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Volumn 6, Issue 12, 2011, Pages

Evolution of microRNA genes in Oryza sativa and Arabidopsis thaliana: An update of the inverted duplication model

Author keywords

[No Author keywords available]

Indexed keywords

ARABIDOPSIS; ARTICLE; CONTROLLED STUDY; GENE DOSAGE; GENE DUPLICATION; GENE EXPRESSION REGULATION; GENE FUNCTION; GENE REGULATORY NETWORK; GENE SEQUENCE; GENE TARGETING; GENETIC ASSOCIATION; GENETIC VARIABILITY; GENOME ANALYSIS; MICRORNA GENE; NONHUMAN; PLANT EVOLUTION; PLANT GENE; PLANT GENETICS; PLANT GENOME; PLANT YIELD; PSEUDOGENE; RICE; BIOLOGICAL MODEL; GENETICS; METABOLISM; MOLECULAR EVOLUTION; NUCLEOTIDE SEQUENCE; TRANSPOSON;

EID: 83355173057     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0028073     Document Type: Article
Times cited : (27)

References (58)
  • 1
    • 58449134534 scopus 로고    scopus 로고
    • Small silencing RNAs: an expanding universe
    • Ghildiyal M, Zamore PD, (2009) Small silencing RNAs: an expanding universe. Nat Rev Genet 10: 94-108.
    • (2009) Nat Rev Genet , vol.10 , pp. 94-108
    • Ghildiyal, M.1    Zamore, P.D.2
  • 2
    • 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
  • 5
    • 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
  • 6
    • 33745271035 scopus 로고    scopus 로고
    • Functions of microRNAs and related small RNAs in plants
    • Mallory AC, Vaucheret H, (2006) Functions of microRNAs and related small RNAs in plants. Nat Genet 38 (Suppl): S31-36.
    • (2006) Nat Genet , vol.38 , Issue.SUPPL.
    • Mallory, A.C.1    Vaucheret, H.2
  • 7
    • 77952821615 scopus 로고    scopus 로고
    • Regulation of OsSPL14 by OsmiR156 defines ideal plant architecture in rice
    • Jiao Y, Wang Y, Xue D, Wang J, Yan M, et al. (2010) Regulation of OsSPL14 by OsmiR156 defines ideal plant architecture in rice. Nat Genet 42: 541-544.
    • (2010) Nat Genet , vol.42 , pp. 541-544
    • Jiao, Y.1    Wang, Y.2    Xue, D.3    Wang, J.4    Yan, M.5
  • 8
    • 33750853059 scopus 로고    scopus 로고
    • Expression of artificial microRNAs in transgenic Arabidopsis thaliana confers virus resistance
    • Niu QW, Lin SS, Reyes JL, Chen KC, Wu HW, et al. (2006) Expression of artificial microRNAs in transgenic Arabidopsis thaliana confers virus resistance. Nat Biotechnol 24: 1420-1428.
    • (2006) Nat Biotechnol , vol.24 , pp. 1420-1428
    • Niu, Q.W.1    Lin, S.S.2    Reyes, J.L.3    Chen, K.C.4    Wu, H.W.5
  • 10
    • 9644272448 scopus 로고    scopus 로고
    • Evolution of microRNA genes by inverted duplication of target gene sequences in Arabidopsis thaliana
    • Allen E, Xie Z, Gustafson AM, Sung GH, Spatafora JW, et al. (2004) Evolution of microRNA genes by inverted duplication of target gene sequences in Arabidopsis thaliana. Nat Genet 36: 1282-1290.
    • (2004) Nat Genet , vol.36 , pp. 1282-1290
    • Allen, E.1    Xie, Z.2    Gustafson, A.M.3    Sung, G.H.4    Spatafora, J.W.5
  • 11
    • 34250729886 scopus 로고    scopus 로고
    • Origin and evolution of human microRNAs from transposable elements
    • Piriyapongsa J, Marino-Ramirez L, Jordan IK, (2007) Origin and evolution of human microRNAs from transposable elements. Genetics 176: 1323-1337.
