulates microRNA expression in Chinese yew (Taxus chinensis)
    • Qiu D, Pan X, Wilson IW, Li F, Liu M, et al. (2009) High throughput sequencing technology reveals that the taxoid elicitor methyl jasmonate regulates microRNA expression in Chinese yew (Taxus chinensis). Gene 436: 37-44.
    • (2009) Gene , vol.436 , pp. 37-44
    • Qiu, D.1    Pan, X.2    Wilson, I.W.3    Li, F.4    Liu, M.5
  • 20
    • 44049105115 scopus 로고    scopus 로고
    • An EST database for Liriodendron tulipifera L. floral buds: the first EST resource for functional and comparative genomics in Liriodendron
    • Liang H, Carlson JE, Leebens-Mack JH, Wall PK, Mueller LA, et al. (2008) An EST database for Liriodendron tulipifera L. floral buds: the first EST resource for functional and comparative genomics in Liriodendron. Tree Genetics & Genomes 4: 419-433.
    • (2008) Tree Genetics & Genomes , vol.4 , pp. 419-433
    • Liang, H.1    Carlson, J.E.2    Leebens-Mack, J.H.3    Wall, P.K.4    Mueller, L.A.5
  • 22
    • 77955883388 scopus 로고    scopus 로고
    • Biases in Illumina transcriptome sequencing caused by random hexamer priming
    • Hansen KD, Brenner SE, Dudoit S, (2010) Biases in Illumina transcriptome sequencing caused by random hexamer priming. Nucleic Acids Research 38.
    • (2010) Nucleic Acids Research , vol.38
    • Hansen, K.D.1    Brenner, S.E.2    Dudoit, S.3
  • 23
    • 79957665988 scopus 로고    scopus 로고
    • Microarrays, deep sequencing and the true measure of the transcriptome
    • Malone JH, Oliver B, (2011) Microarrays, deep sequencing and the true measure of the transcriptome. BMC Biology 9.
    • (2011) BMC Biology , vol.9
    • Malone, J.H.1    Oliver, B.2
  • 24
    • 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 & Development 20: 3407-3425.
    • (2006) Genes & Development , vol.20 , pp. 3407-3425
    • Rajagopalan, R.1    Vaucheret, H.2    Trejo, J.3    Bartel, D.P.4
  • 25
    • 41649102715 scopus 로고    scopus 로고
    • Comparative analysis of the small RNA transcriptomes of Pinus contorta and Oryza sativa
    • Morin RD, Aksay G, Dolgosheina E, Ebhardt HA, Magrini V, et al. (2008) Comparative analysis of the small RNA transcriptomes of Pinus contorta and Oryza sativa. Genome Research 18: 571-584.
    • (2008) Genome Research , vol.18 , pp. 571-584
    • Morin, R.D.1    Aksay, G.2    Dolgosheina, E.3    Ebhardt, H.A.4    Magrini, V.5
  • 26
    • 53549106068 scopus 로고    scopus 로고
    • Deep sequencing of tomato short RNAs identifies microRNAs targeting genes involved in fruit ripening
    • Moxon S, Jing RC, Szittya G, Schwach F, Pilcher RLR, et al. (2008) Deep sequencing of tomato short RNAs identifies microRNAs targeting genes involved in fruit ripening. Genome Research 18: 1602-1609.
    • (2008) Genome Research , vol.18 , pp. 1602-1609
    • Moxon, S.1    Jing, R.C.2    Szittya, G.3    Schwach, F.4    Pilcher, R.L.R.5
  • 27
    • 58249118839 scopus 로고    scopus 로고
    • High-throughput sequencing of Medicago truncatula short RNAs identifies eight new miRNA families
    • Szittya G, Moxon S, Santos DM, Jing R, Fevereiro MPS, et al. (2008) High-throughput sequencing of Medicago truncatula short RNAs identifies eight new miRNA families. BMC Genomics 9.
    • (2008) BMC Genomics , vol.9
    • Szittya, G.1    Moxon, S.2    Santos, D.M.3    Jing, R.4    Fevereiro, M.P.S.5
  • 28
    • 77955375546 scopus 로고    scopus 로고
    • Deep sequencing discovery of novel and conserved microRNAs in trifoliate orange (Citrus trifoliata)
    • Song C, Wang C, Zhang C, Korir NK, Yu H, et al. (2010) Deep sequencing discovery of novel and conserved microRNAs in trifoliate orange (Citrus trifoliata). BMC Genomics 11.
