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Volumn 17, Issue 3, 2005, Pages 665-675

The rice nuclear genome continuously integrates, shuffles, and eliminates the chloroplast genome to cause chloroplast-nuclear DNA flux

Author keywords

[No Author keywords available]

Indexed keywords

CELLS; CROPS; FLUXES; GENES; PLANTS (BOTANY);

EID: 27244457663     PISSN: 10404651     EISSN: None     Source Type: Journal    
DOI: 10.1105/tpc.104.027706     Document Type: Article
Times cited : (130)

References (53)
  • 1
    • 0037162534 scopus 로고    scopus 로고
    • Punctuated evolution of mitochondrial gene content: High and variable rates of mitochondrial gene loss and transfer to the nucleus during angiosperm evolution
    • USA
    • Adams, K.L., Qiu, Y.-L., Stoutemyer, M., and Palmer, J.D. (2002). Punctuated evolution of mitochondrial gene content: High and variable rates of mitochondrial gene loss and transfer to the nucleus during angiosperm evolution. Proc. Natl. Acad. Sci. USA 99, 9905-9912.
    • (2002) Proc. Natl. Acad. Sci. , vol.99 , pp. 9905-9912
    • Adams, K.L.1    Qiu, Y.-L.2    Stoutemyer, M.3    Palmer, J.D.4
  • 2
    • 0033598682 scopus 로고    scopus 로고
    • Intracellular gene transfer in action: Dual transcription and multiple silencings of nuclear and mitochondrial cox2 genes in legumes
    • USA
    • Adams, K.L., Song, K., Roessler, P.G., Nugent, J.M., Doyle, J.L., Doyle, J.J., and Palmer, J.D. (1999). Intracellular gene transfer in action: Dual transcription and multiple silencings of nuclear and mitochondrial cox2 genes in legumes. Proc. Natl. Acad. Sci. USA 96, 13863-13868.
    • (1999) Proc. Natl. Acad. Sci. , vol.96 , pp. 13863-13868
    • Adams, K.L.1    Song, K.2    Roessler, P.G.3    Nugent, J.M.4    Doyle, J.L.5    Doyle, J.J.6    Palmer, J.D.7
  • 4
    • 0034649566 scopus 로고    scopus 로고
    • Analysis of the genome sequence of the flowering plant Arabidopsis thaliana
    • Arabidopsis Genome Initiative (2000). Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408, 796-815.
    • (2000) Nature , vol.408 , pp. 796-815
  • 5
    • 0031813884 scopus 로고    scopus 로고
    • Analysis of plastid DNA-like sequences within the nuclear genomes of higher plants
    • Ayliffe, M.A., Scott, N.S., and Timmis, J.N. (1998). Analysis of plastid DNA-like sequences within the nuclear genomes of higher plants. Mol. Biol. Evol. 15, 738-745.
    • (1998) Mol. Biol. Evol. , vol.15 , pp. 738-745
    • Ayliffe, M.A.1    Scott, N.S.2    Timmis, J.N.3
  • 9
    • 0033601285 scopus 로고    scopus 로고
    • Genetic definition and sequence analysis of Arabidopsis centromeres
    • Copenhaver, G.P., et al. (1999). Genetic definition and sequence analysis of Arabidopsis centromeres. Science 286, 2468-2474.
    • (1999) Science , vol.286 , pp. 2468-2474
    • Copenhaver, G.P.1
  • 10
    • 0020488498 scopus 로고
    • Promiscuous DNA-Chloroplast genes inside plant mitochondria
    • Ellis, R.J. (1982). Promiscuous DNA-Chloroplast genes inside plant mitochondria. Nature 299, 678-679.
    • (1982) Nature , vol.299 , pp. 678-679
    • Ellis, R.J.1
  • 11
    • 0037153127 scopus 로고    scopus 로고
    • Sequence and analysis of rice chromosome 4
    • Feng, Q., et al. (2002). Sequence and analysis of rice chromosome 4. Nature 420, 316-320.
