메뉴 건너뛰기




Volumn 32, Issue 6, 2015, Pages 1487-1506

Discovery of novel genes derived from transposable elements using integrative genomic analysis

Author keywords

Arabidopsis; Brassicaceae; exaptation; molecular domestication; tandem arrays of genes; transposable elements

Indexed keywords

ARABIDOPSIS THALIANA; ARTICLE; CLASSIFICATION; CONTROLLED STUDY; GENE CLUSTER; GENE EXPRESSION; GENE IDENTIFICATION; GENE LOCATION; GENE SEQUENCE; GENETIC ANALYSIS; GENOMICS; NONHUMAN; PHYLOGENY; TRANSPOSON; ARABIDOPSIS; EXON; GENETIC VARIABILITY; GENETICS; MOLECULAR EVOLUTION; MULTIGENE FAMILY; PLANT CHROMOSOME; PLANT GENOME; PROCEDURES; SEQUENCE ALIGNMENT;

EID: 84930731121     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/molbev/msv042     Document Type: Article
Times cited : (46)

References (156)
  • 1
    • 0034649566 scopus 로고    scopus 로고
    • Analysis of the genome sequence of the flowering plant arabidopsis thaliana
    • AGI.
    • AGI. 2000. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408:796-815.
    • (2000) Nature , vol.408 , pp. 796-815
  • 2
    • 0032551829 scopus 로고    scopus 로고
    • Transposition mediated by RAG1 and RAG2 and its implications for the evolution of the immune system
    • Agrawal A, Eastman QM, Schatz DG. 1998. Transposition mediated by RAG1 and RAG2 and its implications for the evolution of the immune system. Nature 394:744-751.
    • (1998) Nature , vol.394 , pp. 744-751
    • Agrawal, A.1    Eastman, Q.M.2    Schatz, D.G.3
  • 4
    • 24644485994 scopus 로고    scopus 로고
    • JIGSAW: Integration of multiple sources of evidence for gene prediction
    • Allen JE, Salzberg SL. 2005. JIGSAW: integration of multiple sources of evidence for gene prediction. Bioinformatics 21:3596-3603.
    • (2005) Bioinformatics , vol.21 , pp. 3596-3603
    • Allen, J.E.1    Salzberg, S.L.2
  • 5
    • 84890829647 scopus 로고    scopus 로고
    • The Amborella genome and the evolution of flowering plants
    • Amborella Genome Project. 2013. The Amborella genome and the evolution of flowering plants. Science 342:1241089.
    • (2013) Science , vol.342 , pp. 1241089
    • Genome Project, A.1
  • 6
    • 33845873578 scopus 로고    scopus 로고
    • The natural history of the WRKY-GCM1 zinc fingers and the relationship between transcription factors and transposons
    • Babu MM, Iyer LM, Balaji S, Aravind L. 2006. The natural history of the WRKY-GCM1 zinc fingers and the relationship between transcription factors and transposons. Nucleic Acids Res. 34:6505-6520.
    • (2006) Nucleic Acids Res. , vol.34 , pp. 6505-6520
    • Babu, M.M.1    Iyer, L.M.2    Balaji, S.3    Aravind, L.4
  • 8
    • 70350639013 scopus 로고    scopus 로고
    • PiggyMac, a domesticated piggyBac transposase involved in programmed genome rearrangements in the ciliate Paramecium tetraurelia
    • Baudry C, Malinsky S, Restituito M, Kapusta A, Rosa S, Meyer E, Betermier M. 2009. PiggyMac, a domesticated piggyBac transposase involved in programmed genome rearrangements in the ciliate Paramecium tetraurelia. Genes Dev. 23:2478-2483.
    • (2009) Genes Dev. , vol.23 , pp. 2478-2483
    • Baudry, C.1    Malinsky, S.2    Restituito, M.3    Kapusta, A.4    Rosa, S.5    Meyer, E.6    Betermier, M.7
  • 9
    • 52349120967 scopus 로고    scopus 로고
    • Genome-wide analysis of the "cut-And-paste" transposons of grapevine
    • Benjak A, Forneck A, Casacuberta JM. 2008. Genome-wide analysis of the "cut-And-paste" transposons of grapevine. PLoS One 3:e3107.
    • (2008) PLoS One , vol.3 , pp. e3107
    • Benjak, A.1    Forneck, A.2    Casacuberta, J.M.3
  • 12
    • 79251581868 scopus 로고    scopus 로고
    • A brief history of the status of transposable elements: From junk DNA to major players in evolution
    • Biemont C. 2010. A brief history of the status of transposable elements: from junk DNA to major players in evolution. Genetics 186: 1085-1093.
    • (2010) Genetics , vol.186 , pp. 1085-1093
    • Biemont, C.1
  • 14
    • 13444257816 scopus 로고    scopus 로고
    • Transposable elements as a source of genetic innovation: Expression and evolution of a family of retrotransposon-derived neogenes in mammals
    • Brandt J, Schrauth S, Veith A-M, Froschauer A, Haneke T, Schultheis C, Gessler M, Leimeister C, Volff J-N. 2005. Transposable elements as a source of genetic innovation: expression and evolution of a family of retrotransposon-derived neogenes in mammals. Gene 345:101-111.
    • (2005) Gene , vol.345 , pp. 101-111
    • Brandt, J.1    Schrauth, S.2    Veith, A.-M.3    Froschauer, A.4    Haneke, T.5    Schultheis, C.6    Gessler, M.7    Leimeister, C.8    Volff, J.-N.9
  • 15
    • 23844431910 scopus 로고    scopus 로고
    • A family of neofunctionalized Ty3/ gypsy retrotransposon genes in mammalian genomes
    • Brandt J, Veith AM, Volff JN. 2005. A family of neofunctionalized Ty3/ gypsy retrotransposon genes in mammalian genomes. Cytogenet Genome Res. 110:307-317.