    • (2010) BMC Genomics , vol.11
    • Song, C.1    Wang, C.2    Zhang, C.3    Korir, N.K.4    Yu, H.5
  • 29
    • 77950484612 scopus 로고    scopus 로고
    • Deep sequencing identifies novel and conserved microRNAs in peanuts (Arachis hypogaea L.)
    • Zhao C-Z, Xia H, Frazier TP, Yao Y-Y, Bi Y-P, et al. (2010) Deep sequencing identifies novel and conserved microRNAs in peanuts (Arachis hypogaea L.). Bmc Plant Biology 10.
    • (2010) Bmc Plant Biology , vol.10
    • Zhao, C.-Z.1    Xia, H.2    Frazier, T.P.3    Yao, Y.-Y.4    Bi, Y.-P.5
  • 32
    • 84859746460 scopus 로고    scopus 로고
    • Identification and characterization of the microRNAs and their targets in Salmo salar
    • Barozai MYK, (2012) Identification and characterization of the microRNAs and their targets in Salmo salar. Gene 499: 163-168.
    • (2012) Gene , vol.499 , pp. 163-168
    • Barozai, M.Y.K.1
  • 33
    • 69949115080 scopus 로고    scopus 로고
    • Repression of apical homeobox genes is required for embryonic root development in Arabidopsis
    • Grigg SP, Galinha C, Kornet N, Canales C, Scheres B, et al. (2009) Repression of apical homeobox genes is required for embryonic root development in Arabidopsis. Current Biology 19: 1485-1490.
    • (2009) Current Biology , vol.19 , pp. 1485-1490
    • Grigg, S.P.1    Galinha, C.2    Kornet, N.3    Canales, C.4    Scheres, B.5
  • 39
    • 24644476482 scopus 로고    scopus 로고
    • MicroRNA identification based on sequence and structure alignment
    • Wang XW, Zhang J, Gu J, He T, Zhang XG, et al. (2005) MicroRNA identification based on sequence and structure alignment. Bioinformatics 21: 3610-3614.
    • (2005) Bioinformatics , vol.21 , pp. 3610-3614
    • Wang, X.W.1    Zhang, J.2    Gu, J.3    He, T.4    Zhang, X.G.5
  • 40
    • 0033591465 scopus 로고    scopus 로고
    • Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure
    • Mathews DH, Sabina J, Zuker M, Turner DH, (1999) Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. Journal of molecular biology 288: 911-940.
    • (1999) Journal of Molecular Biology , vol.288 , pp. 911-940
    • Mathews, D.H.1    Sabina, J.2    Zuker, M.3    Turner, D.H.4
  • 41
    • 10244243802 scopus 로고    scopus 로고
    • Evidence that microRNA precursors, unlike other non-coding RNAs, have lower folding free energies than random sequences
    • Bonnet E, Wuyts J, Rouze P, Van de Peer Y, (2004) Evidence that microRNA precursors, unlike other non-coding RNAs, have lower folding free energies than random sequences. Bioinformatics 20: 2911-2917.
    • (2004) Bioinformatics , vol.20 , pp. 2911-2917
    • Bonnet, E.1    Wuyts, J.2    Rouze, P.3    van de Peer, Y.4
  • 42
    • 27844495281 scopus 로고    scopus 로고
    • Identification and characterization of new plant microRNAs using EST analysis
    • Zhang BH, Pan XP, Wang QL, Cobb GP, Anderson TA, (2005) Identification and characterization of new plant microRNAs using EST analysis. Cell Research 15: 336-360.
    • (2005) Cell Research , vol.15 , pp. 336-360
    • Zhang, B.H.1    Pan, X.P.2    Wang, Q.L.3    Cobb, G.P.4    Anderson, T.A.5
  • 44
    • 33745156778 scopus 로고    scopus 로고
    • Identification of 188 conserved maize microRNAs and their targets
    • Zhang BH, Pan XP, Anderson TA, (2006) Identification of 188 conserved maize microRNAs and their targets. Febs Letters 580: 3753-3762.