    • (2007) Genetics , vol.176 , pp. 1323-1337
    • Piriyapongsa, J.1    Marino-Ramirez, L.2    Jordan, I.K.3
  • 12
    • 19444367079 scopus 로고    scopus 로고
    • Mammalian microRNAs derived from genomic repeats
    • Smalheiser NR, Torvik VI, (2005) Mammalian microRNAs derived from genomic repeats. Trends Genet 21: 322-326.
    • (2005) Trends Genet , vol.21 , pp. 322-326
    • Smalheiser, N.R.1    Torvik, V.I.2
  • 13
    • 33748577987 scopus 로고    scopus 로고
    • Alu elements within human mRNAs are probable microRNA targets
    • Smalheiser NR, Torvik VI, (2006) Alu elements within human mRNAs are probable microRNA targets. Trends Genet 22: 532-536.
    • (2006) Trends Genet , vol.22 , pp. 532-536
    • Smalheiser, N.R.1    Torvik, V.I.2
  • 14
    • 42449099982 scopus 로고    scopus 로고
    • Dual coding of siRNAs and miRNAs by plant transposable elements
    • Piriyapongsa J, Jordan IK, (2008) Dual coding of siRNAs and miRNAs by plant transposable elements. RNA 14: 814-821.
    • (2008) RNA , vol.14 , pp. 814-821
    • Piriyapongsa, J.1    Jordan, I.K.2
  • 15
    • 33644919969 scopus 로고    scopus 로고
    • Primate microRNAs miR-220 and miR-492 lie within processed pseudogenes
    • Devor EJ, (2006) Primate microRNAs miR-220 and miR-492 lie within processed pseudogenes. J Hered 97: 186-190.
    • (2006) J Hered , vol.97 , pp. 186-190
    • Devor, E.J.1
  • 16
    • 44849127601 scopus 로고    scopus 로고
    • Genomics: protein fossils live on as RNA
    • Sasidharan R, Gerstein M, (2008) Genomics: protein fossils live on as RNA. Nature 453: 729-731.
    • (2008) Nature , vol.453 , pp. 729-731
    • Sasidharan, R.1    Gerstein, M.2
  • 17
    • 68249084505 scopus 로고    scopus 로고
    • Small RNAs originated from pseudogenes: cis- or trans-acting?
    • Guo X, Zhang Z, Gerstein MB, Zheng D, (2009) Small RNAs originated from pseudogenes: cis- or trans-acting? PLoS Comput Biol 5: e1000449.
    • (2009) PLoS Comput Biol , vol.5
    • Guo, X.1    Zhang, Z.2    Gerstein, M.B.3    Zheng, D.4
  • 18
    • 33645509923 scopus 로고    scopus 로고
    • Evolution of Arabidopsis microRNA families through duplication events
    • Maher C, Stein L, Ware D, (2006) Evolution of Arabidopsis microRNA families through duplication events. Genome Res 16: 510-519.
    • (2006) Genome Res , vol.16 , pp. 510-519
    • Maher, C.1    Stein, L.2    Ware, D.3
  • 19
    • 57049169777 scopus 로고    scopus 로고
    • Evolution of Arabidopsis thaliana microRNAs from random sequences
    • Felippes FF, Schneeberger K, Dezulian T, Huson DH, Weigel D, (2008) Evolution of Arabidopsis thaliana microRNAs from random sequences. RNA 14: 2455-2459.
    • (2008) RNA , vol.14 , pp. 2455-2459
    • Felippes, F.F.1    Schneeberger, K.2    Dezulian, T.3    Huson, D.H.4    Weigel, D.5
  • 20
    • 0037023384 scopus 로고    scopus 로고
    • A draft sequence of the rice genome (Oryza sativa L. ssp. indica)
    • Yu J, Hu S, Wang J, Wong GK, Li S, et al. (2002) A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science 296: 79-92.
