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Volumn 17, Issue 2, 2007, Pages 184-191

Highly efficient concerted evolution in the ribosomal DNA repeats: Total rDNA repeat variation revealed by whole-genome shotgun sequence data

Author keywords

[No Author keywords available]

Indexed keywords

RIBOSOME DNA;

EID: 33846880495     PISSN: 10889051     EISSN: 15495469     Source Type: Journal    
DOI: 10.1101/gr.5457707     Document Type: Article
Times cited : (298)

References (60)
  • 2
    • 0032491390 scopus 로고    scopus 로고
    • Evidence that gene amplification underlies adaptive mutability of the bacterial lac operon
    • Andersson, D.I., Slechta, E.S., and Roth, J.R. 1998. Evidence that gene amplification underlies adaptive mutability of the bacterial lac operon. Science 282: 1133-1135.
    • (1998) Science , vol.282 , pp. 1133-1135
    • Andersson, D.I.1    Slechta, E.S.2    Roth, J.R.3
  • 3
    • 33645113551 scopus 로고    scopus 로고
    • Monitoring the mode and tempo of concerted evolution in the Drosophila melanogaster rDNA locus
    • Averbeck, K.T. and Eickbush, T.H. 2005. Monitoring the mode and tempo of concerted evolution in the Drosophila melanogaster rDNA locus. Genetics 171: 1837-1846.
    • (2005) Genetics , vol.171 , pp. 1837-1846
    • Averbeck, K.T.1    Eickbush, T.H.2
  • 4
    • 0345518003 scopus 로고    scopus 로고
    • Construction of a variability map for eukaryotic large subunit ribosomal RNA
    • Ben Ali, A., Wuyts, J., De Wachter, R., Meyer, A., and Van de Peer, Y. 1999. Construction of a variability map for eukaryotic large subunit ribosomal RNA. Nucleic Acids Res. 27: 2825-2831.
    • (1999) Nucleic Acids Res , vol.27 , pp. 2825-2831
    • Ben Ali, A.1    Wuyts, J.2    De Wachter, R.3    Meyer, A.4    Van de Peer, Y.5
  • 5
    • 0001225414 scopus 로고    scopus 로고
    • Fungal molecular evolution: Gene trees and geologic time
    • eds. D.J. McLaughlin, E. McLaughlin, and P.A. Lemke, pp, Springer, Berlin
    • Berbee, M.L. and Taylor, J.W. 2001. Fungal molecular evolution: Gene trees and geologic time. In The Mycota (eds. D.J. McLaughlin, E. McLaughlin, and P.A. Lemke), pp. 229-246. Springer, Berlin.
    • (2001) The Mycota , pp. 229-246
    • Berbee, M.L.1    Taylor, J.W.2
  • 6
    • 0004034223 scopus 로고    scopus 로고
    • Analyzing DNA
    • eds. E.D. Green, B. Birren, S. Klapholz, R.M. Myers, and P. Hieter, pp, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York
    • Birren, B., Green, E.D., Klapholz, S., Myers, R.M., and Roskams, J. 1997. Analyzing DNA. In Genome analysis: A laboratory manual. (eds. E.D. Green, B. Birren, S. Klapholz, R.M. Myers, and P. Hieter), pp 125-127. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York.
    • (1997) Genome analysis: A laboratory manual , pp. 125-127
    • Birren, B.1    Green, E.D.2    Klapholz, S.3    Myers, R.M.4    Roskams, J.5
  • 7
    • 0014407722 scopus 로고
    • Repeated sequences in DNA
    • Britten, R.J. and Kohne, D.E. 1968. Repeated sequences in DNA. Science 161: 529-540.
    • (1968) Science , vol.161 , pp. 529-540
    • Britten, R.J.1    Kohne, D.E.2
  • 8
    • 0015505278 scopus 로고
    • A comparison of the ribosomal DNA's of Xenopus laevis and Xenopus mulleri: The evolution of tandem genes
    • Brown, D.D., Wensink, P.C., and Jordan, E. 1972. A comparison of the ribosomal DNA's of Xenopus laevis and Xenopus mulleri: The evolution of tandem genes. J. Mol. Biol. 63: 57-73.