    • (2002) Nature , vol.420 , pp. 316-320
    • Feng, Q.1
  • 12
    • 0002557518 scopus 로고    scopus 로고
    • Molecular clocks and nucleotide substitution rate in higher plants
    • Gaut, B.S. (1998). Molecular clocks and nucleotide substitution rate in higher plants. Evol. Biol. 30, 93-120.
    • (1998) Evol. Biol. , vol.30 , pp. 93-120
    • Gaut, B.S.1
  • 13
    • 0029812835 scopus 로고    scopus 로고
    • Substitution rate comparisons between grasses and palms: Synonymous rate differences at the nuclear gene Adh parallel rate difference at the plastid gene rbcL
    • USA
    • Gaut, B.S., Morton, B.R., McCaig, B., and Clegg, M.T. (1996). Substitution rate comparisons between grasses and palms: Synonymous rate differences at the nuclear gene Adh parallel rate difference at the plastid gene rbcL. Proc. Natl. Acad. Sci. USA 93, 10274-10279.
    • (1996) Proc. Natl. Acad. Sci. , vol.93 , pp. 10274-10279
    • Gaut, B.S.1    Morton, B.R.2    McCaig, B.3    Clegg, M.T.4
  • 14
    • 0037047355 scopus 로고    scopus 로고
    • Genomic deletion created upon LINE-1 retrotransposition
    • Gilbert, N., Lutz-Prigge, S., and Moran, J.V. (2002). Genomic deletion created upon LINE-1 retrotransposition. Cell 110, 315-325.
    • (2002) Cell , vol.110 , pp. 315-325
    • Gilbert, N.1    Lutz-Prigge, S.2    Moran, J.V.3
  • 15
    • 0034307716 scopus 로고    scopus 로고
    • It takes two transposons to tango
    • Gray, Y.H. (2000). It takes two transposons to tango. Trends Genet. 16, 461-468.
    • (2000) Trends Genet. , vol.16 , pp. 461-468
    • Gray, Y.H.1
  • 16
    • 0038028675 scopus 로고    scopus 로고
    • Conserved noncoding sequences among cultivated cereal genomes identify candidate regulatory sequence elements and patterns of promoter evolution
    • Guo, H., and Moose, S. (2003). Conserved noncoding sequences among cultivated cereal genomes identify candidate regulatory sequence elements and patterns of promoter evolution. Plant Cell 15, 1143-1158.
    • (2003) Plant Cell , vol.15 , pp. 1143-1158
    • Guo, H.1    Moose, S.2
  • 17
    • 0031908205 scopus 로고    scopus 로고
    • 2 population
    • 2 population. Genetics 148, 479-494.
    • (1998) Genetics , vol.148 , pp. 479-494
    • Harushima, Y.1
  • 18
    • 0024674380 scopus 로고
    • The complete sequence of the rice (Oryza sativa) chloroplast genome: Intermolecular recombination between distinct tRNA genes accounts for a major plastid DNA inversion during the evolution of the cereals
    • Hiratsuka, J., et al. (1989). The complete sequence of the rice (Oryza sativa) chloroplast genome: Intermolecular recombination between distinct tRNA genes accounts for a major plastid DNA inversion during the evolution of the cereals. Mol. Gen. Genet. 217, 185-194.
    • (1989) Mol. Gen. Genet. , vol.217 , pp. 185-194
    • Hiratsuka, J.1
  • 19
    • 0242669385 scopus 로고    scopus 로고
    • Direct measurement of the transfer rate of chloroplast DNA into the nucleus
    • Huang, C.Y., Ayliffe, M.A., and Timmis, J.N. (2003). Direct measurement of the transfer rate of chloroplast DNA into the nucleus. Nature 422, 72-76.