    • (2002) Science , vol.296 , pp. 79-92
    • Yu, J.1    Hu, S.2    Wang, J.3    Wong, G.K.4    Li, S.5
  • 21
    • 53349160132 scopus 로고    scopus 로고
    • Rates of molecular evolution are linked to life history in flowering plants
    • Smith SA, Donoghue MJ, (2008) Rates of molecular evolution are linked to life history in flowering plants. Science 322: 86-89.
    • (2008) Science , vol.322 , pp. 86-89
    • Smith, S.A.1    Donoghue, M.J.2
  • 22
    • 20144366003 scopus 로고    scopus 로고
    • The Genomes of Oryza sativa: a history of duplications
    • Yu J, Wang J, Lin W, Li S, Li H, et al. (2005) The Genomes of Oryza sativa: a history of duplications. PLoS Biol 3: e38.
    • (2005) PLoS Biol , vol.3
    • Yu, J.1    Wang, J.2    Lin, W.3    Li, S.4    Li, H.5
  • 23
    • 37649007931 scopus 로고    scopus 로고
    • Analysis of 81 genes from 64 plastid genomes resolves relationships in angiosperms and identifies genome-scale evolutionary patterns
    • Jansen RK, Cai Z, Raubeson LA, Daniell H, Depamphilis CW, et al. (2007) Analysis of 81 genes from 64 plastid genomes resolves relationships in angiosperms and identifies genome-scale evolutionary patterns. Proc Natl Acad Sci U S A 104: 19369-19374.
    • (2007) Proc Natl Acad Sci U S A , vol.104 , pp. 19369-19374
    • Jansen, R.K.1    Cai, Z.2    Raubeson, L.A.3    Daniell, H.4    Depamphilis, C.W.5
  • 24
    • 70350515004 scopus 로고    scopus 로고
    • Unexpected consequences of a sudden and massive transposon amplification on rice gene expression
    • Naito K, Zhang F, Tsukiyama T, Saito H, Hancock CN, et al. (2009) Unexpected consequences of a sudden and massive transposon amplification on rice gene expression. Nature 461: 1130-1134.
    • (2009) Nature , vol.461 , pp. 1130-1134
    • Naito, K.1    Zhang, F.2    Tsukiyama, T.3    Saito, H.4    Hancock, C.N.5
  • 25
    • 73249125240 scopus 로고    scopus 로고
    • Rice MicroRNA effector complexes and targets
    • Wu L, Zhang Q, Zhou H, Ni F, Wu X, et al. (2009) Rice MicroRNA effector complexes and targets. Plant Cell 21: 3421-3435.
    • (2009) Plant Cell , vol.21 , pp. 3421-3435
    • Wu, L.1    Zhang, Q.2    Zhou, H.3    Ni, F.4    Wu, X.5
  • 26
    • 77955844575 scopus 로고    scopus 로고
    • Robustness and evolvability
    • Masel J, Trotter MV, (2010) Robustness and evolvability. Trends Genet 26: 406-414.
    • (2010) Trends Genet , vol.26 , pp. 406-414
    • Masel, J.1    Trotter, M.V.2
  • 27
    • 60149103676 scopus 로고    scopus 로고
    • The centrality of RNA
    • Sharp PA, (2009) The centrality of RNA. Cell 136: 577-580.
    • (2009) Cell , vol.136 , pp. 577-580
    • Sharp, P.A.1
  • 28
    • 36249010911 scopus 로고    scopus 로고
    • Return to the RNAi world: rethinking gene expression and evolution
    • Mello CC, (2007) Return to the RNAi world: rethinking gene expression and evolution. Cell Death Differ 14: 2013-2020.
    • (2007) Cell Death Differ , vol.14 , pp. 2013-2020
    • Mello, C.C.1
  • 29
    • 60149098474 scopus 로고    scopus 로고
    • Small RNAs as guardians of the genome
    • Malone CD, Hannon GJ, (2009) Small RNAs as guardians of the genome. Cell 136: 656-668.