    • (2005) Cytogenet Genome Res. , vol.110 , pp. 307-317
    • Brandt, J.1    Veith, A.M.2    Volff, J.N.3
  • 16
    • 80053386792 scopus 로고    scopus 로고
    • The genome of the mesopolyploid crop species Brassica rapa
    • Brassica rapa Genome Sequencing Project Consortium
    • Brassica rapa Genome Sequencing Project Consortium, Wang X, Wang H, Wang J, Sun R, Wu J, Liu S, Bai Y, Mun J-H, Bancroft I, et al. 2011. The genome of the mesopolyploid crop species Brassica rapa. Nat Genet. 43:1035-1039.
    • (2011) Nat Genet , vol.43 , pp. 1035-1039
    • Wang, X.1    Wang, H.2    Wang, J.3    Sun, R.4    Wu, J.5    Liu, S.6    Bai, Y.7    Mun, J.-H.8    Bancroft, I.9
  • 17
    • 32444444701 scopus 로고    scopus 로고
    • Transposable elements have contributed to thousands of human proteins
    • Britten R. 2006. Transposable elements have contributed to thousands of human proteins. Proc Natl Acad Sci U S A. 103:1798-1803.
    • (2006) Proc Natl Acad Sci U S A. , vol.103 , pp. 1798-1803
    • Britten, R.1
  • 18
    • 13144255696 scopus 로고    scopus 로고
    • The ecology of the genome-mobile DNA elements and their hosts
    • Brookfield JF. 2005. The ecology of the genome-mobile DNA elements and their hosts. Nat Rev Genet. 6:128-136.
    • (2005) Nat Rev Genet. , vol.6 , pp. 128-136
    • Brookfield, J.F.1
  • 19
    • 34547576613 scopus 로고    scopus 로고
    • Multiple whole genome alignments and novel biomedical applications at the VISTA portal
    • BrudnoM, Poliakov A, Minovitsky S, Ratnere I, Dubchak I. 2007. Multiple whole genome alignments and novel biomedical applications at the VISTA portal. Nucleic Acids Res. 35:W669-W674.
    • (2007) Nucleic Acids Res. , vol.35 , pp. W669-W674
    • Brudno, M.1    Poliakov, A.2    Minovitsky, S.3    Ratnere, I.4    Dubchak, I.5
  • 20
    • 42149187766 scopus 로고    scopus 로고
    • Improved detection and annotation of transposable elements in sequenced genomes using multiple reference sequence sets
    • Buisine N, Quesneville H, Colot V. 2008. Improved detection and annotation of transposable elements in sequenced genomes using multiple reference sequence sets. Genomics 91:467-475.
    • (2008) Genomics , vol.91 , pp. 467-475
    • Buisine, N.1    Quesneville, H.2    Colot, V.3
  • 21
    • 22444439135 scopus 로고    scopus 로고
    • An Arabidopsis hAT-like transposase is essential for plant development
    • Bundock P, Hooykaas P. 2005. An Arabidopsis hAT-like transposase is essential for plant development. Nature 436:282-284.
    • (2005) Nature , vol.436 , pp. 282-284
    • Bundock, P.1    Hooykaas, P.2
  • 22
    • 46149104377 scopus 로고    scopus 로고
    • Evo-devo and an expanding evolutionary synthesis: A genetic theory of morphological evolution
    • Carroll SB. 2008. Evo-devo and an expanding evolutionary synthesis: A genetic theory of morphological evolution. Cell 134:25-36.
    • (2008) Cell , vol.134 , pp. 25-36
    • Carroll, S.B.1
  • 24
    • 84866181273 scopus 로고    scopus 로고
    • The impact of transposable elements on eukaryotic genomes: From genome size increase to genetic adaptation to stressful environments
    • Chenais B, Caruso A, Hiard S, Casse N. 2012. The impact of transposable elements on eukaryotic genomes: from genome size increase to genetic adaptation to stressful environments. Gene 509:7-15.
    • (2012) Gene , vol.509 , pp. 7-15
    • Chenais, B.1    Caruso, A.2    Hiard, S.3    Casse, N.4
  • 25
    • 77952326283 scopus 로고    scopus 로고
    • A domesticated piggyBac transposase plays key roles in heterochromatin dynamics and DNA cleavage during programmed DNA deletion in Tetrahymena thermophila
    • Cheng C-Y, Vogt A, Mochizuki K, Yao M-C. 2010. A domesticated piggyBac transposase plays key roles in heterochromatin dynamics and DNA cleavage during programmed DNA deletion in Tetrahymena thermophila. Mol Biol Cell. 21:1753-1762.
    • (2010) Mol Biol Cell. , vol.21 , pp. 1753-1762
    • Cheng, C.-Y.1    Vogt, A.2    Mochizuki, K.3    Yao, M.-C.4
  • 26
    • 18744396089 scopus 로고    scopus 로고
    • The THAP domain of THAP1 is a large C2CH module with zinc-dependent sequence-specific DNA-binding activity
    • Clouaire T, Roussigne M, Ecochard V, Mathe C, Amalric F, Girard JP. 2005. The THAP domain of THAP1 is a large C2CH module with zinc-dependent sequence-specific DNA-binding activity. Proc Natl Acad Sci U S A. 102:6907-6912.
