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Volumn 13, Issue 5, 2006, Pages 197-204

Pattern and rate of indel evolution inferred from whole chloroplast intergenic regions in sugarcane, maize and rice

Author keywords

Chloroplast genome; Evolutionary rate; Indels; Intergenic region; Non coding DNA sequence

Indexed keywords

CHLOROPLAST DNA; NUCLEOTIDE; SPACER DNA;

EID: 33845887966     PISSN: 13402838     EISSN: 13402838     Source Type: Journal    
DOI: 10.1093/dnares/dsl012     Document Type: Article
Times cited : (108)

References (35)
  • 1
    • 0345668476 scopus 로고    scopus 로고
    • Majority of divergence between closely related DNA samples is due to indels
    • Britten, R. J., Rowen, L., Williams, J., and Cameron, R. A. 2003, Majority of divergence between closely related DNA samples is due to indels, Proc. Natl Acad. Sci. USA, 100, 4661-4665.
    • (2003) Proc. Natl Acad. Sci. USA , vol.100 , pp. 4661-4665
    • Britten, R.J.1    Rowen, L.2    Williams, J.3    Cameron, R.A.4
  • 2
    • 0034491886 scopus 로고    scopus 로고
    • The evolution of non-coding chloroplast DNA and its application in plant systematics
    • Kelchner, S. A. 2000, The evolution of non-coding chloroplast DNA and its application in plant systematics, Ann. Missouri Bot. Gard., 87, 499-527.
    • (2000) Ann. Missouri Bot. Gard , vol.87 , pp. 499-527
    • Kelchner, S.A.1
  • 3
    • 0242582442 scopus 로고    scopus 로고
    • Molecular evolution of insertions and deletions in the chloroplast genome of Silene
    • Ingvarsson, P. K., Ribstein, S., and Taylor, D. R. 2003, Molecular evolution of insertions and deletions in the chloroplast genome of Silene, Mol. Biol. Evol., 20, 1737-1740.
    • (2003) Mol. Biol. Evol , vol.20 , pp. 1737-1740
    • Ingvarsson, P.K.1    Ribstein, S.2    Taylor, D.R.3
  • 4
    • 3342931347 scopus 로고    scopus 로고
    • Patterns and relative rates of nucleotide and insertion/deletion evolution at six chloroplast intergenic regions in New World species of the Lecythidaceae
    • Hamilton, M. B., Braverman, J. M., and Soria-Hernanz, D. F. 2003, Patterns and relative rates of nucleotide and insertion/deletion evolution at six chloroplast intergenic regions in New World species of the Lecythidaceae, Mol. Biol. Evol., 20, 1710-1721.
    • (2003) Mol. Biol. Evol , vol.20 , pp. 1710-1721
    • Hamilton, M.B.1    Braverman, J.M.2    Soria-Hernanz, D.F.3
  • 5
    • 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., Shimada, H., Whittier, R., 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    Shimada, H.2    Whittier, R.3
  • 6
    • 0029160870 scopus 로고
    • Complete sequence of the maize chloroplast genome: Gene content, hotspots of divergence and fine tuning of genetic information by transcript editing
    • Maier, R. M., Neckermann, K., Igloi, G. L., and Kossel, H. 1995, Complete sequence of the maize chloroplast genome: gene content, hotspots 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    Kossel, H.4
  • 7
    • 0035674196 scopus 로고    scopus 로고
    • Ogihara, Y., Isono, K., Kojim, T., et al. (19 co-authors) 2002, Structural features of a wheat plastome as revealed by complete sequencing of chloroplast DNA, Mol. Gen. Genet., 266, 740-746.
    • Ogihara, Y., Isono, K., Kojim, T., et al. (19 co-authors) 2002, Structural features of a wheat plastome as revealed by complete sequencing of chloroplast DNA, Mol. Gen. Genet., 266, 740-746.
  • 8
    • 0036899796 scopus 로고    scopus 로고
    • Whole chloroplast genome comparison of rice, maize, and wheat: Implications for chloroplast gene diversification and phylogeny of cereals
    • Matsuoka, Y., Yamazaki, Y., Ogihara, Y., and Tsunewaki, K. 2002, Whole chloroplast genome comparison of rice, maize, and wheat: implications for chloroplast gene diversification and phylogeny of cereals, Mol. Biol. Evol., 19, 2084-2091.
    • (2002) Mol. Biol. Evol , vol.19 , pp. 2084-2091
    • Matsuoka, Y.1    Yamazaki, Y.2    Ogihara, Y.3    Tsunewaki, K.4
  • 9
    • 11144263232 scopus 로고    scopus 로고
    • Complete nucleotide sequence of the sugarcane (Saccharum officinarum) chloroplast genome: A comparative analysis of four monocot chloroplast genomes
    • Asano, T., Tsudzuki, T., Takahashi, S., Shimada, H., and Kadowaki, K. 2004, Complete nucleotide sequence of the sugarcane (Saccharum officinarum) chloroplast genome: a comparative analysis of four monocot chloroplast genomes, DNA res., 11, 93-99.
    • (2004) DNA res , vol.11 , pp. 93-99
    • Asano, T.1    Tsudzuki, T.2    Takahashi, S.3    Shimada, H.4    Kadowaki, K.5
  • 10
    • 0035739420 scopus 로고    scopus 로고
    • A search for markers of sugarcane evolution
    • Bacci, M., Miranda, V. F. O., Martins, V. G., et al. 2001, A search for markers of sugarcane evolution, Genet. Mol. Biol., 24, 169-174.
    • (2001) Genet. Mol. Biol , vol.24 , pp. 169-174
    • Bacci, M.1    Miranda, V.F.O.2    Martins, V.G.3
  • 11
    • 23044533391 scopus 로고    scopus 로고
    • Molecular phylogeny of Miscanthus s.l., Saccharum and related genera (Saccharinae, Andropogoneae, Poaceae) using DNA sequences from ITS nuclear ribosomal DNA and the plastid trnL-F regions
    • Hodkinson, T. R.l., Chase, M. W., Lledo, D., Salamin, N., and Renvoize, S. A. 2002, Molecular phylogeny of Miscanthus s.l., Saccharum and related genera (Saccharinae, Andropogoneae, Poaceae) using DNA sequences from ITS nuclear ribosomal DNA and the plastid trnL-F regions, J. Plant Res., 115, 381-392.
    • (2002) J. Plant Res , vol.115 , pp. 381-392
    • Hodkinson, T.R.L.1    Chase, M.W.2    Lledo, D.3    Salamin, N.4    Renvoize, S.A.5
  • 12
    • 2442645495 scopus 로고    scopus 로고
    • A comparison of rice chloroplast genomes
    • Tang, J., Xia, H., Cao, M., et al. 2004, A comparison of rice chloroplast genomes, Plant Phys., 135, 412-420.
    • (2004) Plant Phys , vol.135 , pp. 412-420
    • Tang, J.1    Xia, H.2    Cao, M.3
  • 13
    • 0029610067 scopus 로고
    • Uniparental inheritance of mitochondrial aid chloroplast genes: Mechanisms and evolution
    • Birky, C. W. J. 1995, Uniparental inheritance of mitochondrial aid chloroplast genes: mechanisms and evolution, Proc. Natl Acad. Sci. USA, 92, 11331-11338.
    • (1995) Proc. Natl Acad. Sci. USA , vol.92 , pp. 11331-11338
    • Birky, C.W.J.1
  • 14
    • 0027968068 scopus 로고
    • CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positions-specific gap penalties and weight matrix choice
    • Thompson, J. D., Higgins, D. G., and Gibson, T. J. 1994, CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positions-specific gap penalties and weight matrix choice, Nucleic Acids Res., 22, 4673-4680.
    • (1994) Nucleic Acids Res , vol.22 , pp. 4673-4680
    • Thompson, J.D.1    Higgins, D.G.2    Gibson, T.J.3
  • 15
    • 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
  • 16
    • 0030267939 scopus 로고    scopus 로고
    • Regulation of gene expression in chloroplasts of higher plants
    • Sugita, M., and Sugiura, M. 1996, Regulation of gene expression in chloroplasts of higher plants, Plant Mol. Biol., 32, 315-26.