    • (1972) J. Mol. Biol , vol.63 , pp. 57-73
    • Brown, D.D.1    Wensink, P.C.2    Jordan, E.3
  • 9
    • 23744470383 scopus 로고    scopus 로고
    • Human ribosomal RNA gene arrays display a broad range of palindromic structures
    • Caburet, S., Conti, C., Schurra, C., Lebofsky, R., Edelstein, S.J., and Bensimon, A. 2005. Human ribosomal RNA gene arrays display a broad range of palindromic structures. Genome Res. 15: 1079-1085.
    • (2005) Genome Res , vol.15 , pp. 1079-1085
    • Caburet, S.1    Conti, C.2    Schurra, C.3    Lebofsky, R.4    Edelstein, S.J.5    Bensimon, A.6
  • 10
    • 0035046735 scopus 로고    scopus 로고
    • A microbial population-species interface: Nested cladistic and coalescent inference with multilocus data
    • Carbone, I. and Kohn, L.M. 2001. A microbial population-species interface: Nested cladistic and coalescent inference with multilocus data. Mol. Ecol. 10: 947-964.
    • (2001) Mol. Ecol , vol.10 , pp. 947-964
    • Carbone, I.1    Kohn, L.M.2
  • 11
    • 0030087851 scopus 로고    scopus 로고
    • Two-dimensional RFLP analyses reveal megabase-sized clusters of rRNA gene variants in Arabidopsis thaliana, suggesting local spreading of variants as the mode for gene homogenization during concerted evolution
    • Copenhaver, G.P. and Pikaard, C.S. 1996. Two-dimensional RFLP analyses reveal megabase-sized clusters of rRNA gene variants in Arabidopsis thaliana, suggesting local spreading of variants as the mode for gene homogenization during concerted evolution. Plant J. 9: 273-282.
    • (1996) Plant J , vol.9 , pp. 273-282
    • Copenhaver, G.P.1    Pikaard, C.S.2
  • 14
    • 0020478245 scopus 로고
    • Molecular drive: A cohesive mode of species evolution
    • Dover, G.A. 1982. Molecular drive: A cohesive mode of species evolution. Nature 299: 111-117.
    • (1982) Nature , vol.299 , pp. 111-117
    • Dover, G.A.1
  • 15
    • 0029880961 scopus 로고    scopus 로고
    • Gene conversion plays the major role in controlling the stability of large tandem repeats in yeast
    • Gangloff, S., Zou, H., and Rothstein, R. 1996. Gene conversion plays the major role in controlling the stability of large tandem repeats in yeast. EMBO J. 15: 1715-1725.
    • (1996) EMBO J , vol.15 , pp. 1715-1725
    • Gangloff, S.1    Zou, H.2    Rothstein, R.3
  • 16
    • 0031732104 scopus 로고    scopus 로고
    • Extraordinary ribosomal spacer length heterogeneity in a Neotyphodium endophyte hybrid: Implications for concerted evolution
    • Ganley, A.R.D. and Scott, B. 1998. Extraordinary ribosomal spacer length heterogeneity in a Neotyphodium endophyte hybrid: Implications for concerted evolution. Genetics 150: 1625-1637.
    • (1998) Genetics , vol.150 , pp. 1625-1637
    • Ganley, A.R.D.1    Scott, B.2
  • 17
    • 0036350618 scopus 로고    scopus 로고
    • Concerted evolution in the ribosomal RNA genes of an Epichloë endophyte hybrid: Comparison between tandemly-arranged rDNA and dispersed 5S rrn genes
    • Ganley, A.R.D. and Scott, B. 2002. Concerted evolution in the ribosomal RNA genes of an Epichloë endophyte hybrid: Comparison between tandemly-arranged rDNA and dispersed 5S rrn genes. Fungal Genet. Biol. 35: 39-51.
    • (2002) Fungal Genet. Biol , vol.35 , pp. 39-51
    • Ganley, A.R.D.1    Scott, B.2
  • 18
    • 23844492486 scopus 로고    scopus 로고
    • Identifying gene-independent noncoding functional elements in the yeast ribosomal DNA by phylogenetic footprinting
    • Ganley, A.R.D., Hayashi, K., Horiuchi, T., and Kobayashi, T. 2005. Identifying gene-independent noncoding functional elements in the yeast ribosomal DNA by phylogenetic footprinting. Proc. Natl. Acad. Sci. 102: 11787-11792.