    • (2005) Proc Natl Acad Sci U S A. , vol.102 , pp. 6907-6912
    • Clouaire, T.1    Roussigne, M.2    Ecochard, V.3    Mathe, C.4    Amalric, F.5    Girard, J.P.6
  • 27
    • 33744497802 scopus 로고    scopus 로고
    • Birth of a chimeric primate gene by capture of the transposase gene from a mobile element
    • Cordaux R, Udit S, Batzer MA, Feschotte C. 2006. Birth of a chimeric primate gene by capture of the transposase gene from a mobile element. Proc Natl Acad Sci U S A. 103:8101-8106.
    • (2006) Proc Natl Acad Sci U S A. , vol.103 , pp. 8101-8106
    • Cordaux, R.1    Udit, S.2    Batzer, M.A.3    Feschotte, C.4
  • 28
    • 24744464809 scopus 로고    scopus 로고
    • MUSTANG is a novel family of domesticated transposase genes found in diverse angiosperms
    • Cowan RK, Hoen DR, Schoen DJ, Bureau TE. 2005. MUSTANG is a novel family of domesticated transposase genes found in diverse angiosperms. Mol Biol Evol. 22:2084-2089.
    • (2005) Mol Biol Evol. , vol.22 , pp. 2084-2089
    • Cowan, R.K.1    Hoen, D.R.2    Schoen, D.J.3    Bureau, T.E.4
  • 31
    • 81355139585 scopus 로고    scopus 로고
    • Controlling gene expression in response to stress
    • de Nadal E, Ammerer G, Posas F. 2011. Controlling gene expression in response to stress. Nat Rev Genet. 12:833-845.
    • (2011) Nat Rev Genet. , vol.12 , pp. 833-845
    • De Nadal, E.1    Ammerer, G.2    Posas, F.3
  • 35
    • 0018894384 scopus 로고
    • Selfish genes, the phenotype paradigm and genome evolution
    • Doolittle WF, Sapienza C. 1980. Selfish genes, the phenotype paradigm and genome evolution. Nature 284:601-603.
    • (1980) Nature , vol.284 , pp. 601-603
    • Doolittle, W.F.1    Sapienza, C.2
  • 37
    • 77952988108 scopus 로고    scopus 로고
    • A new generation of homology search tools based on probabilistic inference
    • Eddy SR. 2009. A new generation of homology search tools based on probabilistic inference. Genome Inform. 23:205-211.
    • (2009) Genome Inform. , vol.23 , pp. 205-211
    • Eddy, S.R.1
  • 38
    • 0030848018 scopus 로고    scopus 로고
    • Telomerase and retrotransposons: Which came first
    • Eickbush TH. 1997. Telomerase and retrotransposons: which came first? Science 277:911-912.
    • (1997) Science , vol.277 , pp. 911-912
    • Eickbush, T.H.1
  • 39
    • 80655143442 scopus 로고    scopus 로고
    • Gypsy and the birth of the SCAN domain
    • Emerson RO, Thomas JH. 2011. Gypsy and the birth of the SCAN domain. J Virol. 85:12043-12052.
    • (2011) J Virol. , vol.85 , pp. 12043-12052
    • Emerson, R.O.1    Thomas, J.H.2
  • 40
    • 84868534630 scopus 로고    scopus 로고
    • Presidential address. Transposable elements, epigenetics, and genome evolution
    • Fedoroff NV. 2012. Presidential address. Transposable elements, epigenetics, and genome evolution. Science 338:758-767.
    • (2012) Science , vol.338 , pp. 758-767
    • Fedoroff, N.V.1
  • 41
    • 42349096534 scopus 로고    scopus 로고
    • Transposable elements and the evolution of regulatory networks
    • Feschotte C. 2008. Transposable elements and the evolution of regulatory networks. Nat Rev Genet. 9:397-405.
    • (2008) Nat Rev Genet. , vol.9 , pp. 397-405
    • Feschotte, C.1
  • 42
    • 37549029474 scopus 로고    scopus 로고
    • DNA transposons and the evolution of eukaryotic genomes
    • Feschotte C, Pritham EJ. 2007. DNA transposons and the evolution of eukaryotic genomes. Annu Rev Genet. 41:331-368.
    • (2007) Annu Rev Genet. , vol.41 , pp. 331-368
    • Feschotte, C.1    Pritham, E.J.2
  • 44
    • 0033593035 scopus 로고    scopus 로고
    • Disruption of the telomerase catalytic subunit gene from Arabidopsis inactivates telomerase and leads to a slow loss of telomeric DNA
    • Fitzgerald MS, Riha K, Gao F, Ren S, McKnight TD, Shippen DE. 1999. Disruption of the telomerase catalytic subunit gene from Arabidopsis inactivates telomerase and leads to a slow loss of telomeric DNA. Proc Natl Acad Sci U S A. 96:14813-14818.
    • (1999) Proc Natl Acad Sci U S A , vol.96 , pp. 14813-14818
    • Fitzgerald, M.S.1    Riha, K.2    Gao, F.3    Ren, S.4    McKnight, T.D.5    Shippen, D.E.6
  • 45
    • 67650915748 scopus 로고    scopus 로고
    • Gene duplication and evolutionary novelty in plants
    • Flagel LE, Wendel JF. 2009. Gene duplication and evolutionary novelty in plants. New Phytol. 183:557-564.
    • (2009) New Phytol. , vol.183 , pp. 557-564
    • Flagel, L.E.1    Wendel, J.F.2
  • 47
    • 13944250322 scopus 로고    scopus 로고
    • A eukaryotic gene family related to retroelement integrases
    • Gao X, Voytas D. 2005. A eukaryotic gene family related to retroelement integrases. Trends Genet. 21:133-137.