    • (1996) Plant Mol. Biol , vol.32 , pp. 315-326
    • Sugita, M.1    Sugiura, M.2
  • 17
    • 0032972599 scopus 로고    scopus 로고
    • DnaSP version 3: An integrated program for molecular population genetics and molecular evolution analysis
    • Rozas, J., and Rozas, R. 1999, DnaSP version 3: an integrated program for molecular population genetics and molecular evolution analysis, Bioinformatics, 15, 174-175.
    • (1999) Bioinformatics , vol.15 , pp. 174-175
    • Rozas, J.1    Rozas, R.2
  • 19
    • 0028943946 scopus 로고
    • The size distribution of insertions and deletions in human and rodent pseudogenes suggests the logarithmic gap penalty for sequence alignment
    • Gu, X. and Li, W.-H. 1995, The size distribution of insertions and deletions in human and rodent pseudogenes suggests the logarithmic gap penalty for sequence alignment, J. Mol. Evol., 40, 464-473.
    • (1995) J. Mol. Evol , vol.40 , pp. 464-473
    • Gu, X.1    Li, W.-H.2
  • 20
    • 0028351405 scopus 로고
    • Evolutionary rates of insertion and deletion in noncoding nucleotide sequences of primates
    • Saitou, N. and Ueda, S. 1994, Evolutionary rates of insertion and deletion in noncoding nucleotide sequences of primates, Mol. Biol. Evol., 11, 504-512.
    • (1994) Mol. Biol. Evol , vol.11 , pp. 504-512
    • Saitou, N.1    Ueda, S.2
  • 21
    • 0024505629 scopus 로고
    • Deletions in processed pseudogenes accumulate faster in rodents than in humans
    • Graur, D., Shauali, Y., and Li, W.-H. 1989, Deletions in processed pseudogenes accumulate faster in rodents than in humans, J. Mol. Evol., 28, 279-285.
    • (1989) J. Mol. Evol , vol.28 , pp. 279-285
    • Graur, D.1    Shauali, Y.2    Li, W.-H.3
  • 23
    • 0023256559 scopus 로고
    • Slipped-strand mispairing: A major mechanism for DNA sequence evolution
    • Levinson, G. and Gutman, G. A. 1987, Slipped-strand mispairing: a major mechanism for DNA sequence evolution, Mol. Biol. Evol., 4, 203-221.
    • (1987) Mol. Biol. Evol , vol.4 , pp. 203-221
    • Levinson, G.1    Gutman, G.A.2
  • 24
    • 5444264308 scopus 로고    scopus 로고
    • The complete nucleotide sequence of wild rice (Oryza nivara) chloroplast genome: First genome wide comparative sequence analysis of wild and cultivated rice
    • Masood, M. S., Nishikawa, T., Fukuoka, S., Njenga, P. K., Tsudzuki, T., and Kadowaki, K. 2004, The complete nucleotide sequence of wild rice (Oryza nivara) chloroplast genome: first genome wide comparative sequence analysis of wild and cultivated rice, Gene, 340, 133-139.
    • (2004) Gene , vol.340 , pp. 133-139
    • Masood, M.S.1    Nishikawa, T.2    Fukuoka, S.3    Njenga, P.K.4    Tsudzuki, T.5    Kadowaki, K.6
  • 25
    • 0028865532 scopus 로고
    • Neighboring base composition and transversion/ transition bias in a comparison of rice and maize chloroplast noncoding regions
    • Morton, B. R. 1995, Neighboring base composition and transversion/ transition bias in a comparison of rice and maize chloroplast noncoding regions, Proc. Natl Acad. Sci. USA, 92, 9717-9721.
    • (1995) Proc. Natl Acad. Sci. USA , vol.92 , pp. 9717-9721
    • Morton, B.R.1
  • 26
    • 25444495267 scopus 로고    scopus 로고
    • Homopolymer tract length dependent enrichments in functional regions of 27 eukaryotes and their novel dependence on the organism DNA (G+C)% composition
    • Zhou, Y., Bizzaro, J. W., and Marx, K. A. 2004, Homopolymer tract length dependent enrichments in functional regions of 27 eukaryotes and their novel dependence on the organism DNA (G+C)% composition, BMC Genomics, 5, 95.