    • (2006) Febs Letters , vol.580 , pp. 3753-3762
    • Zhang, B.H.1    Pan, X.P.2    Anderson, T.A.3
  • 45
    • 79952004220 scopus 로고    scopus 로고
    • Investigation of the microRNAs in safflower seed, leaf, and petal by high-throughput sequencing
    • Li H, Dong Y, Sun Y, Zhu E, Yang J, et al. (2011) Investigation of the microRNAs in safflower seed, leaf, and petal by high-throughput sequencing. Planta 233: 611-619.
    • (2011) Planta , vol.233 , pp. 611-619
    • Li, H.1    Dong, Y.2    Sun, Y.3    Zhu, E.4    Yang, J.5
  • 46
    • 78650971549 scopus 로고    scopus 로고
    • Identification of miRNAs and their target genes in developing soybean seeds by deep sequencing
    • Song Q-X, Liu Y-F, Hu X-Y, Zhang W-K, Ma B, et al. (2011) Identification of miRNAs and their target genes in developing soybean seeds by deep sequencing. BMC Plant Biology 11.
    • (2011) BMC Plant Biology , vol.11
    • Song, Q.-X.1    Liu, Y.-F.2    Hu, X.-Y.3    Zhang, W.-K.4    Ma, B.5
  • 47
    • 9444274025 scopus 로고    scopus 로고
    • Defining signal thresholds in DNA microarrays: exemplary application for invasive cancer
    • Bilban M, Buehler LK, Head S, Desoye G, Quaranta V, (2002) Defining signal thresholds in DNA microarrays: exemplary application for invasive cancer. BMC Genomics 3.
    • (2002) BMC Genomics , vol.3
    • Bilban, M.1    Buehler, L.K.2    Head, S.3    Desoye, G.4    Quaranta, V.5
  • 48
    • 0037318307 scopus 로고    scopus 로고
    • A variable fold-change threshold determines significance for expression microarrays
    • Mariani TJ, Budhraja V, Mecham BH, Gu CC, Watson MA, et al. (2002) A variable fold-change threshold determines significance for expression microarrays. Faseb Journal 16: 321-334.
    • (2002) Faseb Journal , vol.16 , pp. 321-334
    • Mariani, T.J.1    Budhraja, V.2    Mecham, B.H.3    Gu, C.C.4    Watson, M.A.5
  • 49
    • 79953086307 scopus 로고    scopus 로고
    • Evolution and functional diversification of miRNA genes
    • Cuperus JT, Fahlgren N, Carrington JC, (2011) Evolution and functional diversification of miRNA genes. Plant Cell 23: 431-442.
    • (2011) Plant Cell , vol.23 , pp. 431-442
    • Cuperus, J.T.1    Fahlgren, N.2    Carrington, J.C.3
  • 51
    • 27744471144 scopus 로고    scopus 로고
    • Novel and mechanical stress-responsive microRNAs in Populus trichocarpa that are absent from Arabidopsis
    • Lu SF, Sun YH, Shi R, Clark C, Li LG, 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.F.1    Sun, Y.H.2    Shi, R.3    Clark, C.4    Li, L.G.5
  • 52
    • 0036000026 scopus 로고    scopus 로고
    • Laccase down-regulation causes alterations in phenolic metabolism and cell wall structure in poplar
    • Ranocha P, Chabannes M, Chamayou S, Danoun S, Jauneau A, et al. (2002) Laccase down-regulation causes alterations in phenolic metabolism and cell wall structure in poplar. Plant Physiology 129: 145-155.
    • (2002) Plant Physiology , vol.129 , pp. 145-155
    • Ranocha, P.1    Chabannes, M.2    Chamayou, S.3    Danoun, S.4    Jauneau, A.5
  • 53
    • 0028353864 scopus 로고
    • Cell fate determination by the cell wall in early fucus development
    • Berger F, Taylor A, Brownlee C, (1994) Cell fate determination by the cell wall in early fucus development. Science (New York, NY) 263: 1421-1423.
    • (1994) Science (New York, NY) , vol.263 , pp. 1421-1423
    • Berger, F.1    Taylor, A.2    Brownlee, C.3
  • 54
    • 0035042137 scopus 로고    scopus 로고
    • Cell wall deposition during morphogenesis in fucoid algae
    • Bisgrove SR, Kropf DL, (2001) Cell wall deposition during morphogenesis in fucoid algae. Planta 212: 648-658.
