메뉴 건너뛰기




Volumn 11, Issue 1, 2013, Pages

The Oxytricha trifallax Macronuclear Genome: A Complex Eukaryotic Genome with 16,000 Tiny Chromosomes

(29)  Swart, Estienne C a   Bracht, John R a   Magrini, Vincent b   Minx, Patrick b   Chen, Xiao a   Zhou, Yi a   Khurana, Jaspreet S a   Goldman, Aaron D a   Nowacki, Mariusz a,c   Schotanus, Klaas a   Jung, Seolkyoung d   Fulton, Robert S b   Ly, Amy b   McGrath, Sean b   Haub, Kevin b   Wiggins, Jessica L a   Storton, Donna a   Matese, John C a   Parsons, Lance a   Chang, Wei Jen e   more..


Author keywords

[No Author keywords available]

Indexed keywords

TRANSPOSASE;

EID: 84873111080     PISSN: 15449173     EISSN: 15457885     Source Type: Journal    
DOI: 10.1371/journal.pbio.1001473     Document Type: Article
Times cited : (181)

References (133)
  • 1
    • 84861330255 scopus 로고    scopus 로고
    • Characterization and taxonomic validity of the ciliate Oxytricha trifallax (class spirotrichea) based on multiple gene sequences: limitations in identifying genera solely by morphology
    • Zoller SD, Hammersmith RL, Swart EC, Higgins BP, Doak TG, et al. (2012) Characterization and taxonomic validity of the ciliate Oxytricha trifallax (class spirotrichea) based on multiple gene sequences: limitations in identifying genera solely by morphology. Protist 163 (4) (): 643-657.
    • (2012) Protist , vol.163 , Issue.4 , pp. 643-657
    • Zoller, S.D.1    Hammersmith, R.L.2    Swart, E.C.3    Higgins, B.P.4    Doak, T.G.5
  • 2
    • 0028231010 scopus 로고
    • The DNA of ciliated protozoa
    • Prescott DM, (1994) The DNA of ciliated protozoa. Microbiol Rev 58: 233-267.
    • (1994) Microbiol Rev , vol.58 , pp. 233-267
    • Prescott, D.M.1
  • 3
    • 0016204893 scopus 로고
    • The development of the macronucleus in the ciliated protozoan Stylonychia mytilus
    • Ammermann D, Steinbruck G, von Berger L, Hennig W, (1974) The development of the macronucleus in the ciliated protozoan Stylonychia mytilus. Chromosoma 45: 401-429.
    • (1974) Chromosoma , vol.45 , pp. 401-429
    • Ammermann, D.1    Steinbruck, G.2    von Berger, L.3    Hennig, W.4
  • 5
    • 84868089881 scopus 로고    scopus 로고
    • The Paramecium germline genome provides a niche for intragenic parasitic DNA: evolutionary dynamics of internal eliminated sequences
    • doi:10.1371/journal.pgen.1002984
    • Arnaiz O, Mathy N, Baudry C, Malinsky S, Aury JM, et al. (2012) The Paramecium germline genome provides a niche for intragenic parasitic DNA: evolutionary dynamics of internal eliminated sequences. PLoS Genet 8: e1002984 doi:10.1371/journal.pgen.1002984.
    • (2012) PLoS Genet , vol.8
    • Arnaiz, O.1    Mathy, N.2    Baudry, C.3    Malinsky, S.4    Aury, J.M.5
  • 8
    • 0025877940 scopus 로고
    • Overamplification of macronuclear linear DNA molecules during prolonged vegetative growth of Oxytricha nova
    • Harper DS, Song K, Jahn CL, (1991) Overamplification of macronuclear linear DNA molecules during prolonged vegetative growth of Oxytricha nova. Gene 99: 55-61.
    • (1991) Gene , vol.99 , pp. 55-61
    • Harper, D.S.1    Song, K.2    Jahn, C.L.3
  • 10
    • 0023445717 scopus 로고
    • Multiple sequence versions of the Oxytricha fallax 81-MAC alternate processing family
    • Herrick G, Cartinhour SW, Williams KR, Kotter KP, (1987) Multiple sequence versions of the Oxytricha fallax 81-MAC alternate processing family. J Protozool 34: 429-434.
    • (1987) J Protozool , vol.34 , pp. 429-434
    • Herrick, G.1    Cartinhour, S.W.2    Williams, K.R.3    Kotter, K.P.4
  • 11
    • 0021436486 scopus 로고
    • Three different macronuclear DNAs in Oxytricha fallax share a common sequence block
    • Cartinhour SW, Herrick GA, (1984) Three different macronuclear DNAs in Oxytricha fallax share a common sequence block. Mol Cell Biol 4: 931-938.
    • (1984) Mol Cell Biol , vol.4 , pp. 931-938
    • Cartinhour, S.W.1    Herrick, G.A.2
  • 12
    • 0024283923 scopus 로고
    • Alternative use of chromosome fragmentation sites in the ciliated protozoan Oxytricha nova
    • Klobutcher LA, Huff ME, Gonye GE, (1988) Alternative use of chromosome fragmentation sites in the ciliated protozoan Oxytricha nova. Nucleic Acids Res 16: 251-264.
    • (1988) Nucleic Acids Res , vol.16 , pp. 251-264
    • Klobutcher, L.A.1    Huff, M.E.2    Gonye, G.E.3
  • 13
    • 0023474129 scopus 로고
    • Alternative processing during development of a macronuclear chromosome family in Oxytricha fallax
    • Herrick G, Hunter D, Williams K, Kotter K, (1987) Alternative processing during development of a macronuclear chromosome family in Oxytricha fallax. Genes Dev 1: 1047-1058.
    • (1987) Genes Dev , vol.1 , pp. 1047-1058
    • Herrick, G.1    Hunter, D.2    Williams, K.3    Kotter, K.4
  • 14
    • 84863882682 scopus 로고    scopus 로고
    • Copy number variations of 11 macronuclear chromosomes and their gene expression in Oxytricha trifallax
    • Xu K, Doak TG, Lipps HJ, Wang J, Swart EC, et al. (2012) Copy number variations of 11 macronuclear chromosomes and their gene expression in Oxytricha trifallax. Gene 505 (1) (): 75-80.
    • (2012) Gene , vol.505 , Issue.1 , pp. 75-80
    • Xu, K.1    Doak, T.G.2    Lipps, H.J.3    Wang, J.4    Swart, E.C.5
  • 15
    • 0040450087 scopus 로고
    • Structural aspects of amitosis: a light and electron microscope study of the isolated macronuclei of Paramecium aurelia and Tetrahymena pyriformis
    • Wolfe J, (1967) Structural aspects of amitosis: a light and electron microscope study of the isolated macronuclei of Paramecium aurelia and Tetrahymena pyriformis. Chromosoma 23: 59-79.
