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Volumn 31, Issue 1, 2004, Pages 50-65

Complete mitochondrial genome DNA sequence for two ophiuroids and a holothuroid: The utility of protein gene sequence and gene maps in the analyses of deep deuterostome phylogeny

Author keywords

[No Author keywords available]

Indexed keywords

ACULEATA; ASTEROIDEA; CUCUMARIA; CUCUMARIA MINIATA; ECHINODERMATA; HOLOTHUROIDEA; OPHIOPHOLIS ACULEATA; OPHIURA; OPHIURA LUTKENI; OPHIUROIDEA; PISASTER; PISASTER OCHRACEUS;

EID: 1642546958     PISSN: 10557903     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.ympev.2003.07.005     Document Type: Article
Times cited : (45)

References (52)
  • 2
    • 0029974748 scopus 로고    scopus 로고
    • Model of amino acid substitution in proteins encoded by mitochondrial DNA
    • Adachi, J., Hasegawa, M., 1996b. Model of amino acid substitution in proteins encoded by mitochondrial DNA. J. Mol. Evol. 42, 459-468.
    • (1996) J. Mol. Evol. , vol.42 , pp. 459-468
    • Adachi, J.1    Hasegawa, M.2
  • 3
    • 0030339735 scopus 로고    scopus 로고
    • Molecular phylogeny of eastern Pacific sea cucumbers (Echinodermata: Holothuroidea) based on mitochondrial DNA sequence
    • Arndt, A., Marquez, C., Lambert, P., Smith, M.J., 1996. Molecular phylogeny of eastern Pacific sea cucumbers (Echinodermata: Holothuroidea) based on mitochondrial DNA sequence. Mol. Phylogenet. Evol. 6, 425-437.
    • (1996) Mol. Phylogenet. Evol. , vol.6 , pp. 425-437
    • Arndt, A.1    Marquez, C.2    Lambert, P.3    Smith, M.J.4
  • 4
    • 0031904632 scopus 로고    scopus 로고
    • Mitochondrial gene rearrangement in the sea cucumber genus, Cucumaria
    • Arndt, A., Smith, M.J., 1998. Mitochondrial gene rearrangement in the sea cucumber genus, Cucumaria. Mol. Biol. Evol. 15, 1009-1016.
    • (1998) Mol. Biol. Evol. , vol.15 , pp. 1009-1016
    • Arndt, A.1    Smith, M.J.2
  • 5
    • 0029069238 scopus 로고
    • Nucleotide sequence and gene organization of the starfish Asterina pectinifera mitochondrial genome
    • Asakawa, S., Himeno, H., Miura, K., Watanabe, K., 1995. Nucleotide sequence and gene organization of the starfish Asterina pectinifera mitochondrial genome. Genetics 140, 1047-1060.
    • (1995) Genetics , vol.140 , pp. 1047-1060
    • Asakawa, S.1    Himeno, H.2    Miura, K.3    Watanabe, K.4
  • 6
    • 0025881012 scopus 로고
    • Strand-specific nucleotide composition bias in echinoderm and vertebrate mitochondrial genomes
    • Asakawa, S., Kumazawa, Y., Araki, T., Himeno, H., Miura, K., Watanabe, K., 1991. Strand-specific nucleotide composition bias in echinoderm and vertebrate mitochondrial genomes. J. Mol. Evol. 32, 511-520.
    • (1991) J. Mol. Evol. , vol.32 , pp. 511-520
    • Asakawa, S.1    Kumazawa, Y.2    Araki, T.3    Himeno, H.4    Miura, K.5    Watanabe, K.6
  • 8
    • 0343340115 scopus 로고    scopus 로고
    • Mitochondrial genomic rearrangements in songbirds
    • Bensch, S., Härlid, A., 2000. Mitochondrial genomic rearrangements in songbirds. Mol. Biol. Evol. 17, 107-113.
    • (2000) Mol. Biol. Evol. , vol.17 , pp. 107-113
    • Bensch, S.1    Härlid, A.2
  • 10
    • 0033561361 scopus 로고    scopus 로고
    • Animal mitochondrial genomes
    • Boore, J.L., 1999. Animal mitochondrial genomes. Nucleic Acids Res. 27, 1767-1780.
    • (1999) Nucleic Acids Res. , vol.27 , pp. 1767-1780
    • Boore, J.L.1
  • 11
    • 0031769998 scopus 로고    scopus 로고
    • Big trees from little genomes: Mitochondrial gene order as a phylogenetic tool
    • Boore, J.L., Brown, W.M., 1998. Big trees from little genomes: mitochondrial gene order as a phylogenetic tool. Curr. Opin. Genet. Dev. 8, 668-674.
    • (1998) Curr. Opin. Genet. Dev. , vol.8 , pp. 668-674
    • Boore, J.L.1    Brown, W.M.2
  • 12
    • 0002135777 scopus 로고
    • The mitochondrial genome of animals
    • Maclntyre, R.J. (Ed.), Plenum Press, New York
    • Brown, W.M., 1985. The mitochondrial genome of animals. In: Maclntyre, R.J. (Ed.), Molecular Evolutionary Genetics. Plenum Press, New York, pp. 95-130.
    • (1985) Molecular Evolutionary Genetics , pp. 95-130
    • Brown, W.M.1
  • 13
    • 0024379859 scopus 로고
    • Simultaneous editing of multiple nucleic acid and protein sequences with ESEE, version 3.2
    • Cabot, E.L., Beckenbach, A.T., 1989. Simultaneous editing of multiple nucleic acid and protein sequences with ESEE, version 3.2. Comput. Appl. Biosci. 5, 233-234.
    • (1989) Comput. Appl. Biosci. , vol.5 , pp. 233-234
    • Cabot, E.L.1    Beckenbach, A.T.2
  • 14
    • 0024962173 scopus 로고
    • The complete nucleotide sequence, gene organization, and genetic code of the mitochondrial genome of Paracentrotus lividus
    • Cantatore, P., Roberti, M., Rainaldi, G., Gadaleta, M.N., Saccone, C., 1989. The complete nucleotide sequence, gene organization, and genetic code of the mitochondrial genome of Paracentrotus lividus. J. Biol. Chem. 264, 10965-10975.
    • (1989) J. Biol. Chem. , vol.264 , pp. 10965-10975
    • Cantatore, P.1    Roberti, M.2    Rainaldi, G.3    Gadaleta, M.N.4    Saccone, C.5
  • 15
    • 0031770677 scopus 로고    scopus 로고
    • The mitochondrial genome of the hemichordate Balanoglossus carnosus and the evolution of deuterostome mitochondria
    • Castresana, J., Feldmaier-Fuchs, G., Yokobori, S., Satoh, N., Pääbo, S., 1998. The mitochondrial genome of the hemichordate Balanoglossus carnosus and the evolution of deuterostome mitochondria. Genetics 150, 1115-1123.
    • (1998) Genetics , vol.150 , pp. 1115-1123
    • Castresana, J.1    Feldmaier-Fuchs, G.2    Yokobori, S.3    Satoh, N.4    Pääbo, S.5
  • 16
    • 0033213874 scopus 로고    scopus 로고
    • Mitogenomics: Digging deeper with complete mitochondrial genomes
    • Curole, J.P., Kocher, T.D., 1999. Mitogenomics: digging deeper with complete mitochondrial genomes. Trends Ecol. Evol. 14, 394-398.
    • (1999) Trends Ecol. Evol. , vol.14 , pp. 394-398
    • Curole, J.P.1    Kocher, T.D.2
  • 17
    • 0030122559 scopus 로고    scopus 로고
    • Complete sequence of the mitochondrial DNA in the sea urchin Arbacia lixula: Conserved features of the echinoid mitochondrial genome
    • De Giorgi, C., Martiradonna, A., Lanave, C., Saccone, C., 1996. Complete sequence of the mitochondrial DNA in the sea urchin Arbacia lixula: conserved features of the echinoid mitochondrial genome. Mol. Phylogenet. Evol. 5, 323-332.
    • (1996) Mol. Phylogenet. Evol. , vol.5 , pp. 323-332
    • De Giorgi, C.1    Martiradonna, A.2    Lanave, C.3    Saccone, C.4
  • 18
    • 0033004743 scopus 로고    scopus 로고
    • Compositional bias may affect both DNA-based and protein-based phylogenetic reconstructions
    • Foster, P.G., Hickey, D.A., 1999. Compositional bias may affect both DNA-based and protein-based phylogenetic reconstructions. J. Mol. Evol. 48, 284-290.
    • (1999) J. Mol. Evol. , vol.48 , pp. 284-290
    • Foster, P.G.1    Hickey, D.A.2
  • 19
    • 0022376704 scopus 로고
    • Dating of the human-ape splitting by a molecular clock of mitochondrial DNA
    • Hasegawa, M., Kishino, H., Yano, T., 1985. Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. J. Mol. Evol. 22, 160-172.
    • (1985) J. Mol. Evol. , vol.22 , pp. 160-172
    • Hasegawa, M.1    Kishino, H.2    Yano, T.3
  • 21
    • 0035049036 scopus 로고    scopus 로고
    • Complete mitochondrial DNA sequence of Conger myriaster (Teleostei: Anguilliformes): Novel gene order for vertebrate mitochondrial genomes and the phylogenetic implications for Anguilliform families
    • Inoue, J.G., Miya, M., Tsukamoto, K., Nishida, M., 2001. Complete mitochondrial DNA sequence of Conger myriaster (Teleostei: Anguilliformes): novel gene order for vertebrate mitochondrial genomes and the phylogenetic implications for Anguilliform families. J. Mol. Evol. 52, 311-320.
    • (2001) J. Mol. Evol. , vol.52 , pp. 311-320
    • Inoue, J.G.1    Miya, M.2    Tsukamoto, K.3    Nishida, M.4
  • 23
    • 0001822670 scopus 로고
    • Phylogenetic implications of genome rearrangement and sequence evolution in echinoderm mitochondrial DNA
    • Paul, C.R.C., Smith, A.B. (Eds.), Oxford University Press, Oxford
    • Jacobs, H.T., Balfe, P., Cohen, B.L., Farquharson, A., Comito, L., 1988a. Phylogenetic implications of genome rearrangement and sequence evolution in echinoderm mitochondrial DNA. In: Paul, C.R.C., Smith, A.B. (Eds.), Echinoderm Phylogeny and Evolutionary Biology. Oxford University Press, Oxford, pp. 121-137.
    • (1988) Echinoderm Phylogeny and Evolutionary Biology , pp. 121-137
    • Jacobs, H.T.1    Balfe, P.2    Cohen, B.L.3    Farquharson, A.4    Comito, L.5
  • 24
    • 0024292930 scopus 로고
    • Nucleotide sequence and gene organization of sea urchin mitochondrial DNA
    • Jacobs, H.T., Elliott, D.J., Math, V.B., Farquharson, A., 1988b. Nucleotide sequence and gene organization of sea urchin mitochondrial DNA. J. Mol. Biol. 202, 185-217.
    • (1988) J. Mol. Biol. , vol.202 , pp. 185-217
    • Jacobs, H.T.1    Elliott, D.J.2    Math, V.B.3    Farquharson, A.4
  • 25
    • 0029000323 scopus 로고
    • Evidence from analyses of intergenic regions for strand-specific directional mutation pressure in metazoan mitochondrial DNA
    • Jermiin, L.S., Graur, D., Crozier, R.H., 1995. Evidence from analyses of intergenic regions for strand-specific directional mutation pressure in metazoan mitochondrial DNA. Mol. Biol. Evol. 12, 558-563.
    • (1995) Mol. Biol. Evol. , vol.12 , pp. 558-563
    • Jermiin, L.S.1    Graur, D.2    Crozier, R.H.3
  • 26
    • 0019296687 scopus 로고
    • A simple method for estimating evolutionary rates of substitutions through comparative studies of nucleotide sequences
    • Kimura, M., 1980. A simple method for estimating evolutionary rates of substitutions through comparative studies of nucleotide sequences. J. Mol. Evol. 16, 111-120.
    • (1980) J. Mol. Evol. , vol.16 , pp. 111-120
    • Kimura, M.1
  • 27
    • 0024307824 scopus 로고
    • Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data, and the branching order in Hominoidea
    • Kishino, H., Hasegawa, M., 1989. Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data, and the branching order in Hominoidea. J. Mol. Evol. 29, 170-179.
    • (1989) J. Mol. Evol. , vol.29 , pp. 170-179
    • Kishino, H.1    Hasegawa, M.2
  • 29
    • 0030746467 scopus 로고    scopus 로고
    • The interrelationships of the echinoderm classes: Morphological and molecular evidence
    • Littlewood, D.T.J., Smith, A.B., Clough, K.A., Emson, R.H., 1997. The interrelationships of the echinoderm classes: morphological and molecular evidence. Biol. J. Linn. Soc. Lond. 61, 409-438.
    • (1997) Biol. J. Linn. Soc. Lond. , vol.61 , pp. 409-438
    • Littlewood, D.T.J.1    Smith, A.B.2    Clough, K.A.3    Emson, R.H.4
  • 30
    • 0028361182 scopus 로고
    • Recovering evolutionary trees under a more realistic model of sequence evolution
    • Lockhart, P.J., Steel, M.A., Hendy, M.D., Penny, D., 1994. Recovering evolutionary trees under a more realistic model of sequence evolution. Mol. Biol. Evol. 11, 605-612.
    • (1994) Mol. Biol. Evol. , vol.11 , pp. 605-612
    • Lockhart, P.J.1    Steel, M.A.2    Hendy, M.D.3    Penny, D.4
  • 31
    • 0031012089 scopus 로고    scopus 로고
    • Two novel gene orders and the role of light-strand replication in rearrangement of the vertebrate mitochondrial genome
    • Macey, J.R., Larson, A., Ananjeva, N.B., Fang, Z., Papenfuss, T.J., 1997. Two novel gene orders and the role of light-strand replication in rearrangement of the vertebrate mitochondrial genome. Mol. Biol. Evol. 14, 91-104.
    • (1997) Mol. Biol. Evol. , vol.14 , pp. 91-104
    • Macey, J.R.1    Larson, A.2    Ananjeva, N.B.3    Fang, Z.4    Papenfuss, T.J.5
  • 32
    • 0025982062 scopus 로고
    • Construction of T-vectors, a rapid and general system for direct cloning of unmodified PCR products
    • Marchuk, D., Drumm, M., Saulino, A., Collins, F.S., 1990. Construction of T-vectors, a rapid and general system for direct cloning of unmodified PCR products. Nucleic Acids Res. 19, 1154.
    • (1990) Nucleic Acids Res. , vol.19 , pp. 1154
    • Marchuk, D.1    Drumm, M.2    Saulino, A.3    Collins, F.S.4
  • 33
    • 0032169857 scopus 로고    scopus 로고
    • Multiple independent origins of mitochondrial gene order in birds
    • Mindell, D.P., Sorenson, M.D., Dimcheff, D.E., 1998. Multiple independent origins of mitochondrial gene order in birds. Proc. Natl. Acad. Sci. USA 95, 10693-10697.
    • (1998) Proc. Natl. Acad. Sci. USA , vol.95 , pp. 10693-10697
    • Mindell, D.P.1    Sorenson, M.D.2    Dimcheff, D.E.3
  • 34
    • 0031773680 scopus 로고    scopus 로고
    • MODELTEST: Testing the model of DNA substitution
    • Posada, D., Crandall, K.A., 1998. MODELTEST: testing the model of DNA substitution. Bioinformatics 14, 817-818.
    • (1998) Bioinformatics , vol.14 , pp. 817-818
    • Posada, D.1    Crandall, K.A.2
  • 35
    • 0032860013 scopus 로고    scopus 로고
    • Evolutionary genomics in Metazoa: The mitochondrial DNA as a model system
    • Saccone, C., De Giorgi, C., Gissi, C., Pesole, G., Reyes, A., 1999. Evolutionary genomics in Metazoa: the mitochondrial DNA as a model system. Gene 238, 195-209.
    • (1999) Gene , vol.238 , pp. 195-209
    • Saccone, C.1    De Giorgi, C.2    Gissi, C.3    Pesole, G.4    Reyes, A.5
  • 36
    • 0025317141 scopus 로고
    • Influence of base composition on quantitative estimates of gene evolution
    • Saccone, C., Lanave, C., Pesole, G., Preparata, G., 1990. Influence of base composition on quantitative estimates of gene evolution. Methods Enzymol. 183, 570-583.
    • (1990) Methods Enzymol. , vol.183 , pp. 570-583
    • Saccone, C.1    Lanave, C.2    Pesole, G.3    Preparata, G.4
  • 38
    • 0035148476 scopus 로고    scopus 로고
    • A novel mitochondrial gene order in the crinoid echinoderm Florometra serratissima
    • Scouras, A., Smith, M.J., 2001. A novel mitochondrial gene order in the crinoid echinoderm Florometra serratissima. Mol. Biol. Evol. 18, 61-73.
    • (2001) Mol. Biol. Evol. , vol.18 , pp. 61-73
    • Scouras, A.1    Smith, M.J.2
  • 39
    • 0033745103 scopus 로고    scopus 로고
    • Nucleotide bias causes a genomewide bias in the amino acid composition of proteins
    • Singer, G.A.C., Hickey, D.A., 2000. Nucleotide bias causes a genomewide bias in the amino acid composition of proteins. Mol. Biol. Evol. 17, 1581-1588.
    • (2000) