메뉴 건너뛰기




Volumn 3, Issue 1, 2011, Pages 309-319

Comparative chloroplast genomes of pinaceae: Insights into the mechanism of diversified genomic organizations

Author keywords

Chloroplast genome; Isoform; Pinaceae; Repeat; Structural evolution

Indexed keywords

CHLOROPLAST DNA;

EID: 79960108509     PISSN: None     EISSN: 17596653     Source Type: Journal    
DOI: 10.1093/gbe/evr026     Document Type: Article
Times cited : (95)

References (45)
  • 1
    • 0008350412 scopus 로고
    • Cyanelle DNA from Cyanophora paradoxa exists in two forms due to intramolecular recombination
    • Bohnert HJ, Loffelhardt W. 1982. Cyanelle DNA from Cyanophora paradoxa exists in two forms due to intramolecular recombination. EBS Lett. 150:403-406.
    • (1982) EBS Lett , vol.150 , pp. 403-406
    • Bohnert, H.J.1    Loffelhardt, W.2
  • 2
    • 65349104518 scopus 로고    scopus 로고
    • Extensive reorganization of the plastid genome of Trifolium subterraneum (Fabaceae) is associated with numerous repeated sequences and novel DNA insertions
    • Cai Z, et al. 2008. Extensive reorganization of the plastid genome of Trifolium subterraneum (Fabaceae) is associated with numerous repeated sequences and novel DNA insertions. J Mol Evol. 67: 696-704.
    • (2008) J Mol Evol , vol.67 , pp. 696-704
    • Cai, Z.1
  • 3
    • 44849092579 scopus 로고    scopus 로고
    • Chloroplast genome sequencing analysis of Heterosigma akashiwo CCMP452 (West Atlantic) and NIES293 (West Pacific) strains
    • Cattolico RA, et al. 2008. Chloroplast genome sequencing analysis of Heterosigma akashiwo CCMP452 (West Atlantic) and NIES293 (West Pacific) strains. BMC Genomics. 9:211.
    • (2008) BMC Genomics , vol.9 , pp. 211
    • Cattolico, R.A.1
  • 4
    • 33749336062 scopus 로고    scopus 로고
    • The complete chloroplast genome sequence of Pelargonium hortorum: Organization and evolution of the largest and most highly rearranged chloroplast genome of land plants
    • DOI 10.1093/molbev/msl089
    • Chumley TW, et al. 2006. The complete chloroplast genome sequence of Pelargonium x hortorum: organization and evolution of the largest and most highly rearranged chloroplast genome of land plants. Mol Biol Evol. 23:2175-2190. (Pubitemid 44536825)
    • (2006) Molecular Biology and Evolution , vol.23 , Issue.11 , pp. 2175-2190
    • Chumley, T.W.1    Palmer, J.D.2    Mower, J.P.3    Fourcade, H.M.4    Calie, P.J.5    Boore, J.L.6    Jansen, R.K.7
  • 5
    • 56149096455 scopus 로고    scopus 로고
    • Multiplex sequencing of plant chloroplast genomes using Solexa sequencing-by-synthesis technology
    • Cronn R, et al. 2008. Multiplex sequencing of plant chloroplast genomes using Solexa sequencing-by-synthesis technology. Nucleic Acids Res. 36:e122.
    • (2008) Nucleic Acids Res , vol.36
    • Cronn, R.1
  • 6
    • 1842362834 scopus 로고
    • Divergence of chloroplast gene organization in three legumes
    • Crouse EJ, et al. 1986. Divergence of chloroplast gene organization in three legumes. Plant Mol Biol. 7:143-150.
    • (1986) Plant Mol Biol. , vol.7 , pp. 143-150
    • Crouse, E.J.1
  • 7
    • 34548841706 scopus 로고    scopus 로고
    • DNA replication, recombination, and repair in plastids
    • Bock R, editor. Heidelberg (Germany): Springer
    • Day A, Madesis P. 2007. DNA replication, recombination, and repair in plastids. In: Bock R, editor. Cell and molecular biology of plastids. Topics in current genetics. Vol. 19. Heidelberg (Germany): Springer. p. 65-119.
    • (2007) Cell and Molecular Biology of Plastids. Topics in Current Genetics , vol.19 , pp. 65-119
    • Day, A.1    Madesis, P.2
  • 8
    • 54949123062 scopus 로고    scopus 로고
    • Use of simultaneous analyses to guide fossilbased calibrations of Pinaceae phylogeny
    • Gernandt DS, et al. 2008. Use of simultaneous analyses to guide fossilbased calibrations of Pinaceae phylogeny. Int J Plant Sci. 169:1086-1099.