    • (1967) Chromosoma , vol.23 , pp. 59-79
    • Wolfe, J.1
  • 16
    • 0014982957 scopus 로고
    • Morphology and development of the macronuclei of the ciliates Stylonychia mytilus and Euplotes aediculatus
    • Ammermann D, (1971) Morphology and development of the macronuclei of the ciliates Stylonychia mytilus and Euplotes aediculatus. Chromosoma 33: 209-238.
    • (1971) Chromosoma , vol.33 , pp. 209-238
    • Ammermann, D.1
  • 17
    • 0026665577 scopus 로고
    • Rate of phenotypic assortment in Tetrahymena thermophila
    • Doerder FP, Deak JC, Lief JH, (1992) Rate of phenotypic assortment in Tetrahymena thermophila. Dev Genet 13: 126-132.
    • (1992) Dev Genet , vol.13 , pp. 126-132
    • Doerder, F.P.1    Deak, J.C.2    Lief, J.H.3
  • 19
    • 0343620719 scopus 로고
    • Appendix model of subnuclear segregation in the macronucleus of ciliates
    • Schensted IV, (1958) Appendix model of subnuclear segregation in the macronucleus of ciliates. The American Naturalist 92: 161-170.
    • (1958) The American Naturalist , vol.92 , pp. 161-170
    • Schensted, I.V.1
  • 20
    • 0005959661 scopus 로고
    • An analysis of nuclear differentiation in the selfers of Tetrahymena
    • Allen SL, Nanney DL, (1958) An analysis of nuclear differentiation in the selfers of Tetrahymena. The American Naturalist 92: 139-160.
    • (1958) The American Naturalist , vol.92 , pp. 139-160
    • Allen, S.L.1    Nanney, D.L.2
  • 21
    • 0034810263 scopus 로고    scopus 로고
    • Minichromosomal DNA replication in the macronucleus of the hypotrichous ciliate Stylonychia lemnae is independent of chromosome-internal sequences
    • Skovorodkin IN, Zassoukhina IB, Hojak S, Ammermann D, Gunzl A, (2001) Minichromosomal DNA replication in the macronucleus of the hypotrichous ciliate Stylonychia lemnae is independent of chromosome-internal sequences. Chromosoma 110: 352-359.
    • (2001) Chromosoma , vol.110 , pp. 352-359
    • Skovorodkin, I.N.1    Zassoukhina, I.B.2    Hojak, S.3    Ammermann, D.4    Gunzl, A.5
  • 22
    • 1942444653 scopus 로고    scopus 로고
    • Modeling senescence in hypotrichous ciliates
    • Duerr HP, Eichner M, Ammermann D, (2004) Modeling senescence in hypotrichous ciliates. Protist 155: 45-52.
    • (2004) Protist , vol.155 , pp. 45-52
    • Duerr, H.P.1    Eichner, M.2    Ammermann, D.3
  • 23
    • 0023056214 scopus 로고
    • Control of rDNA replication in Tetrahymena involves a cis-acting upstream repeat of a promoter element
    • Larson DD, Blackburn EH, Yaeger PC, Orias E, (1986) Control of rDNA replication in Tetrahymena involves a cis-acting upstream repeat of a promoter element. Cell 47: 229-240.
    • (1986) Cell , vol.47 , pp. 229-240
    • Larson, D.D.1    Blackburn, E.H.2    Yaeger, P.C.3    Orias, E.4
  • 24
    • 0028006325 scopus 로고
    • A weak germ-line excision mutation blocks developmentally controlled amplification of the rDNA minichromosome of Tetrahymena thermophila
    • Kapler GM, Blackburn EH, (1994) A weak germ-line excision mutation blocks developmentally controlled amplification of the rDNA minichromosome of Tetrahymena thermophila. Genes Dev 8: 84-95.
    • (1994) Genes Dev , vol.8 , pp. 84-95
    • Kapler, G.M.1    Blackburn, E.H.2
  • 25
    • 0029812439 scopus 로고    scopus 로고
    • Timing of differential amplification of macronucleus-destined sequences during macronuclear development in the hypotrichous ciliate Euplotes crassus
    • Donhoff T, Klein A, (1996) Timing of differential amplification of macronucleus-destined sequences during macronuclear development in the hypotrichous ciliate Euplotes crassus. Chromosoma 105: 172-179.
    • (1996) Chromosoma , vol.105 , pp. 172-179
    • Donhoff, T.1    Klein, A.2
  • 27
    • 0023037564 scopus 로고
    • Telomere proteins: specific recognition and protection of the natural termini of Oxytricha macronuclear DNA
    • Gottschling DE, Zakian VA, (1986) Telomere proteins: specific recognition and protection of the natural termini of Oxytricha macronuclear DNA. Cell 47: 195-205.
    • (1986) Cell , vol.47 , pp. 195-205
    • Gottschling, D.E.1    Zakian, V.A.2
  • 28
    • 0023433713 scopus 로고
    • Telomeric DNA-protein interactions of Oxytricha macronuclear DNA
    • Price CM, Cech TR, (1987) Telomeric DNA-protein interactions of Oxytricha macronuclear DNA. Genes Dev 1: 783-793.
    • (1987) Genes Dev , vol.1 , pp. 783-793
    • Price, C.M.1    Cech, T.R.2
  • 29
    • 0022328483 scopus 로고
    • Mobile elements bounded by C4A4 telomeric repeats in Oxytricha fallax
    • Herrick G, Cartinhour S, Dawson D, Ang D, Sheets R, et al. (1985) Mobile elements bounded by C4A4 telomeric repeats in Oxytricha fallax. Cell 43: 759-768.
    • (1985) Cell , vol.43 , pp. 759-768
    • Herrick, G.1    Cartinhour, S.2    Dawson, D.3    Ang, D.4    Sheets, R.5
  • 30
    • 66149132301 scopus 로고    scopus 로고
    • A functional role for transposases in a large eukaryotic genome
    • Nowacki M, Higgins BP, Maquilan GM, Swart EC, Doak TG, et al. (2009) A functional role for transposases in a large eukaryotic genome. Science 324: 935-938.
    • (2009) Science , vol.324 , pp. 935-938
    • Nowacki, M.1    Higgins, B.P.2    Maquilan, G.M.3    Swart, E.C.4    Doak, T.G.5
  • 31
    • 2942520153 scopus 로고    scopus 로고
    • Telomere formation on macronuclear chromosomes of Oxytricha trifallax and O. fallax: alternatively processed regions have multiple telomere addition sites
    • Williams KR, Doak TG, Herrick G, (2002) Telomere formation on macronuclear chromosomes of Oxytricha trifallax and O. fallax: alternatively processed regions have multiple telomere addition sites. BMC Genet 3: 16.
    • (2002) BMC Genet , vol.3 , pp. 16
    • Williams, K.R.1    Doak, T.G.2    Herrick, G.3
  • 32
    • 0034548911 scopus 로고    scopus 로고
    • A unique pattern of intrastrand anomalies in base composition of the DNA in hypotrichs
    • Prescott DM, Dizick SJ, (2000) A unique pattern of intrastrand anomalies in base composition of the DNA in hypotrichs. Nucleic Acids Res 28: 4679-4688.