    • (2005) Trends Genet. , vol.21 , pp. 133-137
    • Gao, X.1    Voytas, D.2
  • 48
    • 33646145936 scopus 로고    scopus 로고
    • Do transposable elements really contribute to proteomes
    • Gotea V, Makalowski W. 2006. Do transposable elements really contribute to proteomes? Trends Genet. 22:260-267.
    • (2006) Trends Genet , vol.22 , pp. 260-267
    • Gotea, V.1    Makalowski, W.2
  • 49
    • 0032738801 scopus 로고    scopus 로고
    • Individuality and adaptation across levels of selection: How shall we name and generalize the unit of Darwinism
    • Gould SJ, Lloyd EA. 1999. Individuality and adaptation across levels of selection: how shall we name and generalize the unit of Darwinism? Proc Natl Acad Sci U S A. 96:11904-11909.
    • (1999) Proc Natl Acad Sci U S A , vol.96 , pp. 11904-11909
    • Gould, S.J.1    Lloyd, E.A.2
  • 51
    • 16344394793 scopus 로고    scopus 로고
    • Homologs of Drosophila P transposons were mobile in zebrafish but have been domesticated in a common ancestor of chicken and human
    • Hammer SE. 2005. Homologs of Drosophila P transposons were mobile in zebrafish but have been domesticated in a common ancestor of chicken and human. Mol Biol Evol. 22:833-844.
    • (2005) Mol Biol Evol. , vol.22 , pp. 833-844
    • Hammer, S.E.1
  • 52
    • 67649888842 scopus 로고    scopus 로고
    • TARGeT: A web-based pipeline for retrieving and characterizing gene and transposable element families from genomic sequences
    • Han Y, Burnette JM 3rd, Wessler SR. 2009. TARGeT: A web-based pipeline for retrieving and characterizing gene and transposable element families from genomic sequences. Nucleic Acids Res. 37:e78.
    • (2009) Nucleic Acids Res. , vol.37 , pp. e78
    • Han, Y.1    Burnette, J.M.2    Wessler, S.R.3
  • 54
    • 84875303118 scopus 로고    scopus 로고
    • ZBED evolution: Repeated utilization of DNA transposons as regulators of diverse host functions
    • Hayward A, Ghazal A, Andersson G, Andersson L, Jern P. 2013. ZBED evolution: repeated utilization of DNA transposons as regulators of diverse host functions. PLoS One 8:e59940.
    • (2013) PLoS One , vol.8 , pp. e59940
    • Hayward, A.1    Ghazal, A.2    Andersson, G.3    Andersson, L.4    Jern, P.5
  • 58
    • 79952303685 scopus 로고    scopus 로고
    • Transposable elements and small RNAs contribute to gene expression divergence between Arabidopsis thaliana and Arabidopsis lyrata
    • Hollister JD, Smith LM, Guo Y-L, Ott F, Weigel D, Gaut BS. 2011. Transposable elements and small RNAs contribute to gene expression divergence between Arabidopsis thaliana and Arabidopsis lyrata. Proc Natl Acad Sci U S A. 108:2322-2327.
    • (2011) Proc Natl Acad Sci U S A , vol.108 , pp. 2322-2327
    • Hollister, J.D.1    Smith, L.M.2    Guo, Y.-L.3    Ott, F.4    Weigel, D.5    Gaut, B.S.6
  • 61
    • 0038192421 scopus 로고    scopus 로고
    • The FHY3 and FAR1 genes encode transposase-related proteins involved in regulation of gene expression by the phytochrome A-signaling pathway
    • Hudson ME, Lisch DR, Quail PH. 2003. The FHY3 and FAR1 genes encode transposase-related proteins involved in regulation of gene expression by the phytochrome A-signaling pathway. Plant J. 34:453-471.
    • (2003) Plant J. , vol.34 , pp. 453-471
    • Hudson, M.E.1    Lisch, D.R.2    Quail, P.H.3
  • 62
    • 76749150030 scopus 로고    scopus 로고
    • Genome sequencing and analysis of the model grass Brachypodium distachyon
    • International Brachypodium Initiative.
    • International Brachypodium Initiative. 2010. Genome sequencing and analysis of the model grass Brachypodium distachyon. Nature 463: 763-768.
    • (2010) Nature , vol.463 , pp. 763-768
  • 63
    • 84878553926 scopus 로고    scopus 로고
    • The high-quality draft genome of peach (Prunus persica) identifies unique patterns of genetic diversity, domestication and genome evolution
    • Verde I, Abbott AG, Scalabrin S, Jung S, Shu S, Marroni F, Zhebentyayeva T, Dettori MT, Grimwood J, et al. 2013. The high-quality draft genome of peach (Prunus persica) identifies unique patterns of genetic diversity, domestication and genome evolution. Nat Genet. 45:487-494.
    • (2013) Nat Genet. , vol.45 , pp. 487-494
    • Verde, I.1    Abbott, A.G.2    Scalabrin, S.3    Jung, S.4    Shu, S.5    Marroni, F.6    Zhebentyayeva, T.7    Dettori, M.T.8    Grimwood, J.9
  • 64
    • 84868664246 scopus 로고    scopus 로고
    • ALOG domains: Provenance of plant homeotic and developmental regulators from the DNA-binding domain of a novel class of DIRS1-Type retroposons
    • Iyer LM, Aravind L. 2012. ALOG domains: provenance of plant homeotic and developmental regulators from the DNA-binding domain of a novel class of DIRS1-Type retroposons. Biol Direct. 7:39.
