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Volumn 190, Issue , 2012, Pages 62-73

The comparative chloroplast genomic analysis of photosynthetic orchids and developing DNA markers to distinguish Phalaenopsis orchids

Author keywords

Chloroplast DNA marker; Comparative chloroplast genome; Moth orchids; Phalaenopsis

Indexed keywords

CHLOROPLAST DNA; NUCLEOTIDE;

EID: 84860137960     PISSN: 01689452     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.plantsci.2012.04.001     Document Type: Article
Times cited : (83)

References (44)
  • 7
    • 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. Complete nucleotide sequence of the Cryptomeria japonica D. Don. chloroplast genome and comparative chloroplast genomics: diversified genomic structure of coniferous species. BMC Plant Biology 2008, 8:70.
    • (2008) BMC Plant Biology , vol.8 , pp. 70
    • Hirao, T.1    Watanabe, A.2    Kurita, M.3    Kondo, T.4    Takata, K.5
  • 9
    • 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., Ishibashi T., Sakamoto M., Mori M., Kondo C., Honji Y., Sun C.R., Meng B.Y. 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. Molecular Genetics and Genomics 1989, 217:185-194.
    • (1989) Molecular Genetics and Genomics , vol.217 , pp. 185-194
    • Hiratsuka, J.1    Shimada, H.2    Whittier, R.3    Ishibashi, T.4    Sakamoto, M.5    Mori, M.6    Kondo, C.7    Honji, Y.8    Sun, C.R.9    Meng, B.Y.10
  • 10
    • 77951914538 scopus 로고    scopus 로고
    • The chloroplast genome sequence of mungbean (Vigna radiata) determined by high-throughput pyrosequencing: structural organization and phylogenetic relationships
    • Tangphatsornruang S., Sangsrakru D., Chanprasert J., Uthaipaisanwong P., Yoocha P., Jomchai T.N., Tragoonrung S. The chloroplast genome sequence of mungbean (Vigna radiata) determined by high-throughput pyrosequencing: structural organization and phylogenetic relationships. DNA Research 2010, 17:11-22.
    • (2010) DNA Research , vol.17 , pp. 11-22
    • Tangphatsornruang, S.1    Sangsrakru, D.2    Chanprasert, J.3    Uthaipaisanwong, P.4    Yoocha, P.5    Jomchai, T.N.6    Tragoonrung, S.7
  • 11
    • 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., Kadowaki K. Complete nucleotide sequence of the sugarcane (Saccharum officinarum) chloroplast genome: a comparative analysis of four monocot chloroplast genomes. DNA Research 2004, 11:93-99.
    • (2004) DNA Research , vol.11 , pp. 93-99
    • Asano, T.1    Tsudzuki, T.2    Takahashi, S.3    Shimada, H.4    Kadowaki, K.5
  • 12
    • 11144284040 scopus 로고    scopus 로고
    • Complete chloroplast genome sequences from Korean ginseng (Panax schinseng Nees) and comparative analysis of sequence evolution among 17 vascular plants
    • Kim K.J., Lee H.L. Complete chloroplast genome sequences from Korean ginseng (Panax schinseng Nees) and comparative analysis of sequence evolution among 17 vascular plants. DNA Research 2004, 11:247-261.
    • (2004) DNA Research , vol.11 , pp. 247-261
    • Kim, K.J.1    Lee, H.L.2
  • 14
    • 77950794398 scopus 로고    scopus 로고
    • Complete chloroplast genome of Oncidium Gower Ramsey and evaluation of molecular markers for identification and breeding in Oncidiinae
    • Wu F.H., Chan M.T., Liao D.C., Hsu C.T., Lee Y.W., Daniell H., Duvall M.R., Lin C.S. Complete chloroplast genome of Oncidium Gower Ramsey and evaluation of molecular markers for identification and breeding in Oncidiinae. BMC Plant Biology 2010, 10:68.
    • (2010) BMC Plant Biology , vol.10 , pp. 68
    • Wu, F.H.1    Chan, M.T.2    Liao, D.C.3    Hsu, C.T.4    Lee, Y.W.5    Daniell, H.6    Duvall, M.R.7    Lin, C.S.8
  • 15
    • 2442517979 scopus 로고    scopus 로고
    • Dating the monocot-dicot divergence and the origin of core eudicots using whole chloroplast genomes
    • Chaw S.M., Chang C.C., Chen H.L., Li W.H. Dating the monocot-dicot divergence and the origin of core eudicots using whole chloroplast genomes. Journal of Molecular Evolution 2004, 58:424-441.