    • (2000) Nucleic Acids Res , vol.28 , pp. 4679-4688
    • Prescott, D.M.1    Dizick, S.J.2
  • 33
    • 4644345013 scopus 로고    scopus 로고
    • Coding properties of Oxytricha trifallax (Sterkiella histriomuscorum) macronuclear chromosomes: analysis of a pilot genome project
    • Cavalcanti AR, Stover NA, Orecchia L, Doak TG, Landweber LF, (2004) Coding properties of Oxytricha trifallax (Sterkiella histriomuscorum) macronuclear chromosomes: analysis of a pilot genome project. Chromosoma 113: 69-76.
    • (2004) Chromosoma , vol.113 , pp. 69-76
    • Cavalcanti, A.R.1    Stover, N.A.2    Orecchia, L.3    Doak, T.G.4    Landweber, L.F.5
  • 36
    • 78651433774 scopus 로고    scopus 로고
    • PE-Assembler: de novo assembler using short paired-end reads
    • Ariyaratne PN, Sung WK, (2011) PE-Assembler: de novo assembler using short paired-end reads. Bioinformatics 27: 167-174.
    • (2011) Bioinformatics , vol.27 , pp. 167-174
    • Ariyaratne, P.N.1    Sung, W.K.2
  • 38
    • 77956279237 scopus 로고    scopus 로고
    • Assembly of large genomes using second-generation sequencing
    • Schatz MC, Delcher AL, Salzberg SL, (2010) Assembly of large genomes using second-generation sequencing. Genome Res 20 (9) (): 1165-1173.
    • (2010) Genome Res , vol.20 , Issue.9 , pp. 1165-1173
    • Schatz, M.C.1    Delcher, A.L.2    Salzberg, S.L.3
  • 39
    • 0032849859 scopus 로고    scopus 로고
    • CAP3: a DNA sequence assembly program
    • Huang X, Madan A, (1999) CAP3: a DNA sequence assembly program. Genome Res 9: 868-877.
    • (1999) Genome Res , vol.9 , pp. 868-877
    • Huang, X.1    Madan, A.2
  • 41
    • 33244477927 scopus 로고    scopus 로고
    • Patterns of protein evolution in Tetrahymena thermophila: implications for estimates of effective population size
    • Katz LA, Snoeyenbos-West O, Doerder FP, (2006) Patterns of protein evolution in Tetrahymena thermophila: implications for estimates of effective population size. Mol Biol Evol 23: 608-614.
    • (2006) Mol Biol Evol , vol.23 , pp. 608-614
    • Katz, L.A.1    Snoeyenbos-West, O.2    Doerder, F.P.3
  • 42
    • 33750936273 scopus 로고    scopus 로고
    • Large global effective population sizes in Paramecium
    • Snoke MS, Berendonk TU, Barth D, Lynch M, (2006) Large global effective population sizes in Paramecium. Mol Biol Evol 23: 2474-2479.
    • (2006) Mol Biol Evol , vol.23 , pp. 2474-2479
    • Snoke, M.S.1    Berendonk, T.U.2    Barth, D.3    Lynch, M.4
  • 43
    • 0029857126 scopus 로고    scopus 로고
    • Internal eliminated sequences interrupting the Oxytricha 81 locus: allelic divergence, conservation, conversions, and possible transposon origins
    • Seegmiller A, Williams KR, Hammersmith RL, Doak TG, Witherspoon D, et al. (1996) Internal eliminated sequences interrupting the Oxytricha 81 locus: allelic divergence, conservation, conversions, and possible transposon origins. Mol Biol Evol 13: 1351-1362.
    • (1996) Mol Biol Evol , vol.13 , pp. 1351-1362
    • Seegmiller, A.1    Williams, K.R.2    Hammersmith, R.L.3    Doak, T.G.4    Witherspoon, D.5
  • 44
    • 0036226603 scopus 로고    scopus 로고
    • BLAT-the BLAST-like alignment tool
    • Kent WJ, (2002) BLAT-the BLAST-like alignment tool. Genome Res 12: 656-664.
    • (2002) Genome Res , vol.12 , pp. 656-664
    • Kent, W.J.1
  • 45
    • 0029071631 scopus 로고
    • Scrambling of the actin I gene in two Oxytricha species
    • DuBois M, Prescott DM, (1995) Scrambling of the actin I gene in two Oxytricha species. Proc Natl Acad Sci U S A 92: 3888-3892.
    • (1995) Proc Natl Acad Sci U S A , vol.92 , pp. 3888-3892
    • DuBois, M.1    Prescott, D.M.2
  • 46
    • 0020071908 scopus 로고
    • Nucleotide sequence of a macronuclear gene for actin in Oxytricha fallax
    • Kaine BP, Spear BB, (1982) Nucleotide sequence of a macronuclear gene for actin in Oxytricha fallax. Nature 295: 430-432.
    • (1982) Nature , vol.295 , pp. 430-432
    • Kaine, B.P.1    Spear, B.B.2
  • 47
    • 84861330255 scopus 로고    scopus 로고
    • Characterization and taxonomic validity of the ciliate Oxytricha trifallax (Class Spirotrichea) based on multiple gene sequences: limitations in identifying genera solely by morphology
    • Zoller SD, Hammersmith RL, Swart EC, Higgins BP, Doak TG, et al. (2012) Characterization and taxonomic validity of the ciliate Oxytricha trifallax (Class Spirotrichea) based on multiple gene sequences: limitations in identifying genera solely by morphology. Protist 163: 643-657.
    • (2012) Protist , vol.163 , pp. 643-657
    • Zoller, S.D.1    Hammersmith, R.L.2    Swart, E.C.3    Higgins, B.P.4    Doak, T.G.5
  • 49
    • 0041817555 scopus 로고    scopus 로고
    • The population genetics of clonal and partially clonal diploids
    • Balloux F, Lehmann L, de Meeus T, (2003) The population genetics of clonal and partially clonal diploids. Genetics 164: 1635-1644.
    • (2003) Genetics , vol.164 , pp. 1635-1644
    • Balloux, F.1    Lehmann, L.2    de Meeus, T.3
  • 50
    • 1942485893 scopus 로고    scopus 로고
    • The effective size of mixed sexually and asexually reproducing populations
    • Yonezawa K, Ishii T, Nagamine T, (2004) The effective size of mixed sexually and asexually reproducing populations. Genetics 166: 1529-1539.
    • (2004) Genetics , vol.166 , pp. 1529-1539
    • Yonezawa, K.1    Ishii, T.2    Nagamine, T.3
  • 51
    • 70349910898 scopus 로고    scopus 로고
    • Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing data
    • Degner JF, Marioni JC, Pai AA, Pickrell JK, Nkadori E, et al. (2009) Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing data. Bioinformatics 25: 3207-3212.