    • (2008) Int J Plant Sci , vol.169 , pp. 1086-1099
    • Gernandt, D.S.1
  • 9
    • 78650446228 scopus 로고    scopus 로고
    • Extreme reconfiguration of plastid genomes in the angiosperm family Geraniaceae: Rearrangements, repeats, and codon usage
    • Guisinger MM, Kuehl JV, Boore JL, Jansen RK. 2011. Extreme reconfiguration of plastid genomes in the angiosperm family Geraniaceae: rearrangements, repeats, and codon usage. Mol Biol Evol. 28:583-600.
    • (2011) Mol Biol Evol , vol.28 , pp. 583-600
    • Guisinger, M.M.1    Kuehl, J.V.2    Boore, J.L.3    Jansen, R.K.4
  • 10
    • 43149125849 scopus 로고    scopus 로고
    • Extensive rearrangements in the chloroplast genome of Trachelium caeruleum are associated with repeats and tRNA genes
    • Haberle RC, Fourcade HM, Boore JL, Jansen RK. 2008. Extensive rearrangements in the chloroplast genome of Trachelium caeruleum are associated with repeats and tRNA genes. J Mol Evol. 66:350-361.
    • (2008) J Mol Evol , vol.66 , pp. 350-361
    • Haberle, R.C.1    Fourcade, H.M.2    Boore, J.L.3    Jansen, R.K.4
  • 11
    • 0000212728 scopus 로고
    • Organelle genomes in conifers: Structure, evolution, and diversity
    • Hipkins VD, Krutovskii KV, Strauss SH. 1994. Organelle genomes in conifers: structure, evolution, and diversity. For Genet. 1:179-189.
    • (1994) For Genet. , vol.1 , pp. 179-189
    • Hipkins, V.D.1    Krutovskii, K.V.2    Strauss, S.H.3
  • 12
    • 46649088563 scopus 로고    scopus 로고
    • Complete nucleotide sequence of the Cryptomeria japonica D. Don. chloroplast genome and comparative chloroplast genomics: Diversified genomic structure of coniferous species
    • Hirao T, Watanabe A, Kurita M, Kondo T, Takata K. 2008. Complete nucleotide sequence of the Cryptomeria japonica D. Don. chloroplast genome and comparative chloroplast genomics: diversified genomic structure of coniferous species. BMC Plant Biol. 8:70.
    • (2008) BMC Plant Biol. , vol.8 , pp. 70
    • Hirao, T.1    Watanabe, A.2    Kurita, M.3    Kondo, T.4    Takata, K.5
  • 13
    • 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
  • 14
    • 0031059690 scopus 로고    scopus 로고
    • Short inverted repeats function as hotspots of intermolecular recombination giving rise to oligomers of deleted plastid DNAs (ptDNAs)
    • DOI 10.1007/s002940050193
    • Kawata M, Harada T, Shimamoto Y, Oono K, Takaiwa F. 1997. Short inverted repeats function as hotspots of intermolecular recombination giving rise to oligomers of deleted plastid DNAs (ptDNAs). Curr Genet. 31:179-184. (Pubitemid 27116822)
    • (1997) Current Genetics , vol.31 , Issue.2 , pp. 179-184
    • Kawata, M.1    Harada, T.2    Shimamoto, Y.3    Oono, K.4    Takaiwa, F.5
  • 15
    • 23944506347 scopus 로고    scopus 로고
    • Two chloroplast DNA inversions originated simultaneously during the early evolution of the sunflower family (Asteraceae)
    • DOI 10.1093/molbev/msi174
    • Kim KJ, Choi KS, Jansen RK. 2005. Two chloroplast DNA inversions originated simultaneously during early evolution in the sunflower family. Mol Biol Evol. 22:1783-1792. (Pubitemid 41191505)
    • (2005) Molecular Biology and Evolution , vol.22 , Issue.9 , pp. 1783-1792
    • Kim, K.-J.1    Choi, K.-S.2    Jansen, R.K.3
  • 16
    • 22844450753 scopus 로고    scopus 로고
    • Widespread occurrence of small inversions in the chloroplast genomes of land plants
    • Kim KJ, Lee HL. 2005. Widespread occurrence of small inversions in the chloroplast genomes of land plants. Mol Cells. 19:104-113.