    • (2003) Nature , vol.422 , pp. 72-76
    • Huang, C.Y.1    Ayliffe, M.A.2    Timmis, J.N.3
  • 20
    • 2042437650 scopus 로고    scopus 로고
    • Initial sequencing and analysis of the human genome
    • International Human Genome Sequencing Consortium (2001). Initial sequencing and analysis of the human genome. Nature 409, 860-921.
    • (2001) Nature , vol.409 , pp. 860-921
  • 21
    • 0000732090 scopus 로고
    • Evolution of protein molecules
    • H.N. Munro, ed (New York: Academic Press)
    • Jukes, T.H., and Cantor, C.R. (1969). Evolution of protein molecules. In Mammalian Protein Metabolism, H.N. Munro, ed (New York: Academic Press), pp. 21-132.
    • (1969) Mammalian Protein Metabolism , pp. 21-132
    • Jukes, T.H.1    Cantor, C.R.2
  • 22
    • 0037161658 scopus 로고    scopus 로고
    • All genomes great and small
    • Knight, J. (2002). All genomes great and small. Nature 417, 374-376.
    • (2002) Nature , vol.417 , pp. 374-376
    • Knight, J.1
  • 23
    • 0034443285 scopus 로고    scopus 로고
    • Origin and evolution of the mitochondrial proteosome
    • Kurland, C.G., and Andersson, G.E. (2000). Origin and evolution of the mitochondrial proteosome. Microbiol. Mol. Biol. Rev. 64, 786-820.
    • (2000) Microbiol. Mol. Biol. Rev. , vol.64 , pp. 786-820
    • Kurland, C.G.1    Andersson, G.E.2
  • 24
    • 0029160870 scopus 로고
    • Complete sequence of the maize chloroplast genome: Gene content, hot spots of divergence and fine tuning of genetic information by transcript editing
    • Maier, R.M., Neckermann, K., Igloi, G.L., and Kössel, H. (1995). Complete sequence of the maize chloroplast genome: Gene content, hot spots of divergence and fine tuning of genetic information by transcript editing. J. Mol. Biol. 251, 614-628.
    • (1995) J. Mol. Biol. , vol.251 , pp. 614-628
    • Maier, R.M.1    Neckermann, K.2    Igloi, G.L.3    Kössel, H.4
  • 25
    • 0002160837 scopus 로고    scopus 로고
    • Gene transfer from organelles to the nucleus: How much, what happens, and why?
    • Martin, W., and Herrmann, R.G. (1998). Gene transfer from organelles to the nucleus: How much, what happens, and why? Plant Physiol. 118, 9-17.
    • (1998) Plant Physiol. , vol.118 , pp. 9-17
    • Martin, W.1    Herrmann, R.G.2
  • 26
    • 0037126071 scopus 로고    scopus 로고
    • Evolutionary analysis of Arabidopsis, cyanobacterial, and chloroplast genomes reveals plastid phylogeny and thousands of cyanobacterial genes in the nucleus
    • USA
    • Martin, W., Rujan, T., Richly, E., Hansen, A., Cornelsen, S., Lins, T., Leister, D., Stoebe, B., Hasegawa, M., and Penny, D. (2002). Evolutionary analysis of Arabidopsis, cyanobacterial, and chloroplast genomes reveals plastid phylogeny and thousands of cyanobacterial genes in the nucleus. Proc. Natl. Acad. Sci. USA 99, 12246-12251.
    • (2002) Proc. Natl. Acad. Sci. , vol.99 , pp. 12246-12251
    • Martin, W.1    Rujan, T.2    Richly, E.3    Hansen, A.4    Cornelsen, S.5    Lins, T.6    Leister, D.7    Stoebe, B.8    Hasegawa, M.9    Penny, D.10
  • 28
    • 0035056576 scopus 로고    scopus 로고
    • Many parallel losses of infA from chloroplast DNA during angiosperm evolution with multiple independent transfers to the nucleus
    • Millen, R.S., et al. (2001). Many parallel losses of infA from chloroplast DNA during angiosperm evolution with multiple independent transfers to the nucleus. Plant Cell 13, 645-658.
    • (2001) Plant Cell , vol.13 , pp. 645-658
    • Millen, R.S.1
  • 29
    • 0036456491 scopus 로고    scopus 로고
    • The complete sequence of the rice (Oryza sativa L.) mitochondrial genome: Frequent DNA sequence acquisition and loss during the evolution of flowering plants
    • Notsu, Y., Masood, S., Nishikawa, T., Kubo, N., Akiduki, G., Nakazono, M., Hirai, A., and Kadowaki, K. (2002). The complete sequence of the rice (Oryza sativa L.) mitochondrial genome: Frequent DNA sequence acquisition and loss during the evolution of flowering plants. Mol. Genet. Genomics 268, 434-445.
    • (2002) Mol. Genet. Genomics , vol.268 , pp. 434-445
    • Notsu, Y.1    Masood, S.2    Nishikawa, T.3    Kubo, N.4    Akiduki, G.5    Nakazono, M.6    Hirai, A.7    Kadowaki, K.8
  • 30
    • 0026091126 scopus 로고
    • RNA-mediated transfer of the gene coxll from the mitochondrion to the nucleus during flowering plant evolution
    • Nugent, J.M., and Palmer, J.D. (1991). RNA-mediated transfer of the gene coxll from the mitochondrion to the nucleus during flowering plant evolution. Cell 66, 473-481.
    • (1991) Cell , vol.66 , pp. 473-481
    • Nugent, J.M.1    Palmer, J.D.2
  • 31
    • 0036861524 scopus 로고    scopus 로고
    • Different types and rates of genome evolution detected by comparative sequence analysis of orthologous segments from four cereal genomes
    • Ramakrishna, W., Dubcovsky, J., Park, Y.-J., Busso, C., Emberton, J., SanMiguel, P., and Bennetzen, J.L. (2002). Different types and rates of genome evolution detected by comparative sequence analysis of orthologous segments from four cereal genomes. Genetics 162, 1389-1400.
    • (2002) Genetics , vol.162 , pp. 1389-1400
    • Ramakrishna, W.1    Dubcovsky, J.2    Park, Y.-J.3    Busso, C.4    Emberton, J.5    SanMiguel, P.6    Bennetzen, J.L.7
  • 32
    • 0033523903 scopus 로고    scopus 로고
    • Mitochondrial DNA repairs double-strand breaks in yeast chromosomes
    • Ricchetti, M., Fairhead, C., and Dujon, B. (1999). Mitochondrial DNA repairs double-strand breaks in yeast chromosomes. Nature 402, 96-100.
    • (1999) Nature , vol.402 , pp. 96-100
    • Ricchetti, M.1    Fairhead, C.2    Dujon, B.3
  • 33
    • 0038581538 scopus 로고    scopus 로고
    • In-depth view of structure, activity, and evolution of rice chromosome 10
    • Rice Chromosome 10 Sequencing Consortium (2003). In-depth view of structure, activity, and evolution of rice chromosome 10. Science 300, 1566-1569.
    • (2003) Science , vol.300 , pp. 1566-1569
  • 34
    • 0037624063 scopus 로고    scopus 로고
    • Collection, mapping, and annotation of over 28,000 cDNA clones from japonica rice
    • Rice Full-Length cDNA Consortium (2003). Collection, mapping, and annotation of over 28,000 cDNA clones from japonica rice. Science 301, 376-379.
    • (2003) Science , vol.301 , pp. 376-379
  • 35
    • 4944253274 scopus 로고    scopus 로고
    • NUPTs in sequenced eukaryotes and their genomic organization in relation to NUMTs
    • Richly, E., and Leister, D. (2004). NUPTs in sequenced eukaryotes and their genomic organization in relation to NUMTs. Mol. Biol. Evol. 21, 1972-1980.