    • (2009) Bioinformatics , vol.25 , pp. 3207-3212
    • Degner, J.F.1    Marioni, J.C.2    Pai, A.A.3    Pickrell, J.K.4    Nkadori, E.5
  • 52
    • 0017265791 scopus 로고
    • DNA of ciliated protozoa: DNA sequence diminution during macronuclear development of Oxytricha
    • Lauth MR, Spear BB, Heumann J, Prescott DM, (1976) DNA of ciliated protozoa: DNA sequence diminution during macronuclear development of Oxytricha. Cell 7: 67-74.
    • (1976) Cell , vol.7 , pp. 67-74
    • Lauth, M.R.1    Spear, B.B.2    Heumann, J.3    Prescott, D.M.4
  • 53
    • 0019466488 scopus 로고
    • Characterization of macronuclear DNA in five species of ciliates
    • Steinbruck G, Haas I, Hellmer KH, Ammermann D, (1981) Characterization of macronuclear DNA in five species of ciliates. Chromosoma 83: 199-208.
    • (1981) Chromosoma , vol.83 , pp. 199-208
    • Steinbruck, G.1    Haas, I.2    Hellmer, K.H.3    Ammermann, D.4
  • 54
    • 0021958933 scopus 로고
    • Codon usage and tRNA content in unicellular and multicellular organisms
    • Ikemura T, (1985) Codon usage and tRNA content in unicellular and multicellular organisms. Mol Biol Evol 2: 13-34.
    • (1985) Mol Biol Evol , vol.2 , pp. 13-34
    • Ikemura, T.1
  • 56
    • 33748598232 scopus 로고    scopus 로고
    • Macronuclear genome sequence of the ciliate Tetrahymena thermophila, a model eukaryote
    • doi:10.1371/journal.pbio.0040286
    • Eisen JA, Coyne RS, Wu M, Wu D, Thiagarajan M, et al. (2006) Macronuclear genome sequence of the ciliate Tetrahymena thermophila, a model eukaryote. PLoS Biol 4: e286 doi:10.1371/journal.pbio.0040286.
    • (2006) PLoS Biol , vol.4
    • Eisen, J.A.1    Coyne, R.S.2    Wu, M.3    Wu, D.4    Thiagarajan, M.5
  • 59
    • 80052700309 scopus 로고    scopus 로고
    • Exploiting Oxytricha trifallax nanochromosomes to screen for non-coding RNA genes
    • Jung S, Swart EC, Minx PJ, Magrini V, Mardis ER, et al. (2011) Exploiting Oxytricha trifallax nanochromosomes to screen for non-coding RNA genes. Nucleic Acids Res 39: 7529-7547.
    • (2011) Nucleic Acids Res , vol.39 , pp. 7529-7547
    • Jung, S.1    Swart, E.C.2    Minx, P.J.3    Magrini, V.4    Mardis, E.R.5
  • 61
    • 80052019696 scopus 로고    scopus 로고
    • Estimating the timing of early eukaryotic diversification with multigene molecular clocks
    • Parfrey LW, Lahr DJ, Knoll AH, Katz LA, (2011) Estimating the timing of early eukaryotic diversification with multigene molecular clocks. Proc Natl Acad Sci U S A 108: 13624-13629.
    • (2011) Proc Natl Acad Sci U S A , vol.108 , pp. 13624-13629
    • Parfrey, L.W.1    Lahr, D.J.2    Knoll, A.H.3    Katz, L.A.4
  • 62
    • 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
  • 63
    • 0026009964 scopus 로고
    • Feedback control of mitosis in budding yeast
    • Li R, Murray AW, (1991) Feedback control of mitosis in budding yeast. Cell 66: 519-531.
    • (1991) Cell , vol.66 , pp. 519-531
    • Li, R.1    Murray, A.W.2
  • 64
    • 80054058521 scopus 로고    scopus 로고
    • Comparative genomics of the pathogenic ciliate Ichthyophthirius multifiliis, its free-living relatives and a host species provide insights into adoption of a parasitic lifestyle and prospects for disease control
    • Coyne RS, Hannick L, Shanmugam D, Hostetler JB, Brami D, et al. (2011) Comparative genomics of the pathogenic ciliate Ichthyophthirius multifiliis, its free-living relatives and a host species provide insights into adoption of a parasitic lifestyle and prospects for disease control. Genome Biol 12: R100.
    • (2011) Genome Biol , vol.12
    • Coyne, R.S.1    Hannick, L.2    Shanmugam, D.3    Hostetler, J.B.4    Brami, D.5
  • 66
    • 84873121815 scopus 로고
    • An experimental study of an amicronucleate Oxytricha. I. Study of the normal animal, with an account of cannibalism
    • Dawson JA, (1919) An experimental study of an amicronucleate Oxytricha. I. Study of the normal animal, with an account of cannibalism. Journal of Experimental Zoology 29: 473-513.
    • (1919) Journal of Experimental Zoology , vol.29 , pp. 473-513
    • Dawson, J.A.1
  • 67
    • 0026645086 scopus 로고
    • A high degree of macronuclear chromosome polymorphism is generated by variable DNA rearrangements in Paramecium primaurelia during macronuclear differentiation
    • Caron F, (1992) A high degree of macronuclear chromosome polymorphism is generated by variable DNA rearrangements in Paramecium primaurelia during macronuclear differentiation. J Mol Biol 225: 661-678.
    • (1992) J Mol Biol , vol.225 , pp. 661-678
    • Caron, F.1
  • 68
    • 0142184930 scopus 로고    scopus 로고
    • Developmentally regulated chromosome fragmentation linked to imprecise elimination of repeated sequences in paramecia
    • Le Mouel A, Butler A, Caron F, Meyer E, (2003) Developmentally regulated chromosome fragmentation linked to imprecise elimination of repeated sequences in paramecia. Eukaryot Cell 2: 1076-1090.
    • (2003) Eukaryot Cell , vol.2 , pp. 1076-1090
    • Le Mouel, A.1    Butler, A.2    Caron, F.3    Meyer, E.4
  • 69
    • 41649113803 scopus 로고    scopus 로고
    • Analysis of sequence variability in the macronuclear DNA of Paramecium tetraurelia: a somatic view of the germline
    • Duret L, Cohen J, Jubin C, Dessen P, Gout JF, et al. (2008) Analysis of sequence variability in the macronuclear DNA of Paramecium tetraurelia: a somatic view of the germline. Genome Res 18: 585-596.
    • (2008) Genome Res , vol.18 , pp. 585-596
    • Duret, L.1    Cohen, J.2    Jubin, C.3    Dessen, P.4    Gout, J.F.5
  • 70
    • 0018872413 scopus 로고
    • Gene-sized DNA molecules of the macronuclei in three species of hypotrichs: size distributions and absence of nicks. DNA of ciliated protozoa. VIII
    • Swanton MT, Heumann JM, Prescott DM, (1980) Gene-sized DNA molecules of the macronuclei in three species of hypotrichs: size distributions and absence of nicks. DNA of ciliated protozoa. VIII. Chromosoma 77: 217-227.