    • (2004) BMC Genomics , vol.5 , pp. 95
    • Zhou, Y.1    Bizzaro, J.W.2    Marx, K.A.3
  • 27
    • 0027398292 scopus 로고
    • Chloroplast gene sequences and the study of plant evolution
    • Clegg, M. T. 1993, Chloroplast gene sequences and the study of plant evolution, Proc. Natl Acad. Sci. USA, 90, 363-367.
    • (1993) Proc. Natl Acad. Sci. USA , vol.90 , pp. 363-367
    • Clegg, M.T.1
  • 28
    • 21544482014 scopus 로고    scopus 로고
    • Very close relationship of the chloroplast genomes among Saccharum species
    • Takahashi, S., Furukawa, T., Asano, T., et al. 2005, Very close relationship of the chloroplast genomes among Saccharum species, Theor. Appl. Genet., 110, 1523-1529.
    • (2005) Theor. Appl. Genet , vol.110 , pp. 1523-1529
    • Takahashi, S.1    Furukawa, T.2    Asano, T.3
  • 29
    • 4344616881 scopus 로고    scopus 로고
    • Rapid recent growth and divergence of rice nuclear genomes
    • Ma, J. and Bennetzen, J. L. 2004, Rapid recent growth and divergence of rice nuclear genomes, Proc. Natl Acad. Sci. USA, 101, 12404-12410.
    • (2004) Proc. Natl Acad. Sci. USA , vol.101 , pp. 12404-12410
    • Ma, J.1    Bennetzen, J.L.2
  • 30
    • 21244501403 scopus 로고    scopus 로고
    • Phylogenetic relationships among A-genome species of the genus Oryza revealed by intron sequences of four nuclear genes
    • Zhu, Q. H. and Ge, S. 2005, Phylogenetic relationships among A-genome species of the genus Oryza revealed by intron sequences of four nuclear genes, New Phytol., 167, 249-265.
    • (2005) New Phytol , vol.167 , pp. 249-265
    • Zhu, Q.H.1    Ge, S.2
  • 31
    • 0021750971 scopus 로고
    • Molecular evolution of chloroplast DNA sequences
    • Curtis, S. E. and Clegg, M. T. 1984, Molecular evolution of chloroplast DNA sequences, Mol. Biol. Evol., 1, 291-301.
    • (1984) Mol. Biol. Evol , vol.1 , pp. 291-301
    • Curtis, S.E.1    Clegg, M.T.2
  • 32
    • 0022294484 scopus 로고
    • Comparative organization of chloroplast genomes
    • Palmer, J. D. 1985, Comparative organization of chloroplast genomes, Annu. Rev. Genet., 19, 325-354.
    • (1985) Annu. Rev. Genet , vol.19 , pp. 325-354
    • Palmer, J.D.1
  • 33
    • 0023462635 scopus 로고
    • Rates of nucleotide substitution vary greatly across mitochondrial, chloroplast, and nuclear DNAs
    • Wolfe, K. H., Li, W.-H., and Sharp, P. M. 1987, Rates of nucleotide substitution vary greatly across mitochondrial, chloroplast, and nuclear DNAs, Proc. Natl Acad. Sci. USA, 84, 9054-9058.
    • (1987) Proc. Natl Acad. Sci. USA , vol.84 , pp. 9054-9058
    • Wolfe, K.H.1    Li, W.-H.2    Sharp, P.M.3
  • 34
    • 0026582121 scopus 로고
    • Biased gene conversion, copy number, and apparent mutation rate differences within chloroplast and bacterial genomes
    • Birky, C. W. J. and Walsh, J. B. 1992, Biased gene conversion, copy number, and apparent mutation rate differences within chloroplast and bacterial genomes, Genetics, 130, 677-783.
    • (1992) Genetics , vol.130 , pp. 677-783
    • Birky, C.W.J.1    Walsh, J.B.2
  • 35
    • 0036840720 scopus 로고    scopus 로고
    • Nucleotide substitution rates in legume chloroplast DNA depend on the presence of the inverted repeat
    • Perry, A. S. and Wolfe, K. H. 2002, Nucleotide substitution rates in legume chloroplast DNA depend on the presence of the inverted repeat, J. Mol. Evol., 55, 501-508.
    • (2002) J. Mol. Evol , vol.55 , pp. 501-508
    • Perry, A.S.1    Wolfe, K.H.2


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