    • (2009) Cell , vol.136 , pp. 656-668
    • Malone, C.D.1    Hannon, G.J.2
  • 30
    • 38549157506 scopus 로고    scopus 로고
    • Molecular biology: the expanding world of small RNAs
    • Grosshans H, Filipowicz W, (2008) Molecular biology: the expanding world of small RNAs. Nature 451: 414-416.
    • (2008) Nature , vol.451 , pp. 414-416
    • Grosshans, H.1    Filipowicz, W.2
  • 31
    • 16544364568 scopus 로고    scopus 로고
    • The revolution of the biology of the genome
    • Hennig W, (2004) The revolution of the biology of the genome. Cell Res 14: 1-7.
    • (2004) Cell Res , vol.14 , pp. 1-7
    • Hennig, W.1
  • 32
    • 0001359591 scopus 로고
    • Introduction of a Chimeric Chalcone Synthase Gene into Petunia Results in Reversible Co-Suppression of Homologous Genes in trans
    • Napoli C, Lemieux C, Jorgensen R, (1990) Introduction of a Chimeric Chalcone Synthase Gene into Petunia Results in Reversible Co-Suppression of Homologous Genes in trans. Plant Cell 2: 279-289.
    • (1990) Plant Cell , vol.2 , pp. 279-289
    • Napoli, C.1    Lemieux, C.2    Jorgensen, R.3
  • 33
    • 0025405838 scopus 로고
    • Flavonoid genes in petunia: addition of a limited number of gene copies may lead to a suppression of gene expression
    • van der Krol AR, Mur LA, Beld M, Mol JN, Stuitje AR, (1990) Flavonoid genes in petunia: addition of a limited number of gene copies may lead to a suppression of gene expression. Plant Cell 2: 291-299.
    • (1990) Plant Cell , vol.2 , pp. 291-299
    • van der Krol, A.R.1    Mur, L.A.2    Beld, M.3    Mol, J.N.4    Stuitje, A.R.5
  • 34
    • 70449588694 scopus 로고    scopus 로고
    • Small RNAs serve as a genetic buffer against genomic shock in Arabidopsis interspecific hybrids and allopolyploids
    • Ha M, Lu J, Tian L, Ramachandran V, Kasschau KD, et al. (2009) Small RNAs serve as a genetic buffer against genomic shock in Arabidopsis interspecific hybrids and allopolyploids. Proc Natl Acad Sci U S A 106: 17835-17840.
    • (2009) Proc Natl Acad Sci U S A , vol.106 , pp. 17835-17840
    • Ha, M.1    Lu, J.2    Tian, L.3    Ramachandran, V.4    Kasschau, K.D.5
  • 35
    • 33847031363 scopus 로고    scopus 로고
    • Paramutation: from maize to mice
    • Chandler VL, (2007) Paramutation: from maize to mice. Cell 128: 641-645.
    • (2007) Cell , vol.128 , pp. 641-645
    • Chandler, V.L.1
  • 36
    • 84984765621 scopus 로고    scopus 로고
    • Canalization of development by microRNAs
    • Hornstein E, Shomron N, (2006) Canalization of development by microRNAs. Nat Genet 38 (Suppl): S20-24.
    • (2006) Nat Genet , vol.38 , Issue.SUPPL.
    • Hornstein, E.1    Shomron, N.2
  • 37
    • 34547497309 scopus 로고    scopus 로고
    • Target mimicry provides a new mechanism for regulation of microRNA activity
    • Franco-Zorrilla JM, Valli A, Todesco M, Mateos I, Puga MI, et al. (2007) Target mimicry provides a new mechanism for regulation of microRNA activity. Nat Genet 39: 1033-1037.
    • (2007) Nat Genet , vol.39 , pp. 1033-1037
    • Franco-Zorrilla, J.M.1    Valli, A.2    Todesco, M.3    Mateos, I.4    Puga, M.I.5
  • 38
    • 34547938506 scopus 로고    scopus 로고
    • microRNAs: a safeguard against turmoil?
    • Leung AK, Sharp PA, (2007) microRNAs: a safeguard against turmoil? Cell 130: 581-585.