    • (2005) Proc. Natl. Acad. Sci , vol.102 , pp. 11787-11792
    • Ganley, A.R.D.1    Hayashi, K.2    Horiuchi, T.3    Kobayashi, T.4
  • 20
    • 0035338424 scopus 로고    scopus 로고
    • Human rDNA: Evolutionary patterns within the genes and tandem arrays derived from multiple chromosomes
    • Gonzalez, I.L. and Sylvester, J.E. 2001. Human rDNA: Evolutionary patterns within the genes and tandem arrays derived from multiple chromosomes. Genomics 73: 255-263.
    • (2001) Genomics , vol.73 , pp. 255-263
    • Gonzalez, I.L.1    Sylvester, J.E.2
  • 21
    • 0003091268 scopus 로고
    • The nucleolus and ribosome biogenesis
    • eds. M. Alfert et al, Springer-Verlag Wien, New York
    • Hadjiolov, A.A. 1984. The nucleolus and ribosome biogenesis. In Cell biology monographs (eds. M. Alfert et al.), Vol. 12. Springer-Verlag Wien, New York.
    • (1984) Cell biology monographs , vol.12
    • Hadjiolov, A.A.1
  • 22
    • 0023481280 scopus 로고
    • A ten-minute preparation from yeast efficiently releases autonomous plasmids for transformation of Escherichia coli
    • Hoffman, C.S. and Winston, F. 1987. A ten-minute preparation from yeast efficiently releases autonomous plasmids for transformation of Escherichia coli. Gene 57: 267-272.
    • (1987) Gene , vol.57 , pp. 267-272
    • Hoffman, C.S.1    Winston, F.2
  • 23
    • 0028213502 scopus 로고
    • The molecular through ecological genetics of abnormal abdomen in Drosophila mercatorum. VI. The non-neutrality of the Y chromosome rDNA polymorphism
    • Hollocher, H. and Templeton, A.R. 1994. The molecular through ecological genetics of abnormal abdomen in Drosophila mercatorum. VI. The non-neutrality of the Y chromosome rDNA polymorphism. Genetics 136: 1373-1384.
    • (1994) Genetics , vol.136 , pp. 1373-1384
    • Hollocher, H.1    Templeton, A.R.2
  • 24
    • 0035148956 scopus 로고    scopus 로고
    • Polymorphism at the ribosomal DNA spacers and its relation to breeding structure of the widespread mushroom Schizophyllum commune
    • James, T.J., Moncalvo, J.-M., Li, S., and Vilgalys, R. 2001. Polymorphism at the ribosomal DNA spacers and its relation to breeding structure of the widespread mushroom Schizophyllum commune. Genetics 157: 149-161.
    • (2001) Genetics , vol.157 , pp. 149-161
    • James, T.J.1    Moncalvo, J.-M.2    Li, S.3    Vilgalys, R.4
  • 26
    • 0038349948 scopus 로고    scopus 로고
    • Sequencing and comparison of yeast species to identify genes and regulatory elements
    • Kellis, M., Patterson, N., Endrizzi, M., Birren, B., and Lander, E.S. 2003. Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature 423: 241-254.
    • (2003) Nature , vol.423 , pp. 241-254
    • Kellis, M.1    Patterson, N.2    Endrizzi, M.3    Birren, B.4    Lander, E.S.5
  • 27
    • 0032535478 scopus 로고    scopus 로고
    • Expansion and contraction of ribosomal DNA repeats in Saccharomyces cerevisiae: Requirement of replication fork blocking (Fob1) protein and the role of RNA polymerase I
    • Kobayashi, T., Heck, D.J., Nomura, M., and Horiuchi, T. 1998. Expansion and contraction of ribosomal DNA repeats in Saccharomyces cerevisiae: Requirement of replication fork blocking (Fob1) protein and the role of RNA polymerase I. Genes & Dev. 12: 3821-3830.