    • (2001) Planta , vol.212 , pp. 648-658
    • Bisgrove, S.R.1    Kropf, D.L.2
  • 55
    • 33750435234 scopus 로고    scopus 로고
    • Distinct catalytic and non-catalytic roles of ARGONAUTE4 in RNA-directed DNA methylation
    • Qi Y, He X, Wang X-J, Kohany O, Jurka J, et al. (2006) Distinct catalytic and non-catalytic roles of ARGONAUTE4 in RNA-directed DNA methylation. Nature 443: 1008-1012.
    • (2006) Nature , vol.443 , pp. 1008-1012
    • Qi, Y.1    He, X.2    Wang, X.-J.3    Kohany, O.4    Jurka, J.5
  • 56
    • 41349114789 scopus 로고    scopus 로고
    • Sorting of small RNAs into Arabidopsis argonaute complexes is directed by the 5′ terminal nucleotide
    • Mi S, Cai T, Hu Y, Chen Y, Hodges E, et al. (2008) Sorting of small RNAs into Arabidopsis argonaute complexes is directed by the 5′ terminal nucleotide. Cell 133: 116-127.
    • (2008) Cell , vol.133 , pp. 116-127
    • Mi, S.1    Cai, T.2    Hu, Y.3    Chen, Y.4    Hodges, E.5
  • 57
    • 77950342461 scopus 로고    scopus 로고
    • The Arabidopsis RNA-directed DNA methylation argonautes functionally diverge based on their expression and interaction with target loci
    • Havecker ER, Wallbridge LM, Hardcastle TJ, Bush MS, Kelly KA, et al. (2010) The Arabidopsis RNA-directed DNA methylation argonautes functionally diverge based on their expression and interaction with target loci. Plant Cell 22: 321-334.
    • (2010) Plant Cell , vol.22 , pp. 321-334
    • Havecker, E.R.1    Wallbridge, L.M.2    Hardcastle, T.J.3    Bush, M.S.4    Kelly, K.A.5
  • 58
    • 73149089202 scopus 로고    scopus 로고
    • Transcriptional control of gene expression by microRNAs
    • Khraiwesh B, Arif MA, Seumel GI, Ossowski S, Weigel D, et al. (2010) Transcriptional control of gene expression by microRNAs. Cell 140: 111-122.
    • (2010) Cell , vol.140 , pp. 111-122
    • Khraiwesh, B.1    Arif, M.A.2    Seumel, G.I.3    Ossowski, S.4    Weigel, D.5
  • 62
    • 1342294092 scopus 로고    scopus 로고
    • Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation
    • Yang YH, Dudoit S, Luu P, Lin DM, Peng V, et al. (2002) Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation. Nucleic Acids Research 30.
    • (2002) Nucleic Acids Research , vol.30
    • Yang, Y.H.1    Dudoit, S.2    Luu, P.3    Lin, D.M.4    Peng, V.5
  • 63
    • 38849140922 scopus 로고    scopus 로고
    • Protocol: a highly sensitive RT-PCR method for detection and quantification of microRNAs
    • 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.
    • (2007) Plant Methods , vol.3
    • Varkonyi-Gasic, E.1    Wu, R.2    Wood, M.3    Walton, E.F.4    Hellens, R.P.5
  • 64
    • 77954184918 scopus 로고    scopus 로고
    • TAPIR, a web server for the prediction of plant microRNA targets, including target mimics
    • Bonnet E, He Y, Billiau K, Van de Peer Y, (2010) TAPIR, a web server for the prediction of plant microRNA targets, including target mimics. Bioinformatics 26: 1566-1568.
    • (2010) Bioinformatics , vol.26 , pp. 1566-1568
    • Bonnet, E.1    He, Y.2    Billiau, K.3    van de Peer, Y.4
  • 65
    • 79959967431 scopus 로고    scopus 로고
    • psRNATarget: a plant small RNA target analysis server
    • Dai XB, Zhao PX, (2011) psRNATarget: a plant small RNA target analysis server. Nucleic Acids Research 39: 155-159.
    • (2011) Nucleic Acids Research , vol.39 , pp. 155-159
    • Dai, X.B.1    Zhao, P.X.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.