    • (1980) Chromosoma , vol.77 , pp. 217-227
    • Swanton, M.T.1    Heumann, J.M.2    Prescott, D.M.3
  • 71
    • 0018843472 scopus 로고
    • Arrangement of coding and non-coding sequences in the DNA molecules coding for rRNAs in Oxytricha sp. DNA of ciliated protozoa. VII
    • Swanton MT, Greslin AF, Prescott DM, (1980) Arrangement of coding and non-coding sequences in the DNA molecules coding for rRNAs in Oxytricha sp. DNA of ciliated protozoa. VII. Chromosoma 77: 203-215.
    • (1980) Chromosoma , vol.77 , pp. 203-215
    • Swanton, M.T.1    Greslin, A.F.2    Prescott, D.M.3
  • 72
    • 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, et al. (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
  • 73
    • 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 CY, Vogt A, Mochizuki K, Yao MC, (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
  • 74
    • 24944572234 scopus 로고    scopus 로고
    • Nowa1p and Nowa2p: novel putative RNA binding proteins involved in trans-nuclear crosstalk in Paramecium tetraurelia
    • Nowacki M, Zagorski-Ostoja W, Meyer E, (2005) Nowa1p and Nowa2p: novel putative RNA binding proteins involved in trans-nuclear crosstalk in Paramecium tetraurelia. Curr Biol 15: 1616-1628.
    • (2005) Curr Biol , vol.15 , pp. 1616-1628
    • Nowacki, M.1    Zagorski-Ostoja, W.2    Meyer, E.3
  • 75
    • 0036833565 scopus 로고    scopus 로고
    • Mutator transposons
    • Lisch D, (2002) Mutator transposons. Trends Plant Sci 7: 498-504.
    • (2002) Trends Plant Sci , vol.7 , pp. 498-504
    • Lisch, D.1
  • 76
    • 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
  • 77
    • 36448967092 scopus 로고    scopus 로고
    • Transposase-derived transcription factors regulate light signaling in Arabidopsis
    • Lin R, Ding L, Casola C, Ripoll DR, Feschotte C, et al. (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
  • 78
    • 65349130586 scopus 로고    scopus 로고
    • Analysis of the DDE motif in the Mutator superfamily
    • Hua-Van A, Capy P, (2008) Analysis of the DDE motif in the Mutator superfamily. J Mol Evol 67: 670-681.
    • (2008) J Mol Evol , vol.67 , pp. 670-681
    • Hua-Van, A.1    Capy, P.2
  • 79
    • 0020531593 scopus 로고
    • Acquisition of host cell DNA sequences by baculoviruses: relationship between host DNA insertions and FP mutants of Autographa californica and Galleria mellonella nuclear polyhedrosis viruses
    • Fraser MJ, Smith GE, Summers MD, (1983) Acquisition of host cell DNA sequences by baculoviruses: relationship between host DNA insertions and FP mutants of Autographa californica and Galleria mellonella nuclear polyhedrosis viruses. J Virol 47: 287-300.
    • (1983) J Virol , vol.47 , pp. 287-300
    • Fraser, M.J.1    Smith, G.E.2    Summers, M.D.3
  • 80
    • 0030632756 scopus 로고    scopus 로고
    • Developmental genome reorganization in ciliated protozoa: the transposon link
    • Klobutcher LA, Herrick G, (1997) Developmental genome reorganization in ciliated protozoa: the transposon link. Prog Nucleic Acid Res Mol Biol 56: 1-62.
    • (1997) Prog Nucleic Acid Res Mol Biol , vol.56 , pp. 1-62
    • Klobutcher, L.A.1    Herrick, G.2
  • 81
    • 0028053230 scopus 로고
    • A proposed superfamily of transposase genes: transposon-like elements in ciliated protozoa and a common "D35E" motif
    • Doak TG, Doerder FP, Jahn CL, Herrick G, (1994) A proposed superfamily of transposase genes: transposon-like elements in ciliated protozoa and a common "D35E" motif. Proc Natl Acad Sci U S A 91: 942-946.
    • (1994) Proc Natl Acad Sci U S A , vol.91 , pp. 942-946
    • Doak, T.G.1    Doerder, F.P.2    Jahn, C.L.3    Herrick, G.4
  • 82
    • 55349087385 scopus 로고    scopus 로고
    • Evolution of telomere binding proteins
    • In: Nosek J, Tomáska L, editors, Austin, TX: Landes Bioscience
    • Horvath MP (2008) Evolution of telomere binding proteins. In: Nosek J, Tomáska L, editors. Origin and evolution of telomeres. Austin, TX: Landes Bioscience. pp. 83-99.
    • (2008) Origin and evolution of telomeres , pp. 83-99
    • Horvath, M.P.1
  • 83
    • 33846692105 scopus 로고    scopus 로고
    • TPP1 is a homologue of ciliate TEBP-beta and interacts with POT1 to recruit telomerase
    • Xin H, Liu D, Wan M, Safari A, Kim H, et al. (2007) TPP1 is a homologue of ciliate TEBP-beta and interacts with POT1 to recruit telomerase. Nature 445: 559-562.
    • (2007) Nature , vol.445 , pp. 559-562
    • Xin, H.1    Liu, D.2    Wan, M.3    Safari, A.4    Kim, H.5
  • 84
    • 80655128119 scopus 로고    scopus 로고
    • The Pot1a-associated proteins Tpt1 and Pat1 coordinate telomere protection and length regulation in Tetrahymena
    • Linger BR, Morin GB, Price CM, (2011) The Pot1a-associated proteins Tpt1 and Pat1 coordinate telomere protection and length regulation in Tetrahymena. Mol Biol Cell 22: 4161-4170.
    • (2011) Mol Biol Cell , vol.22 , pp. 4161-4170
    • Linger, B.R.1    Morin, G.B.2    Price, C.M.3
  • 85
    • 0027168268 scopus 로고
    • Oxytricha telomere-binding protein: separable DNA-binding and dimerization domains of the alpha-subunit
    • Fang G, Gray JT, Cech TR, (1993) Oxytricha telomere-binding protein: separable DNA-binding and dimerization domains of the alpha-subunit. Genes Dev 7: 870-882.
    • (1993) Genes Dev , vol.7 , pp. 870-882
    • Fang, G.1    Gray, J.T.2    Cech, T.R.3
  • 86
    • 0030447657 scopus 로고    scopus 로고
    • The Saccharomyces CDC13 protein is a single-strand TG1-3 telomeric DNA-binding protein in vitro that affects telomere behavior in vivo
    • Lin JJ, Zakian VA, (1996) The Saccharomyces CDC13 protein is a single-strand TG1-3 telomeric DNA-binding protein in vitro that affects telomere behavior in vivo. Proc Natl Acad Sci U S A 93: 13760-13765.