    • (2005) Mol Cells , vol.19 , pp. 104-113
    • Kim, K.J.1    Lee, H.L.2
  • 17
    • 0002909895 scopus 로고
    • Inverted repeats in chloroplast DNA from higher plants
    • Kolodner R, Tewari KK. 1979. Inverted repeats in chloroplast DNA from higher plants. Proc Natl Acad Sci U S A. 76:41-45.
    • (1979) Proc Natl Acad Sci U S A , vol.76 , pp. 41-45
    • Kolodner, R.1    Tewari, K.K.2
  • 18
    • 34548321590 scopus 로고    scopus 로고
    • Gene relocations within chloroplast genomes of Jasminum and Menodora (Oleaceae) are due to multiple, overlapping inversions
    • DOI 10.1093/molbev/msm036
    • Lee HL, Jansen RK, Chumley TW, Kim KJ. 2007. Gene relocations within chloroplast genomes of Jasminum and Menodora (Oleaceae) are due to multiple, overlapping inversions. Mol Biol Evol. 24: 1161-1180. (Pubitemid 47343642)
    • (2007) Molecular Biology and Evolution , vol.24 , Issue.5 , pp. 1161-1180
    • Lee, H.-L.1    Jansen, R.K.2    Chumley, T.W.3    Kim, K.-J.4
  • 19
    • 77958456904 scopus 로고    scopus 로고
    • Comparative chloroplast genomics reveals the evolution of Pinaceae genera and subfamilies
    • Lin CP, Huang JP, Wu CS, Hsu CY, Chaw SM. 2010. Comparative chloroplast genomics reveals the evolution of Pinaceae genera and subfamilies. Genome Biol Evol. 2:504-517.
    • (2010) Genome Biol Evol , vol.2 , pp. 504-517
    • Lin, C.P.1    Huang, J.P.2    Wu, C.S.3    Hsu, C.Y.4    Chaw, S.M.5
  • 20
    • 44049089159 scopus 로고    scopus 로고
    • The complete plastid genome sequence of Welwitschia mirabilis: An unusually compact plastome with accelerated divergence rates
    • McCoy SR, Kuehl JV, Boore JL, Raubeson LA. 2008. The complete plastid genome sequence of Welwitschia mirabilis: an unusually compact plastome with accelerated divergence rates. BMC Evol Biol. 8:130.
    • (2008) BMC Evol Biol. , vol.8 , pp. 130
    • McCoy, S.R.1    Kuehl, J.V.2    Boore, J.L.3    Raubeson, L.A.4
  • 21
    • 0001741303 scopus 로고    scopus 로고
    • Implications of fossil conifers for the phylogenetic relationships of living families
    • Miller CN. 1999. Implications of fossil conifers for the phylogenetic relationships of living families. Bot Rev. 65:239-277.
    • (1999) Bot Rev , vol.65 , pp. 239-277
    • Miller, C.N.1
  • 22
    • 0024692036 scopus 로고
    • Dispersed repeats and structural reorganization in subclover chloroplast DNA
    • Milligan BG, Hampton JN, Palmer JD. 1989. Dispersed repeats and structural reorganization in subclover chloroplast DNA. Mol Biol Evol. 6:355-368.
    • (1989) Mol Biol Evol , vol.6 , pp. 355-368
    • Milligan, B.G.1    Hampton, J.N.2    Palmer, J.D.3
  • 24
    • 0024110615 scopus 로고
    • Intramolecular recombination of chloroplast genome mediated by short direct-repeat sequences in wheat species
    • Ogihara Y, Terachi T, Sasakuma T. 1988. Intramolecular recombination of chloroplast genome mediated by short direct-repeat sequences in wheat species. Proc Nat Acad Sci U S A. 85:8573-8577.
    • (1988) Proc Nat Acad Sci U S A , vol.85 , pp. 8573-8577
    • Ogihara, Y.1    Terachi, T.2    Sasakuma, T.3
  • 26
    • 0020144964 scopus 로고
    • Chloroplast DNA rearrangements are more frequent when a large inverted repeat sequence is lost
    • Palmer JD, Thompson WF. 1982. Chloroplast DNA rearrangements are more frequent when a large inverted repeat sequence is lost. Cell 29:537-550.
    • (1982) Cell , vol.29 , pp. 537-550
    • Palmer, J.D.1    Thompson, W.F.2
  • 27
    • 0020658540 scopus 로고
    • Chloroplast DNA exists in 2 orientations
    • Palmer JD. 1983. Chloroplast DNA exists in 2 orientations. Nature 301:92-93.