    • (2004) Journal of Molecular Evolution , vol.58 , pp. 424-441
    • Chaw, S.M.1    Chang, C.C.2    Chen, H.L.3    Li, W.H.4
  • 16
    • 33645576010 scopus 로고    scopus 로고
    • The chloroplast genome of Nicotiana sylvestris and Nicotiana tomentosiformis: complete sequencing confirms that the Nicotiana sylvestris progenitor is the maternal genome donor of Nicotiana tabacum
    • Yukawa M., Tsudzuki T., Sugiura M. The chloroplast genome of Nicotiana sylvestris and Nicotiana tomentosiformis: complete sequencing confirms that the Nicotiana sylvestris progenitor is the maternal genome donor of Nicotiana tabacum. Molecular Genetics and Genomics 2006, 275:367-373.
    • (2006) Molecular Genetics and Genomics , vol.275 , pp. 367-373
    • Yukawa, M.1    Tsudzuki, T.2    Sugiura, M.3
  • 17
    • 0033955649 scopus 로고    scopus 로고
    • Examining rates and patterns of nucleotide substitution in plants
    • Muse V.S. Examining rates and patterns of nucleotide substitution in plants. Plant Molecular Biology 2000, 42:25-43.
    • (2000) Plant Molecular Biology , vol.42 , pp. 25-43
    • Muse, V.S.1
  • 18
    • 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., Tsunewaki K. Whole chloroplast genome comparison of rice, maize, and wheat: implications for chloroplast gene diversification and phylogeny of cereals. Molecular Biology and Evolution 2002, 19:2084-2091.
    • (2002) Molecular Biology and Evolution , vol.19 , pp. 2084-2091
    • Matsuoka, Y.1    Yamazaki, Y.2    Ogihara, Y.3    Tsunewaki, K.4
  • 19
    • 18144368560 scopus 로고    scopus 로고
    • Chloroplast genome phylogenetics: why we need independent approaches to plant molecular evolution
    • Martin W., Deusch O., Stawski N., Grunheit N., Goremykin V. Chloroplast genome phylogenetics: why we need independent approaches to plant molecular evolution. Trends in Plant Science 2005, 10:203-209.
    • (2005) Trends in Plant Science , vol.10 , pp. 203-209
    • Martin, W.1    Deusch, O.2    Stawski, N.3    Grunheit, N.4    Goremykin, V.5
  • 20
    • 33845684713 scopus 로고    scopus 로고
    • The evolutionary history of the common chloroplast genome of Arabidopsis thaliana and A. suecica
    • Jakobsson M., Sall T., Lind-Hallden C., Hallden C. The evolutionary history of the common chloroplast genome of Arabidopsis thaliana and A. suecica. Journal of Evolutionary Biology 2007, 20:104-121.
    • (2007) Journal of Evolutionary Biology , vol.20 , pp. 104-121
    • Jakobsson, M.1    Sall, T.2    Lind-Hallden, C.3    Hallden, C.4
  • 21
    • 1542368230 scopus 로고    scopus 로고
    • Plastid transformation in higher plants
    • Maliga P. Plastid transformation in higher plants. Annual Review of Plant Biology 2004, 55:289-313.
    • (2004) Annual Review of Plant Biology , vol.55 , pp. 289-313
    • Maliga, P.1
  • 22
    • 33746761042 scopus 로고    scopus 로고
    • Complete chloroplast genome sequences of Solanum bulbocastanum, Solanum lycopersicum and comparative analyses with other Solanaceae genomes, complete chloroplast genome sequences of Solanum bulbocastanum, Solanum lycopersicum and comparative analyses with other Solanaceae genomes
    • Daniell H., Lee S.B., Grevich J., Saski C., Quesada-Vargas T., Guda C., Tomkins J., Jansen R.K. Complete chloroplast genome sequences of Solanum bulbocastanum, Solanum lycopersicum and comparative analyses with other Solanaceae genomes, complete chloroplast genome sequences of Solanum bulbocastanum, Solanum lycopersicum and comparative analyses with other Solanaceae genomes. Theoretical and Applied Genetics 2006, 112:1503-1518.
    • (2006) Theoretical and Applied Genetics , vol.112 , pp. 1503-1518
    • Daniell, H.1    Lee, S.B.2    Grevich, J.3    Saski, C.4    Quesada-Vargas, T.5    Guda, C.6    Tomkins, J.7    Jansen, R.K.8
  • 23
    • 0001507529 scopus 로고
    • The size of the Orchidaceae and the systematic distribution of epiphytic orchids
    • Atwood J.T. The size of the Orchidaceae and the systematic distribution of epiphytic orchids. Selbyana 1986, 9:171-186.
    • (1986) Selbyana , vol.9 , pp. 171-186
    • Atwood, J.T.1
  • 24
    • 30744447444 scopus 로고    scopus 로고
    • The chloroplast genome of Phalaenopsis aphrodite (Orchidaceae): comparative analysis of evolutionary rate with that of grasses and its phylogenetic implications
    • Chang C.C., Lin H.C., Lin I.P., Chow T.Y., Chen H.H., Chen W.H., Cheng C.H., Lin C.Y., Liu S.M., Chang C.C., et al. The chloroplast genome of Phalaenopsis aphrodite (Orchidaceae): comparative analysis of evolutionary rate with that of grasses and its phylogenetic implications. Molecular Biology and Evolution 2006, 23:279-291.
    • (2006) Molecular Biology and Evolution , vol.23 , pp. 279-291
    • Chang, C.C.1    Lin, H.C.2    Lin, I.P.3    Chow, T.Y.4    Chen, H.H.5    Chen, W.H.6    Cheng, C.H.7    Lin, C.Y.8    Liu, S.M.9    Chang, C.C.10
  • 26
    • 10244240599 scopus 로고    scopus 로고
    • Automatic annotation of organellar genomes with DOGMA
    • Wyman S.K., Jansen R.K., Boore J.L. Automatic annotation of organellar genomes with DOGMA. Bioinfomatics 2004, 20:3252-3255.
    • (2004) Bioinfomatics , vol.20 , pp. 3252-3255
    • Wyman, S.K.1    Jansen, R.K.2    Boore, J.L.3
  • 27
    • 0002511466 scopus 로고    scopus 로고
    • GeneDoc: analysis and visualization of genetic variation
    • Nicholas K.B., Nicholas H.B., Deerfield D.W. GeneDoc: analysis and visualization of genetic variation. EMBNEW News 1997, 4:14.
    • (1997) EMBNEW News , vol.4 , pp. 14
    • Nicholas, K.B.1    Nicholas, H.B.2    Deerfield, D.W.3
  • 28
    • 0019296687 scopus 로고
    • A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences
    • Kimura M. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. Journal of Molecular Evolution 1980, 16:111-120.
    • (1980) Journal of Molecular Evolution , vol.16 , pp. 111-120
    • Kimura, M.1
  • 29
    • 34547781750 scopus 로고    scopus 로고
    • MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0
    • Tamura K., Dudley J., Nei M., Kumar S. MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Molecular Biology and Evolution 2007, 24:1596-1599.
    • (2007) Molecular Biology and Evolution , vol.24 , pp. 1596-1599
    • Tamura, K.1    Dudley, J.2    Nei, M.3    Kumar, S.4
  • 30
    • 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., Kossel H. Complete sequence of the maize chloroplast genome: gene content, hotspots of divergence and fine tuning of genetic information by transcript editing. Journal of Molecular Biology 1995, 251:614-628.
    • (1995) Journal of Molecular Biology , vol.251 , pp. 614-628
    • Maier, R.M.1    Neckermann, K.2    Igloi, G.L.3    Kossel, H.4
  • 31
    • 43549096694 scopus 로고    scopus 로고
    • Dynamics and evolution of the inverted repeat-large single copy junctions in the chloroplast genomes of monocots
    • Wang R.J, Cheng C.L., Chang C.C., Wu C.L., Su T.M., Chaw S.M. Dynamics and evolution of the inverted repeat-large single copy junctions in the chloroplast genomes of monocots. BMC Evolutionary Biology 2008, 8:36.
    • (2008) BMC Evolutionary Biology , vol.8 , pp. 36
    • Wang, R.J.1    Cheng, C.L.2    Chang, C.C.3    Wu, C.L.4    Su, T.M.5    Chaw, S.M.6
  • 32
    • 33847215877 scopus 로고    scopus 로고
    • Identification of RNA editing sites in chloroplast transcripts of Phalaenopsis aphrodite and comparative analysis with those of other seed plants
    • Zeng W.H., Liao S.C., Chang C.C. Identification of RNA editing sites in chloroplast transcripts of Phalaenopsis aphrodite and comparative analysis with those of other seed plants. Plant and Cell Physiology 2007, 48:362-368.
    • (2007) Plant and Cell Physiology , vol.48 , pp. 362-368
    • Zeng, W.H.1    Liao, S.C.2    Chang, C.C.3
  • 33
    • 0029360724 scopus 로고
    • Hypervariable microsatellites provide a general source of polymorphic DNA markers for the chloroplast genome
    • Tingey S.V., Rafalski J.A. Hypervariable microsatellites provide a general source of polymorphic DNA markers for the chloroplast genome. Current Biology 1995, 5:1023-1029.
    • (1995) Current Biology , vol.5 , pp. 1023-1029
    • Tingey, S.V.1    Rafalski, J.A.2
  • 34
    • 12744272172 scopus 로고    scopus 로고
    • Chloroplast DNA inheritance in the orchid Anacamptis palustris using single-seed polymerase chain reaction
    • Cafasso D., Widmer A., Cozzolino S. Chloroplast DNA inheritance in the orchid Anacamptis palustris using single-seed polymerase chain reaction. The Journal of Heredity 2005, 96:66-70.
    • (2005) The Journal of Heredity , vol.96 , pp. 66-70
    • Cafasso, D.1    Widmer, A.2    Cozzolino, S.3
  • 35
    • 66449105849 scopus 로고    scopus 로고
    • CURE-chloroplast: a chloroplast C-to-U RNA editing predictor for seed plants
    • Du P., Jia L., Li Y. CURE-chloroplast: a chloroplast C-to-U RNA editing predictor for seed plants. BMC Bioinformatics 2009, 10:135.
    • (2009) BMC Bioinformatics , vol.10 , pp. 135
    • Du, P.1    Jia, L.2    Li, Y.3
  • 36
    • 67349254201 scopus 로고    scopus 로고
    • Loss of all plastid ndh genes in Gnetales and conifers: extent and evolutionary significance for the seed plant phylogeny
    • Braukmann T.W., Kuzmina M., Stefanovic S. Loss of all plastid ndh genes in Gnetales and conifers: extent and evolutionary significance for the seed plant phylogeny. Current Genetics 2009, 55:323-337.
    • (2009) Current Genetics , vol.55 , pp. 323-337
    • Braukmann, T.W.1    Kuzmina, M.2    Stefanovic, S.3
  • 38
    • 0032481317 scopus 로고    scopus 로고
    • Identification of a functional respiratory complex in chloroplasts through analysis of tobacco mutants containing disrupted plastid ndh genes
    • Burrows P.A., Sazanov L.A., Svab Z., Maliga P., Nixon P.J. Identification of a functional respiratory complex in chloroplasts through analysis of tobacco mutants containing disrupted plastid ndh genes. EMBO Journal 1998, 17:868-876.
    • (1998) EMBO Journal , vol.17 , pp. 868-876
    • Burrows, P.A.1    Sazanov, L.A.2    Svab, Z.3    Maliga, P.4    Nixon, P.J.5
  • 39
    • 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.I., Njenga P.K., Tsudzuki T., Kadowaki K.I. The complete nucleotide sequence of wild rice (Oryza nivara) chloroplast genome: first genome wide comparative sequence analysis of wild and cultivated rice. Gene 2004, 340:133-139.
    • (2004) Gene , vol.340 , pp. 133-139
    • Masood, M.S.1    Nishikawa, T.2    Fukuoka, S.I.3    Njenga, P.K.4    Tsudzuki, T.5    Kadowaki, K.I.6
  • 40
    • 16544362025 scopus 로고    scopus 로고
    • Chloroplast genetic engineering to improve agronomic traits
    • Daniell H., Ruiz O.N., Dhingra A. Chloroplast genetic engineering to improve agronomic traits. Methods in Molecular Biology 2005, 286:111-138.
    • (2005) Methods in Molecular Biology , vol.286 , pp. 111-138
    • Daniell, H.1    Ruiz, O.N.2    Dhingra, A.3
  • 42
    • 0033866085 scopus 로고    scopus 로고
    • Sense from nonsense: how the genetic information of chloroplasts is altered by RNA editing
    • Bock R. Sense from nonsense: how the genetic information of chloroplasts is altered by RNA editing. Biochimie 2000, 82:549-557.
    • (2000) Biochimie , vol.82 , pp. 549-557
    • Bock, R.1
  • 43
    • 0034821617 scopus 로고    scopus 로고
    • Comparative analysis of RNA editing sites in higher plant chloroplasts
    • Tsudzuki T., Wakasugi T., Sugiura M. Comparative analysis of RNA editing sites in higher plant chloroplasts. Journal of Molecular Evolution 2001, 53:327-332.
    • (2001) Journal of Molecular Evolution , vol.53 , pp. 327-332
    • Tsudzuki, T.1    Wakasugi, T.2    Sugiura, M.3
  • 44
    • 33746450368 scopus 로고    scopus 로고
    • Sequence of the tomato chloroplast DNA and evolutionary comparison of solanaceous plastid genomes
    • Kahlau S., Aspinall S., Gray J.C., Bock R. Sequence of the tomato chloroplast DNA and evolutionary comparison of solanaceous plastid genomes. Journal of Molecular Evolution 2006, 63:194-207.
    • (2006) Journal of Molecular Evolution , vol.63 , pp. 194-207
    • Kahlau, S.1    Aspinall, S.2    Gray, J.C.3    Bock, R.4


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