    • (1998) Genes & Dev , vol.12 , pp. 3821-3830
    • Kobayashi, T.1    Heck, D.J.2    Nomura, M.3    Horiuchi, T.4
  • 28
  • 29
    • 0031033604 scopus 로고    scopus 로고
    • Concerted evolution of the tandemly repeated genes encoding human U2 snRNA (the RNU2 locus) involves rapid intrachromosomal homogenization and rare interchromosomal gene conversion
    • Liao, D., Pavelitz, T., Kidd, J.R., Kidd, K.K., and Weiner, A.M. 1997. Concerted evolution of the tandemly repeated genes encoding human U2 snRNA (the RNU2 locus) involves rapid intrachromosomal homogenization and rare interchromosomal gene conversion. EMBO J. 16: 588-598.
    • (1997) EMBO J , vol.16 , pp. 588-598
    • Liao, D.1    Pavelitz, T.2    Kidd, J.R.3    Kidd, K.K.4    Weiner, A.M.5
  • 31
    • 0018814593 scopus 로고
    • Repeated genes in eukaryotes
    • Long, E.O. and Dawid, I.B. 1980. Repeated genes in eukaryotes. Annu. Rev. Biochem. 49: 727-764.
    • (1980) Annu. Rev. Biochem , vol.49 , pp. 727-764
    • Long, E.O.1    Dawid, I.B.2
  • 32
    • 11844291918 scopus 로고    scopus 로고
    • UBF-binding site arrays form pseudo-NORs and sequester the RNA polymerase I transcription machinery
    • Mais, C., Wright, J.E., Prieto, J.-L., Raggett, S.L., and McStay, B. 2005. UBF-binding site arrays form pseudo-NORs and sequester the RNA polymerase I transcription machinery. Genes & Dev. 19: 50-64.
    • (2005) Genes & Dev , vol.19 , pp. 50-64
    • Mais, C.1    Wright, J.E.2    Prieto, J.-L.3    Raggett, S.L.4    McStay, B.5
  • 33
    • 0035479142 scopus 로고    scopus 로고
    • Deletional bias and the evolution of bacterial genomes
    • Mira, A., Ochman, H., and Moran, N.A. 2001. Deletional bias and the evolution of bacterial genomes. Trends Genet. 17: 589-596.
    • (2001) Trends Genet , vol.17 , pp. 589-596
    • Mira, A.1    Ochman, H.2    Moran, N.A.3
  • 34
    • 0005814023 scopus 로고
    • Mathematical model for studying genetic variation in terms of restriction endonucleases
    • Nei, M. and Li, W.-H. 1979. Mathematical model for studying genetic variation in terms of restriction endonucleases. Proc. Natl. Acad. Sci. 76: 5269-5273.
    • (1979) Proc. Natl. Acad. Sci , vol.76 , pp. 5269-5273
    • Nei, M.1    Li, W.-H.2
  • 35
    • 0030791307 scopus 로고    scopus 로고
    • Evolution by the birth-and-death process in multigene families of the vertebrate immune system
    • Nei, M., Gu, X., and Sitnikova, T. 1997. Evolution by the birth-and-death process in multigene families of the vertebrate immune system. Proc. Natl. Acad. Sci. 94: 7799-7806.
    • (1997) Proc. Natl. Acad. Sci , vol.94 , pp. 7799-7806
    • Nei, M.1    Gu, X.2    Sitnikova, T.3
  • 36
    • 0034718504 scopus 로고    scopus 로고
    • Purifying selection and birth-and-death evolution in the ubiquitin gene family
    • Nei, M., Rogozin, I.B., and Piontkivska, H. 2000. Purifying selection and birth-and-death evolution in the ubiquitin gene family. Proc. Natl. Acad. Sci. 97: 10866-10871.
    • (2000) Proc. Natl. Acad. Sci , vol.97 , pp. 10866-10871
    • Nei, M.1    Rogozin, I.B.2    Piontkivska, H.3
  • 37
    • 0031065526 scopus 로고    scopus 로고
    • Two divergent intragenomic rDNA ITS2 types within a monophyletic lineage of the fungus Fusarium are nonorthologous
    • O'Donnell, K. and Cigelnik, E. 1997. Two divergent intragenomic rDNA ITS2 types within a monophyletic lineage of the fungus Fusarium are nonorthologous. Mol. Phylogenet. Evol. 7: 103-116.