    • (2007) Cell , vol.130 , pp. 581-585
    • Leung, A.K.1    Sharp, P.A.2
  • 39
    • 66049153398 scopus 로고    scopus 로고
    • Evolution under canalization and the dual roles of microRNAs: a hypothesis
    • Wu CI, Shen Y, Tang T, (2009) Evolution under canalization and the dual roles of microRNAs: a hypothesis. Genome Res 19: 734-743.
    • (2009) Genome Res , vol.19 , pp. 734-743
    • Wu, C.I.1    Shen, Y.2    Tang, T.3
  • 40
    • 22144472969 scopus 로고    scopus 로고
    • MicroRNAs directing siRNA biogenesis
    • Bartel B, (2005) MicroRNAs directing siRNA biogenesis. Nat Struct Mol Biol 12: 569-571.
    • (2005) Nat Struct Mol Biol , vol.12 , pp. 569-571
    • Bartel, B.1
  • 41
    • 23844495159 scopus 로고    scopus 로고
    • LINEs, SINEs and processed pseudogenes: parasitic strategies for genome modeling
    • Dewannieux M, Heidmann T, (2005) LINEs, SINEs and processed pseudogenes: parasitic strategies for genome modeling. Cytogenet Genome Res 110: 35-48.
    • (2005) Cytogenet Genome Res , vol.110 , pp. 35-48
    • Dewannieux, M.1    Heidmann, T.2
  • 42
  • 43
    • 77953217767 scopus 로고    scopus 로고
    • Arabidopsis lyrata small RNAs: transient MIRNA and small interfering RNA loci within the Arabidopsis genus
    • Ma Z, Coruh C, Axtell MJ, (2010) Arabidopsis lyrata small RNAs: transient MIRNA and small interfering RNA loci within the Arabidopsis genus. Plant Cell 22: 1090-1103.
    • (2010) Plant Cell , vol.22 , pp. 1090-1103
    • Ma, Z.1    Coruh, C.2    Axtell, M.J.3
  • 44
    • 41149149873 scopus 로고    scopus 로고
    • Sorting out small RNAs
    • Kim VN, (2008) Sorting out small RNAs. Cell 133: 25-26.
    • (2008) Cell , vol.133 , pp. 25-26
    • Kim, V.N.1
  • 46
    • 20044383938 scopus 로고    scopus 로고
    • Alternative splicing and gene duplication are inversely correlated evolutionary mechanisms
    • Kopelman NM, Lancet D, Yanai I, (2005) Alternative splicing and gene duplication are inversely correlated evolutionary mechanisms. Nat Genet 37: 588-589.
    • (2005) Nat Genet , vol.37 , pp. 588-589
    • Kopelman, N.M.1    Lancet, D.2    Yanai, I.3
  • 47
    • 33144460646 scopus 로고    scopus 로고
    • In silico discovery of human natural antisense transcripts
    • Li YY, Qin L, Guo ZM, Liu L, Xu H, et al. (2006) In silico discovery of human natural antisense transcripts. BMC Bioinformatics 7: 18.
    • (2006) BMC Bioinformatics , vol.7 , pp. 18
    • Li, Y.Y.1    Qin, L.2    Guo, Z.M.3    Liu, L.4    Xu, H.5
  • 48
    • 66349135632 scopus 로고    scopus 로고
    • Evidence for antisense transcription associated with microRNA target mRNAs in Arabidopsis
    • Luo QJ, Samanta MP, Koksal F, Janda J, Galbraith DW, et al. (2009) Evidence for antisense transcription associated with microRNA target mRNAs in Arabidopsis. PLoS Genet 5: e1000457.
    • (2009) PLoS Genet , vol.5
    • Luo, Q.J.1    Samanta, M.P.2    Koksal, F.3    Janda, J.4    Galbraith, D.W.5
  • 49
    • 34250632677 scopus 로고    scopus 로고
    • The gene balance hypothesis: from classical genetics to modern genomics
    • Birchler JA, Veitia RA, (2007) The gene balance hypothesis: from classical genetics to modern genomics. Plant Cell 19: 395-402.