    • (1983) Nature , vol.301 , pp. 92-93
    • Palmer, J.D.1
  • 28
    • 0001856419 scopus 로고
    • Plastid chromosomes: Structure and evolution
    • Bogorad L, editor. San Diego (CA): Academic Press
    • Palmer JD. 1991. Plastid chromosomes: structure and evolution. In: Bogorad L, editor. Molecular biology of plastids. San Diego (CA): Academic Press. p. 5-53.
    • (1991) Molecular Biology of Plastids , pp. 5-53
    • Palmer, J.D.1
  • 29
    • 23944523620 scopus 로고    scopus 로고
    • The chloroplast genome sequence of the green alga Pseudendoclonium akinetum (Ulvophyceae) reveals unusual structural features and new insights into the branching order of chlorophyte lineages
    • DOI 10.1093/molbev/msi182
    • Pombert JF, Otis C, Lemieux C, Turmel M. 2005. The chloroplast genome sequence of the green alga Pseudendoclonium akinetum (Ulvophyceae) reveals unusual structural features and new insights into the branching order of chlorophyte lineages. Mol Biol Evol. 22:1903-1918. (Pubitemid 41191516)
    • (2005) Molecular Biology and Evolution , vol.22 , Issue.9 , pp. 1903-1918
    • Pombert, J.-F.1    Otis, C.2    Lemieux, C.3    Turmel, M.4
  • 30
    • 33644938217 scopus 로고    scopus 로고
    • The complete chloroplast DNA sequence of the green alga Oltmannsiellopsis viridis reveals a distinctive quadripartite architecture in the chloroplast genome of early diverging ulvophytes
    • Pombert JF, Lemieux C, Turmel M. 2006. The complete chloroplast DNA sequence of the green alga Oltmannsiellopsis viridis reveals a distinctive quadripartite architecture in the chloroplast genome of early diverging ulvophytes. BMC Biol. 4:3.
    • (2006) BMC Biol. , vol.4 , pp. 3
    • Pombert, J.F.1    Lemieux, C.2    Turmel, M.3
  • 31
    • 0002032093 scopus 로고
    • A rare chloroplast DNA structural mutation is shared by all conifers
    • Raubeson LA, Jansen RK. 1992. A rare chloroplast DNA structural mutation is shared by all conifers. Biochem Syst Ecol. 20:17-24.
    • (1992) Biochem Syst Ecol , vol.20 , pp. 17-24
    • Raubeson, L.A.1    Jansen, R.K.2
  • 33
    • 0024311019 scopus 로고
    • Pseudogenes and short repeated sequences in the rice chloroplast genome
    • DOI 10.1007/BF00422116
    • Shimada H, Sugiura M. 1989. Pseudogenes and short repeated sequences in the rice chloroplast genome. Curr Genet. 164:293-301. (Pubitemid 20000961)
    • (1989) Current Genetics , vol.16 , Issue.4 , pp. 293-301
    • Shimada, H.1    Sugiura, M.2
  • 34
    • 1842335092 scopus 로고
    • Structural evolution and flipflop recombination of chloroplast DNA in the fern genus Osmunda
    • Stein DB, Palmer JD, Thompson WF. 1986. Structural evolution and flipflop recombination of chloroplast DNA in the fern genus Osmunda. Curr Genet. 10:835-841.
    • (1986) Curr Genet. , vol.10 , pp. 835-841
    • Stein, D.B.1    Palmer, J.D.2    Thompson, W.F.3
  • 35
    • 0027158760 scopus 로고
    • A rapid CTAB DNA isolation technique useful for RAPD fingerprinting and other PCR applications
    • Stewart CN Jr, Via LE. 1993. A rapid CTAB DNA isolation technique useful for RAPD fingerprinting and other PCR applications. BioTechniques 14:748-751.
    • (1993) BioTechniques , vol.14 , pp. 748-751
    • Stewart Jr., C.N.1    Via, L.E.2
  • 36
    • 0024025601 scopus 로고
    • Chloroplast genomes of two conifers lack a large inverted repeat and are extensively rearranged
    • Strauss SH, Palmer JD, Howe GT, Doerksen AH. 1988. Chloroplast genomes of two conifers lack a large inverted repeat and are extensively rearranged. Proc Natl Acad Sci U S A. 85:3898-3902.
    • (1988) Proc Natl Acad Sci U S A , vol.85 , pp. 3898-3902
    • Strauss, S.H.1    Palmer, J.D.2    Howe, G.T.3    Doerksen, A.H.4
  • 37
    • 0020653446 scopus 로고
    • The complete nucleotide sequence of a 16s ribosomal RNA gene from a blue-green alga, Anacystis nidulans
    • Tomioka N, Sugiura M. 1983. The complete nucleotide sequence of a 16s ribosomal RNA gene from a blue-green alga, Anacystis nidulans. Mol Gen Genet. 191:46-50.
    • (1983) Mol Gen Genet. , vol.191 , pp. 46-50
    • Tomioka, N.1    Sugiura, M.2
  • 38
    • 0024722956 scopus 로고
    • Dispersed repetitive sequences in the chloroplast genome of Douglas-fir
    • Tsai CH, Strauss SH. 1989. Dispersed repetitive sequences in the chloroplast genome of Douglas-fir. Curr Genet. 16:211-218.
    • (1989) Curr Genet. , vol.16 , pp. 211-218
    • Tsai, C.H.1    Strauss, S.H.2
  • 39
    • 0026506180 scopus 로고
    • Chloroplast DNA of black pine retains a residual inverted repeat lacking rRNA genes: Nucleotide sequences of trnQ, trnK, psbA, trnI and trnH and the absence of rps16
    • Tsudzuki J, et al. 1992. Chloroplast DNA of black pine retains a residual inverted repeat lacking rRNA genes: nucleotide sequences of trnQ, trnK, psbA, trnI and trnH and the absence of rps16. Mol Gen Genet. 232:206-214.
    • (1992) Mol Gen Genet. , vol.232 , pp. 206-214
    • Tsudzuki, J.1
  • 40
    • 0033866121 scopus 로고    scopus 로고
    • Chloroplast DNA inversion polymorphism in populations of Abies and Tsuga
    • Tsumura Y, Suyama Y, Yoshimura K. 2000. Chloroplast DNA inversion polymorphism in populations of Abies and Tsuga. Mol Biol Evol. 17:1302-1312.
    • (2000) Mol Biol Evol , vol.17 , pp. 1302-1312
    • Tsumura, Y.1    Suyama, Y.2    Yoshimura, K.3
  • 41
    • 0033621040 scopus 로고    scopus 로고
    • The complete chloroplast DNA sequence of the green alga Nephroselmis olivacea: Insights into the architecture of ancestral chloroplast genomes
    • DOI 10.1073/pnas.96.18.10248
    • Turmel M, Otis C, Lemieux C. 1999. The complete chloroplast DNA sequence of the green alga Nephroselmis olivacea: insights into the architecture of ancestral chloroplast genomes. Proc Natl Acad Sci U S A. 96:10248-10253. (Pubitemid 29422544)
    • (1999) Proceedings of the National Academy of Sciences of the United States of America , vol.96 , Issue.18 , pp. 10248-10253
    • Turmel, M.1
  • 43
    • 0034022645 scopus 로고    scopus 로고
    • Phylogeny and divergence times in pinaceae: Evidence from three genomes
    • Wang XQ, Tank DC, Sang T. 2000. Phylogeny and divergence times in Pinaceae: evidence from three genomes. Mol Biol Evol. 17:773-781. (Pubitemid 30252265)
    • (2000) Molecular Biology and Evolution , vol.17 , Issue.5 , pp. 773-781
    • Wang, X.-Q.1    Tank, D.C.2    Sang, T.3
  • 44
    • 67349273773 scopus 로고    scopus 로고
    • Evolution of reduced and compact chloroplast genomes (cpDNAs) in gnetophytes: Selection toward a lower-cost strategy
    • Wu CS, Lai YT, Lin CP, Wang YN, Chaw SM. 2009. Evolution of reduced and compact chloroplast genomes (cpDNAs) in gnetophytes: selection toward a lower-cost strategy. Mol Phylogenet Evol. 52:115-124.
    • (2009) Mol Phylogenet Evol , vol.52 , pp. 115-124
    • Wu, C.S.1    Lai, Y.T.2    Lin, C.P.3    Wang, Y.N.4    Chaw, S.M.5
  • 45
    • 34548108492 scopus 로고    scopus 로고
    • Chloroplast genome (cpDNA) of Cycas taitungensis and 56 cp protein-coding genes of Gnetum parvifolium: Insights into cpDNA evolution and phylogeny of extant seed plants
    • Wu CS, Wang YN, Liu SM, Chaw SM. 2007. Chloroplast genome (cpDNA) of Cycas taitungensis and 56 cp protein-coding genes of Gnetum parvifolium: insights into cpDNA evolution and phylogeny of extant seed plants. Mol Biol Evol. 24:1366-1379.
    • (2007) Mol Biol Evol , vol.24 , pp. 1366-1379
    • Wu, C.S.1    Wang, Y.N.2    Liu, S.M.3    Chaw, S.M.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.