    • (2012) Biol Direct. , vol.7 , pp. 39
    • Iyer, L.M.1    Aravind, L.2
  • 66
    • 34447544653 scopus 로고    scopus 로고
    • A genome-wide transcriptional activity survey of rice transposable element-related genes
    • Jiao Y, Deng X. 2007. A genome-wide transcriptional activity survey of rice transposable element-related genes. Genome Biol. 8:R28.
    • (2007) Genome Biol. , vol.8 , pp. R28
    • Jiao, Y.1    Deng, X.2
  • 67
    • 84866913795 scopus 로고    scopus 로고
    • A gene family derived from transposable elements during early angiosperm evolution has reproductive fitness benefits in Arabidopsis thaliana
    • Joly-Lopez Z, Forczek E, Hoen DR, Juretic N, Bureau TE. 2012. A gene family derived from transposable elements during early angiosperm evolution has reproductive fitness benefits in Arabidopsis thaliana. PLoS Genet. 8:e1002931.
    • (2012) PLoS Genet. , vol.8 , pp. e1002931
    • Joly-Lopez, Z.1    Forczek, E.2    Hoen, D.R.3    Juretic, N.4    Bureau, T.E.5
  • 68
  • 69
    • 24344459435 scopus 로고    scopus 로고
    • The evolutionary fate of MULE-mediated duplications of host gene fragments in rice
    • Juretic N, Hoen DR, Huynh ML, Harrison PM, Bureau TE. 2005. The evolutionary fate of MULE-mediated duplications of host gene fragments in rice. Genome Res. 15:1292-1297.
    • (2005) Genome Res. , vol.15 , pp. 1292-1297
    • Juretic, N.1    Hoen, D.R.2    Huynh, M.L.3    Harrison, P.M.4    Bureau, T.E.5
  • 70
    • 22744445703 scopus 로고    scopus 로고
    • RAG1 core and V(D)J recombination signal sequences were derived from Transib transposons
    • Kapitonov VV, Jurka J. 2005. RAG1 core and V(D)J recombination signal sequences were derived from Transib transposons. PLoS Biol. 3:e181.
    • (2005) PLoS Biol. , vol.3 , pp. e181
    • Kapitonov, V.V.1    Jurka, J.2
  • 71
    • 84876864345 scopus 로고    scopus 로고
    • Transposable elements are major contributors to the origin, diversification, and regulation of vertebrate long noncoding RNAs
    • Kapusta A, Kronenberg Z, Lynch VJ, Zhuo X, Ramsay L, Bourque G, Yandell M, Feschotte C. 2013. Transposable elements are major contributors to the origin, diversification, and regulation of vertebrate long noncoding RNAs. PLoS Genet. 9:e1003470.
    • (2013) PLoS Genet. , vol.9 , pp. e1003470
    • Kapusta, A.1    Kronenberg, Z.2    Lynch, V.J.3    Zhuo, X.4    Ramsay, L.5    Bourque, G.6    Yandell, M.7    Feschotte, C.8
  • 72
    • 84875619226 scopus 로고    scopus 로고
    • MAFFT multiple sequence alignment software version 7: Improvements in performance and usability
    • Katoh K, Standley DM. 2013. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol. 30:772-780.
    • (2013) Mol Biol Evol. , vol.30 , pp. 772-780
    • Katoh, K.1    Standley, D.M.2
  • 73
    • 77951120000 scopus 로고    scopus 로고
    • Alternative splicing and evolution: Diversification, exon definition and function
    • Keren H, Lev-Maor G, Ast G. 2010. Alternative splicing and evolution: diversification, exon definition and function. Nat Rev Genet. 11: 345-355.
    • (2010) Nat Rev Genet. , vol.11 , pp. 345-355
    • Keren, H.1    Lev-Maor, G.2    Ast, G.3
  • 75
    • 0035105221 scopus 로고    scopus 로고
    • Perspective: Transposable elements, parasitic DNA, and genome evolution
    • KidwellMG, Lisch DR. 2001. Perspective: transposable elements, parasitic DNA, and genome evolution. Evolution 55:1-24.
    • (2001) Evolution , vol.55 , pp. 1-24
    • Kidwell, M.G.1    Lisch, D.R.2
  • 76
    • 84867421104 scopus 로고    scopus 로고
    • The SLEEPER genes: A transposase-derived angiosperm-specific gene family
    • Knip M, de Pater S, Hooykaas PJ. 2012. The SLEEPER genes: A transposase-derived angiosperm-specific gene family. BMC Plant Biol. 12:192.
    • (2012) BMC Plant Biol. , vol.12 , pp. 192
    • Knip, M.1    De Pater, S.2    Hooykaas, P.J.3
  • 77
    • 84889972922 scopus 로고    scopus 로고
    • DAYSLEEPER: A nuclear and vesicular-localized protein that is expressed in proliferating tissues
    • Knip M, Hiemstra S, Sietsma A, Castelein M, de Pater S, Hooykaas P. 2013. DAYSLEEPER: A nuclear and vesicular-localized protein that is expressed in proliferating tissues. BMC Plant Biol. 13:211.
    • (2013) BMC Plant Biol. , vol.13 , pp. 211
    • Knip, M.1    Hiemstra, S.2    Sietsma, A.3    Castelein, M.4    De Pater, S.5    Hooykaas, P.6
  • 80
    • 36448967092 scopus 로고    scopus 로고
    • Transposase-derived transcription factors regulate light signaling in Arabidopsis
    • Lin R, Ding L, Casola C, Ripoll DR, Feschotte C, Wang H. 2007. Transposase-derived transcription factors regulate light signaling in Arabidopsis. Science 318:1302-1305.
    • (2007) Science , vol.318 , pp. 1302-1305
    • Lin, R.1    Ding, L.2    Casola, C.3    Ripoll, D.R.4    Feschotte, C.5    Wang, H.6
  • 81
    • 16644374612 scopus 로고    scopus 로고
    • Arabidopsis FHY3/FAR1 gene family and distinct roles of its members in light control of Arabidopsis development
    • Lin R, Wang H. 2004. Arabidopsis FHY3/FAR1 gene family and distinct roles of its members in light control of Arabidopsis development. Plant Physiol. 136:4010-4022.
    • (2004) Plant Physiol. , vol.136 , pp. 4010-4022
    • Lin, R.1    Wang, H.2
  • 82
    • 84871329875 scopus 로고    scopus 로고
    • How important are transposons for plant evolution
    • Lisch D. 2013. How important are transposons for plant evolution? Nat Rev Genet. 14:49-61.
    • (2013) Nat Rev Genet , vol.14 , pp. 49-61
    • Lisch, D.1
  • 84
    • 84930741386 scopus 로고    scopus 로고
    • On the transposon origins of mammalian SCAND3 and KRBA2, two zincfinger genes carrying an integrase/transposase domain
    • Llorens C, Bernet GP, Ramasamy S, Feschotte C, Moya A. 2012. On the transposon origins of mammalian SCAND3 and KRBA2, two zincfinger genes carrying an integrase/transposase domain. Mob Genet Elements. 2:205-210.
    • (2012) Mob Genet Elements. , vol.2 , pp. 205-210
    • Llorens, C.1    Bernet, G.P.2    Ramasamy, S.3    Feschotte, C.4    Moya, A.5
  • 85
    • 59849128363 scopus 로고    scopus 로고
    • The contribution of transposable elements to expressed coding sequence in Arabidopsis thaliana
    • Lockton S, Gaut BS. 2009. The contribution of transposable elements to expressed coding sequence in Arabidopsis thaliana. J Mol Evol. 68: 80-89.
    • (2009) J Mol Evol. , vol.68 , pp. 80-89
    • Lockton, S.1    Gaut, B.S.2
  • 86
    • 84876554076 scopus 로고    scopus 로고
    • Genomicus: Five genome browsers for comparative genomics in eukaryota
    • Louis A, Muffato M, Roest Crollius H. 2013. Genomicus: five genome browsers for comparative genomics in eukaryota. Nucleic Acids Res. 41:D700-D705.
    • (2013) Nucleic Acids Res. , vol.41 , pp. D700-D705
    • Louis, A.1    Muffato, M.2    Roest Crollius, H.3
  • 87
    • 84865415008 scopus 로고    scopus 로고
    • 29 Mammalian genomes reveal novel exaptations of mobile elements for likely regulatory functions in the human genome
    • Lowe CB, Haussler D. 2012. 29 Mammalian genomes reveal novel exaptations of mobile elements for likely regulatory functions in the human genome. PLoS One 7:e43128.
    • (2012) PLoS One , vol.7 , pp. e43128
    • Lowe, C.B.1    Haussler, D.2
  • 90
    • 84901041535 scopus 로고    scopus 로고
    • RNA-directed DNA methylation: An epigenetic pathway of increasing complexity
    • Matzke MA, Mosher RA. 2014. RNA-directed DNA methylation: An epigenetic pathway of increasing complexity. Nat Rev Genet. 15: 394-408.
    • (2014) Nat Rev Genet. , vol.15 , pp. 394-408
    • Matzke, M.A.1    Mosher, R.A.2
  • 91
    • 0021715393 scopus 로고
    • The significance of responses of the genome to challenge
    • McClintock B. 1984. The significance of responses of the genome to challenge. Science (New York, N. Y.) 226:792-801.
    • (1984) Science (New York, N. Y.) , vol.226 , pp. 792-801
    • McClintock, B.1
  • 92
    • 84869092886 scopus 로고    scopus 로고
    • Transposable element small RNAs as regulators of gene expression
    • McCue ADA, Slotkin RKR. 2012. Transposable element small RNAs as regulators of gene expression. Trends Genet. 28:616-623.
    • (2012) Trends Genet. , vol.28 , pp. 616-623
    • McCue, A.D.A.1    Slotkin, R.K.R.2
  • 96
    • 0026518145 scopus 로고
    • P-element homologous sequences are tandemly repeated in the genome of Drosophila guanche
    • Miller WJ, Hagemann S, Reiter E, Pinsker W. 1992. P-element homologous sequences are tandemly repeated in the genome of Drosophila guanche. Proc Natl Acad Sci U S A. 89:4018-4022.
    • (1992) Proc Natl Acad Sci U S A. , vol.89 , pp. 4018-4022
    • Miller, W.J.1    Hagemann, S.2    Reiter, E.3    Pinsker, W.4
  • 102
    • 0035500898 scopus 로고    scopus 로고
    • Transposable elements are found in a large number of human protein-coding genes
    • Nekrutenko A, Li WH. 2001. Transposable elements are found in a large number of human protein-coding genes. Trends Genet. 17: 619-621.
    • (2001) Trends Genet. , vol.17 , pp. 619-621
    • Nekrutenko, A.1    Li, W.H.2
  • 103
    • 33644555823 scopus 로고    scopus 로고
    • On the origin of telomeres: A glimpse at the pre-Telomerase world
    • Nosek J, Kosa P, Tomaska L. 2006. On the origin of telomeres: A glimpse at the pre-Telomerase world. Bioessays 28:182-190.