    • (1996) Proc Natl Acad Sci U S A , vol.93 , pp. 13760-13765
    • Lin, J.J.1    Zakian, V.A.2
  • 87
    • 0029845892 scopus 로고    scopus 로고
    • Cdc13p: a single-strand telomeric DNA-binding protein with a dual role in yeast telomere maintenance
    • Nugent CI, Hughes TR, Lue NF, Lundblad V, (1996) Cdc13p: a single-strand telomeric DNA-binding protein with a dual role in yeast telomere maintenance. Science 274: 249-252.
    • (1996) Science , vol.274 , pp. 249-252
    • Nugent, C.I.1    Hughes, T.R.2    Lue, N.F.3    Lundblad, V.4
  • 88
    • 75649152043 scopus 로고    scopus 로고
    • POT1 proteins in green algae and land plants: DNA-binding properties and evidence of co-evolution with telomeric DNA
    • Shakirov EV, Song X, Joseph JA, Shippen DE, (2009) POT1 proteins in green algae and land plants: DNA-binding properties and evidence of co-evolution with telomeric DNA. Nucleic Acids Res 37: 7455-7467.
    • (2009) Nucleic Acids Res , vol.37 , pp. 7455-7467
    • Shakirov, E.V.1    Song, X.2    Joseph, J.A.3    Shippen, D.E.4
  • 89
    • 33745685066 scopus 로고    scopus 로고
    • Recent expansion of the telomeric complex in rodents: two distinct POT1 proteins protect mouse telomeres
    • Hockemeyer D, Daniels JP, Takai H, de Lange T, (2006) Recent expansion of the telomeric complex in rodents: two distinct POT1 proteins protect mouse telomeres. Cell 126: 63-77.
    • (2006) Cell , vol.126 , pp. 63-77
    • Hockemeyer, D.1    Daniels, J.P.2    Takai, H.3    de Lange, T.4
  • 90
    • 33847243648 scopus 로고    scopus 로고
    • Tetrahymena POT1a regulates telomere length and prevents activation of a cell cycle checkpoint
    • Jacob NK, Lescasse R, Linger BR, Price CM, (2007) Tetrahymena POT1a regulates telomere length and prevents activation of a cell cycle checkpoint. Mol Cell Biol 27: 1592-1601.
    • (2007) Mol Cell Biol , vol.27 , pp. 1592-1601
    • Jacob, N.K.1    Lescasse, R.2    Linger, B.R.3    Price, C.M.4
  • 92
    • 0027104087 scopus 로고
    • Euplotes crassus has genes encoding telomere-binding proteins and telomere-binding protein homologs
    • Wang W, Skopp R, Scofield M, Price C, (1992) Euplotes crassus has genes encoding telomere-binding proteins and telomere-binding protein homologs. Nucleic Acids Res 20: 6621-6629.
    • (1992) Nucleic Acids Res , vol.20 , pp. 6621-6629
    • Wang, W.1    Skopp, R.2    Scofield, M.3    Price, C.4
  • 93
    • 0028425458 scopus 로고
    • Accumulation of telomerase RNA and telomere protein transcripts during telomere synthesis in Euplotes
    • Price CM, Adams AK, Vermeesch JR, (1994) Accumulation of telomerase RNA and telomere protein transcripts during telomere synthesis in Euplotes. J Eukaryot Microbiol 41: 267-275.
    • (1994) J Eukaryot Microbiol , vol.41 , pp. 267-275
    • Price, C.M.1    Adams, A.K.2    Vermeesch, J.R.3
  • 94
    • 60549108398 scopus 로고    scopus 로고
    • Macronuclear genome structure of the ciliate Nyctotherus ovalis: single-gene chromosomes and tiny introns
    • Ricard G, de Graaf RM, Dutilh BE, Duarte I, van Alen TA, et al. (2008) Macronuclear genome structure of the ciliate Nyctotherus ovalis: single-gene chromosomes and tiny introns. BMC Genomics 9: 587.
    • (2008) BMC Genomics , vol.9 , pp. 587
    • Ricard, G.1    de Graaf, R.M.2    Dutilh, B.E.3    Duarte, I.4    van Alen, T.A.5
  • 95
    • 0034916154 scopus 로고    scopus 로고
    • Widespread distribution of extensive chromosomal fragmentation in ciliates
    • Riley JL, Katz LA, (2001) Widespread distribution of extensive chromosomal fragmentation in ciliates. Mol Biol Evol 18: 1372-1377.
    • (2001) Mol Biol Evol , vol.18 , pp. 1372-1377
    • Riley, J.L.1    Katz, L.A.2
  • 96
    • 0029915525 scopus 로고    scopus 로고
    • Computational method to predict mitochondrially imported proteins and their targeting sequences
    • Claros MG, Vincens P, (1996) Computational method to predict mitochondrially imported proteins and their targeting sequences. Eur J Biochem 241: 779-786.
    • (1996) Eur J Biochem , vol.241 , pp. 779-786
    • Claros, M.G.1    Vincens, P.2
  • 97
    • 2942589051 scopus 로고    scopus 로고
    • Predotar: a tool for rapidly screening proteomes for N-terminal targeting sequences
    • Small I, Peeters N, Legeai F, Lurin C, (2004) Predotar: a tool for rapidly screening proteomes for N-terminal targeting sequences. Proteomics 4: 1581-1590.
    • (2004) Proteomics , vol.4 , pp. 1581-1590
    • Small, I.1    Peeters, N.2    Legeai, F.3    Lurin, C.4
  • 98
    • 0021301340 scopus 로고
    • Telomeric properties of C4A4-homologous sequences in micronuclear DNA of Oxytricha fallax
    • Dawson D, Herrick G, (1984) Telomeric properties of C4A4-homologous sequences in micronuclear DNA of Oxytricha fallax. Cell 36: 171-177.
    • (1984) Cell , vol.36 , pp. 171-177
    • Dawson, D.1    Herrick, G.2
  • 99
    • 0030755832 scopus 로고    scopus 로고
    • The telomere binding protein of Euplotes crassus prevents non-specific transcription initiation but has no role in positioning transcription initiation complexes
    • Bender J, Klein A, (1997) The telomere binding protein of Euplotes crassus prevents non-specific transcription initiation but has no role in positioning transcription initiation complexes. Nucleic Acids Res 25: 2877-2882.
    • (1997) Nucleic Acids Res , vol.25 , pp. 2877-2882
    • Bender, J.1    Klein, A.2
  • 100
    • 0035992028 scopus 로고    scopus 로고
    • Topological organization of DNA molecules in the macronucleus of hypotrichous ciliated protozoa
    • Murti KG, Prescott DM, (2002) Topological organization of DNA molecules in the macronucleus of hypotrichous ciliated protozoa. Chromosome Res 10: 165-173.
    • (2002) Chromosome Res , vol.10 , pp. 165-173
    • Murti, K.G.1    Prescott, D.M.2
  • 101
    • 0034990775 scopus 로고    scopus 로고
    • Association of the telomere-telomere-binding protein complex of hypotrichous ciliates with the nuclear matrix and dissociation during replication
    • Postberg J, Juranek SA, Feiler S, Kortwig H, Jonsson F, et al. (2001) Association of the telomere-telomere-binding protein complex of hypotrichous ciliates with the nuclear matrix and dissociation during replication. J Cell Sci 114: 1861-1866.