    • (2004) Mol. Biol. Evol. , vol.21 , pp. 1972-1980
    • Richly, E.1    Leister, D.2
  • 37
    • 0037153190 scopus 로고    scopus 로고
    • The genome sequence and structure of rice chromosome 1
    • Sasaki, T., et al. (2002). The genome sequence and structure of rice chromosome 1. Nature 420, 312-316.
    • (2002) Nature , vol.420 , pp. 312-316
    • Sasaki, T.1
  • 38
    • 0033852426 scopus 로고    scopus 로고
    • A contiguous 66-kb barley DNA sequence provides evidence for reversible genome expansion
    • Shirasu, K., Shulman, A.H., Lahaye, T., and Schulze-Lefert, P. (2000). A contiguous 66-kb barley DNA sequence provides evidence for reversible genome expansion. Genome Res. 10, 908-915.
    • (2000) Genome Res. , vol.10 , pp. 908-915
    • Shirasu, K.1    Shulman, A.H.2    Lahaye, T.3    Schulze-Lefert, P.4
  • 39
    • 0019887799 scopus 로고
    • Identification of common molecular sequences
    • Smith, T.F., and Waterman, M.S. (1981a). Identification of common molecular sequences. J. Mol. Biol. 147, 195-197.
    • (1981) J. Mol. Biol. , vol.147 , pp. 195-197
    • Smith, T.F.1    Waterman, M.S.2
  • 40
  • 41
    • 0042760348 scopus 로고    scopus 로고
    • High-frequency gene transfer from the chloroplast genome to the nucleus
    • USA
    • Stegemann, S., Hartmann, S., Ruf, S., and Bock, R. (2003). High-frequency gene transfer from the chloroplast genome to the nucleus. Proc. Natl. Acad. Sci. USA 100, 8828-8833.
    • (2003) Proc. Natl. Acad. Sci. , vol.100 , pp. 8828-8833
    • Stegemann, S.1    Hartmann, S.2    Ruf, S.3    Bock, R.4
  • 42
    • 0035942234 scopus 로고    scopus 로고
    • Complex mtDNA constitutes an approximate 620-kb insertion on Arabidopsis thaliana chromosome 2: Implication of potential sequencing errors caused by large-unit repeat
    • USA
    • Stupar, R.M., Lilly, J.W., Town, C.D., Cheng, Z., Kaul, S., Buell, R., and Jiang, J. (2001). Complex mtDNA constitutes an approximate 620-kb insertion on Arabidopsis thaliana chromosome 2: Implication of potential sequencing errors caused by large-unit repeat. Proc. Natl. Acad. Sci. USA 98, 5099-5103.
    • (2001) Proc. Natl. Acad. Sci. , vol.98 , pp. 5099-5103
    • Stupar, R.M.1    Lilly, J.W.2    Town, C.D.3    Cheng, Z.4    Kaul, S.5    Buell, R.6    Jiang, J.7
  • 43
    • 0026860017 scopus 로고
    • The chloroplast genome
    • Sugiura, M. (1992). The chloroplast genome. Plant Mol. Biol. 19, 149-168.
    • (1992) Plant Mol. Biol. , vol.19 , pp. 149-168
    • Sugiura, M.1
  • 45
    • 0031574072 scopus 로고    scopus 로고
    • The CLUSTALX windows interface: Flexible strategies for multiple sequence alignment aided by quality analysis tools
    • Thompson, J.D., Gibson, T.J., Plewniak, F., Jeanmougin, F., and Higgins, D.G. (1997). The CLUSTALX windows interface: Flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 25, 4876-4882.
    • (1997) Nucleic Acids Res. , vol.25 , pp. 4876-4882
    • Thompson, J.D.1    Gibson, T.J.2    Plewniak, F.3    Jeanmougin, F.4    Higgins, D.G.5
  • 46
    • 0037267093 scopus 로고    scopus 로고
    • Pericentromeric duplications in the laboratory mouse
    • Thomas, J.W., et al. (2003). Pericentromeric duplications in the laboratory mouse. Genome Res. 13, 55-63.