    • (1997) Mol. Phylogenet. Evol , vol.7 , pp. 103-116
    • O'Donnell, K.1    Cigelnik, E.2
  • 38
    • 0021191315 scopus 로고
    • The cohesive population genetics of molecular drive
    • Ohta, T. and Dover, G.A. 1984. The cohesive population genetics of molecular drive. Genetics 108: 501-521.
    • (1984) Genetics , vol.108 , pp. 501-521
    • Ohta, T.1    Dover, G.A.2
  • 39
    • 0036811729 scopus 로고    scopus 로고
    • Rates of R1 and R2 retrotransposition and elimination from the rDNA locus of Drosophila melanogaster
    • Pérez-González, C.E. and Eickbush, T.H. 2002. Rates of R1 and R2 retrotransposition and elimination from the rDNA locus of Drosophila melanogaster. Genetics 162: 799-811.
    • (2002) Genetics , vol.162 , pp. 799-811
    • Pérez-González, C.E.1    Eickbush, T.H.2
  • 40
    • 0037310350 scopus 로고    scopus 로고
    • The correlation between rDNA copy number and genome size in eukaryotes
    • Prokopowich, C.D., Gregory, T.R., and Crease, T.J. 2003. The correlation between rDNA copy number and genome size in eukaryotes. Genome 46: 48-50.
    • (2003) Genome , vol.46 , pp. 48-50
    • Prokopowich, C.D.1    Gregory, T.R.2    Crease, T.J.3
  • 41
    • 0013943818 scopus 로고
    • A molecular explanation of the bobbed mutants of Drosophila as partial deficiencies of ribosomal DNA
    • Ritossa, F.M., Atwood, K.C., and Spiegelman, S. 1966. A molecular explanation of the bobbed mutants of Drosophila as partial deficiencies of "ribosomal DNA." Genetics 54: 819-834.
    • (1966) Genetics , vol.54 , pp. 819-834
    • Ritossa, F.M.1    Atwood, K.C.2    Spiegelman, S.3
  • 42
    • 17044401340 scopus 로고    scopus 로고
    • Evolution of a large ribosomal RNA multigene family in filamentous fungi: Birth and death of a concerted evolution paradigm
    • Rooney, A.P. and Ward, T.J. 2005. Evolution of a large ribosomal RNA multigene family in filamentous fungi: Birth and death of a concerted evolution paradigm. Proc. Natl. Acad. Sci. 102: 5084-5089.
    • (2005) Proc. Natl. Acad. Sci , vol.102 , pp. 5084-5089
    • Rooney, A.P.1    Ward, T.J.2
  • 43
    • 0347513220 scopus 로고    scopus 로고
    • DnaSP, DNA polymorphism analyses by the coalescent and other methods
    • Rozas, J., Sánchez-DelBarrio, J.C., Messeguer, X., and Rozas, R. 2003. DnaSP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics 19: 2496-2497.
    • (2003) Bioinformatics , vol.19 , pp. 2496-2497
    • Rozas, J.1    Sánchez-DelBarrio, J.C.2    Messeguer, X.3    Rozas, R.4
  • 44
    • 0022621534 scopus 로고
    • Magnification of rRNA gene number in a Neurospora crassa strain with a partial deletion of the nucleolus organizer
    • Russell, P.J. and Rodland, K.D. 1986. Magnification of rRNA gene number in a Neurospora crassa strain with a partial deletion of the nucleolus organizer. Chromosoma 93: 337-340.
    • (1986) Chromosoma , vol.93 , pp. 337-340
    • Russell, P.J.1    Rodland, K.D.2
  • 45
  • 46
    • 0020382199 scopus 로고
    • Aspergillus nidulans: An organism for detecting a range of genetic damage
    • eds. F.J. deSerres and A. Hollaender, Plenum, New York
    • Scott, B.R. and Kafer, E. 1982. Aspergillus nidulans: An organism for detecting a range of genetic damage. In Chemical mutagens (eds. F.J. deSerres and A. Hollaender), Vol. 7, pp. 447-479. Plenum, New York.