    • (2007) Plant Cell , vol.19 , pp. 395-402
    • Birchler, J.A.1    Veitia, R.A.2
  • 50
    • 38749123986 scopus 로고    scopus 로고
    • Evolution of complexity in miRNA-mediated gene regulation systems
    • Takuno S, Innan H, (2008) Evolution of complexity in miRNA-mediated gene regulation systems. Trends Genet 24: 56-59.
    • (2008) Trends Genet , vol.24 , pp. 56-59
    • Takuno, S.1    Innan, H.2
  • 51
    • 56549119570 scopus 로고    scopus 로고
    • Turning a hobby into a job: how duplicated genes find new functions
    • Conant GC, Wolfe KH, (2008) Turning a hobby into a job: how duplicated genes find new functions. Nat Rev Genet 9: 938-950.
    • (2008) Nat Rev Genet , vol.9 , pp. 938-950
    • Conant, G.C.1    Wolfe, K.H.2
  • 52
    • 54049108505 scopus 로고    scopus 로고
    • Selection and mutation on microRNA target sequences during rice evolution
    • Guo X, Gui Y, Wang Y, Zhu QH, Helliwell C, et al. (2008) Selection and mutation on microRNA target sequences during rice evolution. BMC Genomics 9: 454.
    • (2008) BMC Genomics , vol.9 , pp. 454
    • Guo, X.1    Gui, Y.2    Wang, Y.3    Zhu, Q.H.4    Helliwell, C.5
  • 53
    • 39749083331 scopus 로고    scopus 로고
    • The birth and death of microRNA genes in Drosophila
    • Lu J, Shen Y, Wu Q, Kumar S, He B, et al. (2008) The birth and death of microRNA genes in Drosophila. Nat Genet 40: 351-355.
    • (2008) Nat Genet , vol.40 , pp. 351-355
    • Lu, J.1    Shen, Y.2    Wu, Q.3    Kumar, S.4    He, B.5
  • 54
    • 51749096678 scopus 로고    scopus 로고
    • Preferential regulation of duplicated genes by microRNAs in mammals
    • Li J, Musso G, Zhang Z, (2008) Preferential regulation of duplicated genes by microRNAs in mammals. Genome Biol 9: R132.
    • (2008) Genome Biol , vol.9
    • Li, J.1    Musso, G.2    Zhang, Z.3
  • 55
    • 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
  • 56
    • 78650516640 scopus 로고    scopus 로고
    • Multiple distinct small RNAs originate from the same microRNA precursors
    • Zhang W, Gao S, Zhou X, Xia J, Chellappan P, et al. (2010) Multiple distinct small RNAs originate from the same microRNA precursors. Genome Biol 11: R81.
    • (2010) Genome Biol , vol.11
    • Zhang, W.1    Gao, S.2    Zhou, X.3    Xia, J.4    Chellappan, P.5
  • 57
    • 44849134096 scopus 로고    scopus 로고
    • Detecting polymorphic regions in Arabidopsis thaliana with resequencing microarrays
    • Zeller G, Clark RM, Schneeberger K, Bohlen A, Weigel D, et al. (2008) Detecting polymorphic regions in Arabidopsis thaliana with resequencing microarrays. Genome Res 18: 918-929.
    • (2008) Genome Res , vol.18 , pp. 918-929
    • Zeller, G.1    Clark, R.M.2    Schneeberger, K.3    Bohlen, A.4    Weigel, D.5
  • 58
    • 0036187351 scopus 로고    scopus 로고
    • Extent of gene duplication in the genomes of Drosophila, nematode, and yeast
    • Gu Z, Cavalcanti A, Chen FC, Bouman P, Li WH, (2002) Extent of gene duplication in the genomes of Drosophila, nematode, and yeast. Mol Biol Evol 19: 256-262.
    • (2002) Mol Biol Evol , vol.19 , pp. 256-262
    • Gu, Z.1    Cavalcanti, A.2    Chen, F.C.3    Bouman, P.4    Li, W.H.5


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