    • (2006) Bioessays , vol.28 , pp. 182-190
    • Nosek, J.1    Kosa, P.2    Tomaska, L.3
  • 104
  • 108
    • 80051935853 scopus 로고    scopus 로고
    • Genome-wide binding site analysis of FAR-RED ELONGATED HYPOCOTYL3 reveals its novel function in Arabidopsis development
    • Ouyang X, Li J, Li G, Li B, Chen B, Shen H, Huang X, Mo X, Wan X, Lin R, et al. 2011. Genome-wide binding site analysis of FAR-RED ELONGATED HYPOCOTYL3 reveals its novel function in Arabidopsis development. Plant Cell 23:2514-2535.
    • (2011) Plant Cell , vol.23 , pp. 2514-2535
    • Ouyang, X.1    Li, J.2    Li, G.3    Li, B.4    Chen, B.5    Shen, H.6    Huang, X.7    Mo, X.8    Wan, X.9    Lin, R.10
  • 113
    • 79960422847 scopus 로고    scopus 로고
    • Genome sequence and analysis of the tuber crop potato
    • Potato Genome Sequencing Consortium
    • Potato Genome Sequencing Consortium, Xu X, Pan S, Cheng S, Zhang B, Mu D, Ni P, Zhang G, Yang S, Li R, et al. 2011. Genome sequence and analysis of the tuber crop potato. Nature 475:189-195.
    • (2011) Nature , vol.475 , pp. 189-195
    • Xu, X.1    Pan, S.2    Cheng, S.3    Zhang, B.4    Mu, D.5    Ni, P.6    Zhang, G.7    Yang, S.8    Li, R.9
  • 115
    • 77949718257 scopus 로고    scopus 로고
    • FastTree 2-Approximately maximum-likelihood trees for large alignments
    • Price MN, Dehal PS, Arkin AP. 2010. FastTree 2-Approximately maximum-likelihood trees for large alignments. PLoS One 5:e9490.
    • (2010) PLoS One , vol.5 , pp. e9490
    • Price, M.N.1    Dehal, P.S.2    Arkin, A.P.3
  • 119
    • 14544268717 scopus 로고    scopus 로고
    • Recurrent recruitment of the THAP DNA-binding domain and molecular domestication of the P-Transposable element
    • Quesneville H, Nouaud D, Anxolabehere D. 2005. Recurrent recruitment of the THAP DNA-binding domain and molecular domestication of the P-Transposable element. Mol Biol Evol. 22:741-746.
    • (2005) Mol Biol Evol. , vol.22 , pp. 741-746
    • Quesneville, H.1    Nouaud, D.2    Anxolabehere, D.3
  • 120
    • 84867050577 scopus 로고    scopus 로고
    • Transposable elements: An abundant and natural source of regulatory sequences for host genes
    • Rebollo R, Romanish MT, Mager DL. 2012. Transposable elements: An abundant and natural source of regulatory sequences for host genes. Annu Rev Genet. 46:21-42.
    • (2012) Annu Rev Genet. , vol.46 , pp. 21-42
    • Rebollo, R.1    Romanish, M.T.2    Mager, D.L.3
  • 122
    • 33846857991 scopus 로고    scopus 로고
    • Curated genome annotation of Oryza sativa ssp. Japonica and comparative genome analysis with Arabidopsis thaliana
    • Rice Annotation Project
    • Rice Annotation Project, Itoh T, Tanaka T, Barrero RA, Yamasaki C, Fujii Y, Hilton PB, Antonio BA, Aono H, Apweiler R, et al. 2007. Curated genome annotation of Oryza sativa ssp. japonica and comparative genome analysis with Arabidopsis thaliana. Genome Res. 17: 175-183.
    • (2007) Genome Res. , vol.17 , pp. 175-183
    • Itoh, T.1    Tanaka, T.2    Barrero, R.A.3    Yamasaki, C.4    Fujii, Y.5    Hilton, P.B.6    Antonio, B.A.7    Aono, H.8    Apweiler, R.9
  • 123
    • 33749357831 scopus 로고    scopus 로고
    • Striking similarities in the genomic distribution of tandemly arrayed genes in Arabidopsis and rice
    • Rizzon C, Ponger L, Gaut BS. 2006. Striking similarities in the genomic distribution of tandemly arrayed genes in Arabidopsis and rice. PLoS Comput Biol. 2:e115.
    • (2006) PLoS Comput Biol. , vol.2 , pp. e115
    • Rizzon, C.1    Ponger, L.2    Gaut, B.S.3
  • 124
    • 0031593204 scopus 로고    scopus 로고
    • Molecular evolution of an ancient mariner transposon, Hsmar1, in the human genome
    • Robertson HM, Zumpano KL. 1997. Molecular evolution of an ancient mariner transposon, Hsmar1, in the human genome. Gene 205: 203-217.
    • (1997) Gene , vol.205 , pp. 203-217
    • Robertson, H.M.1    Zumpano, K.L.2
  • 125
    • 34547842495 scopus 로고    scopus 로고
    • ROSINA (RSI) is part of a CACTA transposable element, TamRSI, and links flower development to transposon activity
    • Roccaro M, Li Y, Sommer H, Saedler H. 2007. ROSINA (RSI) is part of a CACTA transposable element, TamRSI, and links flower development to transposon activity. Mol Genet Genomics. 278:243-254.
    • (2007) Mol Genet Genomics. , vol.278 , pp. 243-254
    • Roccaro, M.1    Li, Y.2    Sommer, H.3    Saedler, H.4
  • 126
    • 0344442909 scopus 로고    scopus 로고
    • Molecular evolutionary analysis of the widespread piggyBac transposon family and related "domesticated" sequences
    • Sarkar A, Sim C, Hong YS, Hogan JR, Fraser MJ, Robertson HM, Collins FH. 2003. Molecular evolutionary analysis of the widespread piggyBac transposon family and related "domesticated" sequences. Mol Genet Genomics. 270:173-180.