    • (1982) Chemical mutagens , vol.7 , pp. 447-479
    • Scott, B.R.1    Kafer, E.2
  • 49
    • 0015707780 scopus 로고
    • Unequal crossover and the evolution of multigene families
    • Smith, G.P. 1973. Unequal crossover and the evolution of multigene families. Cold Spring Harb. Symp. Quant. Biol. 38: 507-513.
    • (1973) Cold Spring Harb. Symp. Quant. Biol , vol.38 , pp. 507-513
    • Smith, G.P.1
  • 50
    • 0002062060 scopus 로고
    • Pulsed field gel electrophoresis and the technology of large DNA molecules
    • ed. K.E. Davies, pp, IRL Press, Oxford
    • Smith, C.L., Klco, S.R., and Cantor, C.R. 1988. Pulsed field gel electrophoresis and the technology of large DNA molecules. In Genome analysis: A practical approach (ed. K.E. Davies), pp. 41-72. IRL Press, Oxford.
    • (1988) Genome analysis: A practical approach , pp. 41-72
    • Smith, C.L.1    Klco, S.R.2    Cantor, C.R.3
  • 51
    • 0018869075 scopus 로고
    • Unequal crossing over in the ribosomal DNA of Saccharomyces cerevisiae
    • Szostak, J.W. and Wu, R. 1980. Unequal crossing over in the ribosomal DNA of Saccharomyces cerevisiae. Nature 284: 426-430.
    • (1980) Nature , vol.284 , pp. 426-430
    • Szostak, J.W.1    Wu, R.2
  • 52
    • 0038046165 scopus 로고    scopus 로고
    • Transcription- dependent recombination and the role of fork collision in yeast rDNA
    • Takeuchi, Y., Horiuchi, T., and Kobayashi, T. 2003. Transcription- dependent recombination and the role of fork collision in yeast rDNA. Genes & Dev. 17: 1497-1506.
    • (2003) Genes & Dev , vol.17 , pp. 1497-1506
    • Takeuchi, Y.1    Horiuchi, T.2    Kobayashi, T.3
  • 53
    • 0029789623 scopus 로고    scopus 로고
    • A quantitative map of nucleotide substitution rates in bacterial rRNA
    • Van de Peer, Y., Chapelle, S., and De Wachter, R. 1996. A quantitative map of nucleotide substitution rates in bacterial rRNA. Nucleic Acids Res. 24: 3381-3391.
    • (1996) Nucleic Acids Res , vol.24 , pp. 3381-3391
    • Van de Peer, Y.1    Chapelle, S.2    De Wachter, R.3
  • 56
    • 33644852003 scopus 로고    scopus 로고
    • Trypanosoma cruzi 5S rRNA arrays define five groups and indicate geographic origins of an ancestor of the heterozygous hybrids
    • Westenberger, S.J., Sturm, N.R., and Campbell, D.A. 2006. Trypanosoma cruzi 5S rRNA arrays define five groups and indicate geographic origins of an ancestor of the heterozygous hybrids. Int. J. Parasitol. 36: 337-346.
    • (2006) Int. J. Parasitol , vol.36 , pp. 337-346
    • Westenberger, S.J.1    Sturm, N.R.2    Campbell, D.A.3
  • 58
    • 0021346063 scopus 로고
    • Transformation of Aspergillus nidulans by using a trpC plasmid
    • Yelton, M.M., Hamer, J.E., and Timberlake, W.E. 1984. Transformation of Aspergillus nidulans by using a trpC plasmid. Proc. Natl. Acad. Sci. 81: 1470-1474.
    • (1984) Proc. Natl. Acad. Sci , vol.81 , pp. 1470-1474
    • Yelton, M.M.1    Hamer, J.E.2    Timberlake, W.E.3
  • 59
    • 0035853297 scopus 로고    scopus 로고
    • Directionality of DNA replication fork movement strongly affects the generation of spontaneous mutations in Escherichia coli
    • Yoshiyama, K., Higuchi, K., Matsumura, H., and Maki, H. 2001. Directionality of DNA replication fork movement strongly affects the generation of spontaneous mutations in Escherichia coli. J. Mol. Biol. 307: 1195-1206.
    • (2001) J. Mol. Biol , vol.307 , pp. 1195-1206
    • Yoshiyama, K.1    Higuchi, K.2    Matsumura, H.3    Maki, H.4


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