    • (2003) Genome Res. , vol.13 , pp. 55-63
    • Thomas, J.W.1
  • 47
    • 0025325148 scopus 로고
    • Escape of DNA from mitochondria to the nucleus in Saccharomyces cerevisiae
    • Thorsness, P.E., and Fox, T.D. (1990). Escape of DNA from mitochondria to the nucleus in Saccharomyces cerevisiae. Nature 346, 376-379.
    • (1990) Nature , vol.346 , pp. 376-379
    • Thorsness, P.E.1    Fox, T.D.2
  • 48
    • 0036073133 scopus 로고    scopus 로고
    • Pattern of organization of human mitochondrial pseudogenes in the nuclear genome
    • Woischnik, M., and Moraes, C.T. (2002). Pattern of organization of human mitochondrial pseudogenes in the nuclear genome. Genome Res. 12, 885-893.
    • (2002) Genome Res. , vol.12 , pp. 885-893
    • Woischnik, M.1    Moraes, C.T.2
  • 49
    • 0024712231 scopus 로고
    • Date of the monocot-dicot divergence estimated from chloroplast DNA sequence data
    • USA
    • Wolfe, K.H., Gouy, M., Yang, Y.-W., Sharp, P.M., and Li, W.-H. (1989). Date of the monocot-dicot divergence estimated from chloroplast DNA sequence data. Proc. Natl. Acad. Sci. USA 86, 6201-6205.
    • (1989) Proc. Natl. Acad. Sci. , vol.86 , pp. 6201-6205
    • Wolfe, K.H.1    Gouy, M.2    Yang, Y.-W.3    Sharp, P.M.4    Li, W.-H.5
  • 50
    • 0036009910 scopus 로고    scopus 로고
    • A comprehensive rice transcript map containing 6591 expressed sequence tag sites
    • Wu, J., et al. (2002). A comprehensive rice transcript map containing 6591 expressed sequence tag sites. Plant Cell 14, 525-535.
    • (2002) Plant Cell , vol.14 , pp. 525-535
    • Wu, J.1
  • 51
    • 0033231558 scopus 로고    scopus 로고
    • Patching broken chromosomes with extranuclear cellular DNA
    • Yu, X., and Gabriel, A. (1999). Patching broken chromosomes with extranuclear cellular DNA. Mol. Cell 4, 873-888.
    • (1999) Mol. Cell , vol.4 , pp. 873-888
    • Yu, X.1    Gabriel, A.2
  • 52
    • 0036047666 scopus 로고    scopus 로고
    • Genome sequencing of a 239-kb region of rice chromosome 10L reveals a high frequency of gene duplication and a large chloroplast DNA insertion
    • Yuan, Q., Hill, J., Hsiao, J., Moffat, K., Ouyang, S., Cheng, Z., Jiang, J., and Buell, C.R. (2002). Genome sequencing of a 239-kb region of rice chromosome 10L reveals a high frequency of gene duplication and a large chloroplast DNA insertion. Mol. Genet. Genomics 267, 713-720.
    • (2002) Mol. Genet. Genomics , vol.267 , pp. 713-720
    • Yuan, Q.1    Hill, J.2    Hsiao, J.3    Moffat, K.4    Ouyang, S.5    Cheng, Z.6    Jiang, J.7    Buell, C.R.8
  • 53
    • 0001354070 scopus 로고
    • Evolution of higher-plant chloroplast DNA-encoded genes: Implications for structure-function and phylogenetic studies
    • Zurawski, G., and Clegg, M.T. (1987). Evolution of higher-plant chloroplast DNA-encoded genes: Implications for structure-function and phylogenetic studies. Annu. Rev. Plant Physiol. 38, 391-418.
    • (1987) Annu. Rev. Plant Physiol. , vol.38 , pp. 391-418
    • Zurawski, G.1    Clegg, M.T.2


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