    • (2003) Mol Genet Genomics. , vol.270 , pp. 173-180
    • Sarkar, A.1    Sim, C.2    Hong, Y.S.3    Hogan, J.R.4    Fraser, M.J.5    Robertson, H.M.6    Collins, F.H.7
  • 132
    • 0036944528 scopus 로고    scopus 로고
    • The Drosophila Pipsqueak protein defines a new family of helix-Turn-helix DNA-binding proteins
    • Siegmund T, Lehmann M. 2002. The Drosophila Pipsqueak protein defines a new family of helix-Turn-helix DNA-binding proteins. Dev Genes Evol. 212:152-157.
    • (2002) Dev Genes Evol. , vol.212 , pp. 152-157
    • Siegmund, T.1    Lehmann, M.2
  • 134
    • 62349089758 scopus 로고    scopus 로고
    • Molecular domestication of transposable elements: From detrimental parasites to useful host genes
    • Sinzelle L, Izsvak Z, Ivics Z. 2009. Molecular domestication of transposable elements: from detrimental parasites to useful host genes. Cell Mol Life Sci. 66:1073-1093.
    • (2009) Cell Mol Life Sci. , vol.66 , pp. 1073-1093
    • Sinzelle, L.1    Izsvak, Z.2    Ivics, Z.3
  • 136
    • 0032784908 scopus 로고    scopus 로고
    • Interspersed repeats and other mementos of transposable elements in mammalian genomes
    • Smit AF. 1999. Interspersed repeats and other mementos of transposable elements in mammalian genomes. Curr Opin Genet Dev. 9: 657-663.
    • (1999) Curr Opin Genet Dev. , vol.9 , pp. 657-663
    • Smit, A.F.1
  • 137
    • 0029991222 scopus 로고    scopus 로고
    • Tiggers and DNA transposon fossils in the human genome
    • Smit AF, Riggs AD. 1996. Tiggers and DNA transposon fossils in the human genome. Proc Natl Acad Sci U S A. 93:1443-1448.
    • (1996) Proc Natl Acad Sci U S A. , vol.93 , pp. 1443-1448
    • Smit, A.F.1    Riggs, A.D.2
  • 138
    • 84857990796 scopus 로고    scopus 로고
    • The cutting crew-ribonucleases are key players in the control of plastid gene expression
    • Stoppel R, Meurer J. 2012. The cutting crew-ribonucleases are key players in the control of plastid gene expression. J Exp Bot. 63: 1663-1673.
    • (2012) J Exp Bot. , vol.63 , pp. 1663-1673
    • Stoppel, R.1    Meurer, J.2
  • 140
    • 84863693752 scopus 로고    scopus 로고
    • The tomato genome sequence provides insights into fleshy fruit evolution
    • Tomato Genome Consortium
    • Tomato Genome Consortium. 2012. The tomato genome sequence provides insights into fleshy fruit evolution. Nature 485:635-641.
    • (2012) Nature , vol.485 , pp. 635-641
  • 143
    • 33748936552 scopus 로고    scopus 로고
    • Turning junk into gold: Domestication of transposable elements and the creation of new genes in eukaryotes
    • Volff J-N. 2006. Turning junk into gold: domestication of transposable elements and the creation of new genes in eukaryotes. Bioessays 28: 913-922.
    • (2006) Bioessays , vol.28 , pp. 913-922
    • Volff, J.-N.1
  • 147
    • 84890972951 scopus 로고    scopus 로고
    • Small RNAs, big impact: Small RNA pathways in transposon control and their effect on the host stress response
    • Wheeler BS. 2013. Small RNAs, big impact: small RNA pathways in transposon control and their effect on the host stress response. Chromosome Res. 21:587-600.
    • (2013) Chromosome Res. , vol.21 , pp. 587-600
    • Wheeler, B.S.1
  • 151
    • 34548575149 scopus 로고    scopus 로고
    • Transposable element fragments in proteincoding regions and their contributions to human functional proteins
    • Wu M, Li L, Sun Z. 2007. Transposable element fragments in proteincoding regions and their contributions to human functional proteins. Gene 401:165-171.
    • (2007) Gene , vol.401 , pp. 165-171
    • Wu, M.1    Li, L.2    Sun, Z.3
  • 152
    • 84877107923 scopus 로고    scopus 로고
    • DNAbinding domains of plant-specific transcription factors: Structure, function, and evolution
    • Yamasaki K, Kigawa T, Seki M, Shinozaki K, Yokoyama S. 2013. DNAbinding domains of plant-specific transcription factors: structure, function, and evolution. Trends Plant Sci. 18:267-276.
    • (2013) Trends Plant Sci. , vol.18 , pp. 267-276
    • Yamasaki, K.1    Kigawa, T.2    Seki, M.3    Shinozaki, K.4    Yokoyama, S.5
  • 155
    • 13944250658 scopus 로고    scopus 로고
    • Protein coding potential of retroviruses and other transposable elements in vertebrate genomes
    • Zdobnov EM, Campillos M, Harrington ED, Torrents D, Bork P. 2005. Protein coding potential of retroviruses and other transposable elements in vertebrate genomes. Nucleic Acids Res. 33:946-954.
    • (2005) Nucleic Acids Res , vol.33 , pp. 946-954
    • Zdobnov, E.M.1    Campillos, M.2    Harrington, E.D.3    Torrents, D.4    Bork, P.5
  • 156


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.