    • (2001) J Cell Sci , vol.114 , pp. 1861-1866
    • Postberg, J.1    Juranek, S.A.2    Feiler, S.3    Kortwig, H.4    Jonsson, F.5
  • 102
    • 0036439572 scopus 로고    scopus 로고
    • Organization of the macronuclear gene-sized pieces of stichotrichous ciliates into a higher order structure via telomere-matrix interactions
    • Jonsson F, Postberg J, Schaffitzel C, Lipps HJ, (2002) Organization of the macronuclear gene-sized pieces of stichotrichous ciliates into a higher order structure via telomere-matrix interactions. Chromosome Res 10: 445-453.
    • (2002) Chromosome Res , vol.10 , pp. 445-453
    • Jonsson, F.1    Postberg, J.2    Schaffitzel, C.3    Lipps, H.J.4
  • 103
    • 38049186458 scopus 로고    scopus 로고
    • RNA-mediated epigenetic programming of a genome-rearrangement pathway
    • Nowacki M, Vijayan V, Zhou Y, Schotanus K, Doak TG, et al. (2008) RNA-mediated epigenetic programming of a genome-rearrangement pathway. Nature 451: 153-158.
    • (2008) Nature , vol.451 , pp. 153-158
    • Nowacki, M.1    Vijayan, V.2    Zhou, Y.3    Schotanus, K.4    Doak, T.G.5
  • 104
    • 3042764655 scopus 로고    scopus 로고
    • A micronuclear locus containing three protein-coding genes remains linked during macronuclear development in the spirotrichous ciliate Holosticha
    • Chang WJ, Stover NA, Addis VM, Landweber LF, (2004) A micronuclear locus containing three protein-coding genes remains linked during macronuclear development in the spirotrichous ciliate Holosticha. Protist 155: 245-255.
    • (2004) Protist , vol.155 , pp. 245-255
    • Chang, W.J.1    Stover, N.A.2    Addis, V.M.3    Landweber, L.F.4
  • 107
    • 0035054380 scopus 로고    scopus 로고
    • Automated finishing with autofinish
    • Gordon D, Desmarais C, Green P, (2001) Automated finishing with autofinish. Genome Res 11: 614-625.
    • (2001) Genome Res , vol.11 , pp. 614-625
    • Gordon, D.1    Desmarais, C.2    Green, P.3
  • 108
    • 0031955116 scopus 로고    scopus 로고
    • Consed: a graphical tool for sequence finishing
    • Gordon D, Abajian C, Green P, (1998) Consed: a graphical tool for sequence finishing. Genome Res 8: 195-202.
    • (1998) Genome Res , vol.8 , pp. 195-202
    • Gordon, D.1    Abajian, C.2    Green, P.3
  • 109
    • 0031955518 scopus 로고    scopus 로고
    • Base-calling of automated sequencer traces using phred. I. Accuracy assessment
    • Ewing B, Hillier L, Wendl MC, Green P, (1998) Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res 8: 175-185.
    • (1998) Genome Res , vol.8 , pp. 175-185
    • Ewing, B.1    Hillier, L.2    Wendl, M.C.3    Green, P.4
  • 110
    • 79955919332 scopus 로고    scopus 로고
    • Targeted assembly of short sequence reads
    • doi:10.1371/journal.pone.0019816
    • Warren RL, Holt RA, (2011) Targeted assembly of short sequence reads. PLoS One 6: e19816 doi:10.1371/journal.pone.0019816.
    • (2011) PLoS One , vol.6
    • Warren, R.L.1    Holt, R.A.2
  • 112
    • 69949122158 scopus 로고    scopus 로고
    • VarScan: variant detection in massively parallel sequencing of individual and pooled samples
    • Koboldt DC, Chen K, Wylie T, Larson DE, McLellan MD, et al. (2009) VarScan: variant detection in massively parallel sequencing of individual and pooled samples. Bioinformatics 25: 2283-2285.
    • (2009) Bioinformatics , vol.25 , pp. 2283-2285
    • Koboldt, D.C.1    Chen, K.2    Wylie, T.3    Larson, D.E.4    McLellan, M.D.5
  • 113
    • 80052824121 scopus 로고    scopus 로고
    • MACSE: Multiple Alignment of Coding SEquences accounting for frameshifts and stop codons
    • doi:10.1371/journal.pone.0022594
    • Ranwez V, Harispe S, Delsuc F, Douzery EJ, (2011) MACSE: Multiple Alignment of Coding SEquences accounting for frameshifts and stop codons. PLoS One 6: e22594 doi:10.1371/journal.pone.0022594.
    • (2011) PLoS One , vol.6
    • Ranwez, V.1    Harispe, S.2    Delsuc, F.3    Douzery, E.J.4
  • 114
    • 40049091292 scopus 로고    scopus 로고
    • Using native and syntenically mapped cDNA alignments to improve de novo gene finding
    • Stanke M, Diekhans M, Baertsch R, Haussler D, (2008) Using native and syntenically mapped cDNA alignments to improve de novo gene finding. Bioinformatics 24: 637-644.
    • (2008) Bioinformatics , vol.24 , pp. 637-644
    • Stanke, M.1    Diekhans, M.2    Baertsch, R.3    Haussler, D.4
  • 115
    • 2942527473 scopus 로고    scopus 로고
    • Gene prediction with a hidden Markov model and a new intron submodel
    • Stanke M, Waack S, (2003) Gene prediction with a hidden Markov model and a new intron submodel. Bioinformatics 19 Suppl 2: ii215-ii225.
    • (2003) Bioinformatics , vol.19 , Issue.SUPPL.
    • Stanke, M.1    Waack, S.2
  • 116
    • 0018082198 scopus 로고
    • Chromatin structure in the macronucleus of the ciliate Stylonychia mytilus
    • Lipps HJ, Nock A, Riewe M, Steinbruck G, (1978) Chromatin structure in the macronucleus of the ciliate Stylonychia mytilus. Nucleic Acids Res 5: 4699-4709.
    • (1978) Nucleic Acids Res , vol.5 , pp. 4699-4709
    • Lipps, H.J.1    Nock, A.2    Riewe, M.3    Steinbruck, G.4
  • 117
    • 0019440649 scopus 로고
    • RNA and macronuclear transcription in the ciliate Stylonychia mytilus
    • Nock A, (1981) RNA and macronuclear transcription in the ciliate Stylonychia mytilus. Chromosoma 83: 209-220.
    • (1981) Chromosoma , vol.83 , pp. 209-220
    • Nock, A.1
  • 118
    • 58149307926 scopus 로고    scopus 로고
    • Refined annotation and assembly of the Tetrahymena thermophila genome sequence through EST analysis, comparative genomic hybridization, and targeted gap closure
    • Coyne RS, Thiagarajan M, Jones KM, Wortman JR, Tallon LJ, et al. (2008) Refined annotation and assembly of the Tetrahymena thermophila genome sequence through EST analysis, comparative genomic hybridization, and targeted gap closure. BMC Genomics 9: 562.
    • (2008) BMC Genomics , vol.9 , pp. 562
    • Coyne, R.S.1    Thiagarajan, M.2    Jones, K.M.3    Wortman, J.R.4    Tallon, L.J.5
  • 119
    • 0022666355 scopus 로고
    • Alternative processing of sequences during macronuclear development in Tetrahymena thermophila
    • White TC, Allen SL, (1986) Alternative processing of sequences during macronuclear development in Tetrahymena thermophila. J Protozool 33: 30-38.
    • (1986) J Protozool , vol.33 , pp. 30-38
    • White, T.C.1    Allen, S.L.2
  • 120
    • 0024086714 scopus 로고
    • Sequence structures of two developmentally regulated, alternative DNA deletion junctions in Tetrahymena thermophila
    • Austerberry CF, Yao MC, (1988) Sequence structures of two developmentally regulated, alternative DNA deletion junctions in Tetrahymena thermophila. Mol Cell Biol 8: 3947-3950.
    • (1988) Mol Cell Biol , vol.8 , pp. 3947-3950
    • Austerberry, C.F.1    Yao, M.C.2
  • 121
    • 33750858684 scopus 로고    scopus 로고
    • Global trends of whole-genome duplications revealed by the ciliate Paramecium tetraurelia
    • Aury JM, Jaillon O, Duret L, Noel B, Jubin C, et al. (2006) Global trends of whole-genome duplications revealed by the ciliate Paramecium tetraurelia. Nature 444: 171-178.
    • (2006) Nature , vol.444 , pp. 171-178
    • Aury, J.M.1    Jaillon, O.2    Duret, L.3    Noel, B.4    Jubin, C.5
  • 122
    • 0037015614 scopus 로고    scopus 로고
    • Genome sequence of the human malaria parasite Plasmodium falciparum
    • Gardner MJ, Hall N, Fung E, White O, Berriman M, et al. (2002) Genome sequence of the human malaria parasite Plasmodium falciparum. Nature 419: 498-511.
    • (2002) Nature , vol.419 , pp. 498-511
    • Gardner, M.J.1    Hall, N.2    Fung, E.3    White, O.4    Berriman, M.5
  • 123
    • 0242578620 scopus 로고    scopus 로고
    • A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood
    • Guindon S, Gascuel O, (2003) A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 52: 696-704.
    • (2003) Syst Biol , vol.52 , pp. 696-704
    • Guindon, S.1    Gascuel, O.2
  • 124
    • 45949107473 scopus 로고    scopus 로고
    • Recent developments in the MAFFT multiple sequence alignment program
    • Katoh K, Toh H, (2008) Recent developments in the MAFFT multiple sequence alignment program. Brief Bioinform 9: 286-298.
    • (2008) Brief Bioinform , vol.9 , pp. 286-298
    • Katoh, K.1    Toh, H.2
  • 125
    • 67650757433 scopus 로고    scopus 로고
    • trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses
    • Capella-Gutierrez S, Silla-Martinez JM, Gabaldon T, (2009) trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics 25: 1972-1973.
    • (2009) Bioinformatics , vol.25 , pp. 1972-1973
    • Capella-Gutierrez, S.1    Silla-Martinez, J.M.2    Gabaldon, T.3
  • 126
    • 33644877178 scopus 로고    scopus 로고
    • Tetrahymena Genome Database (TGD): a new genomic resource for Tetrahymena thermophila research
    • Stover NA, Krieger CJ, Binkley G, Dong Q, Fisk DG, et al. (2006) Tetrahymena Genome Database (TGD): a new genomic resource for Tetrahymena thermophila research. Nucleic Acids Res 34: D500-D503.
    • (2006) Nucleic Acids Res , vol.34
    • Stover, N.A.1    Krieger, C.J.2    Binkley, G.3    Dong, Q.4    Fisk, D.G.5
  • 127
    • 78651325661 scopus 로고    scopus 로고
    • ParameciumDB in 2011: new tools and new data for functional and comparative genomics of the model ciliate Paramecium tetraurelia
    • Arnaiz O, Sperling L, (2011) ParameciumDB in 2011: new tools and new data for functional and comparative genomics of the model ciliate Paramecium tetraurelia. Nucleic Acids Res 39: D632-D636.
    • (2011) Nucleic Acids Res , vol.39
    • Arnaiz, O.1    Sperling, L.2
  • 128
    • 84858983547 scopus 로고    scopus 로고
    • KEGG for integration and interpretation of large-scale molecular data sets
    • Kanehisa M, Goto S, Sato Y, Furumichi M, Tanabe M, (2012) KEGG for integration and interpretation of large-scale molecular data sets. Nucleic Acids Res 40: D109-D114.
    • (2012) Nucleic Acids Res , vol.40
    • Kanehisa, M.1    Goto, S.2    Sato, Y.3    Furumichi, M.4    Tanabe, M.5
  • 129
    • 0033982936 scopus 로고    scopus 로고
    • KEGG: kyoto encyclopedia of genes and genomes
    • Kanehisa M, Goto S, (2000) KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res 28: 27-30.
    • (2000) Nucleic Acids Res , vol.28 , pp. 27-30
    • Kanehisa, M.1    Goto, S.2
  • 131
    • 77957244650 scopus 로고    scopus 로고
    • Search and clustering orders of magnitude faster than BLAST
    • Edgar RC, (2010) Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26: 2460-2461.
    • (2010) Bioinformatics , vol.26 , pp. 2460-2461
    • Edgar, R.C.1
  • 132
    • 84873181041 scopus 로고    scopus 로고
    • Data from: the Oxytricha trifallax macronuclear genome: a complex eukaryotic genome with 16,000 tiny chromosomes
    • Swart EC, Bracht J, Magrini V, Minx P, Chen X, et al. Data from: the Oxytricha trifallax macronuclear genome: a complex eukaryotic genome with 16,000 tiny chromosomes. Dryad Digital Repository.
    • Dryad Digital Repository
    • Swart, E.C.1    Bracht, J.2    Magrini, V.3    Minx, P.4    Chen, X.5
  • 133
    • 0037217056 scopus 로고    scopus 로고
    • Multiple protein phylogenies show that Oxyrrhis marina and Perkinsus marinus are early branches of the dinoflagellate lineage
    • Saldarriaga JF, McEwan ML, Fast NM, Taylor FJ, Keeling PJ, (2003) Multiple protein phylogenies show that Oxyrrhis marina and Perkinsus marinus are early branches of the dinoflagellate lineage. Int J Syst Evol Microbiol 53: 355-365.
    • (2003) Int J Syst Evol Microbiol , vol.53 , pp. 355-365
    • Saldarriaga, J.F.1    McEwan, M.L.2    Fast, N.M.3    Taylor, F.J.4    Keeling, P.J.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.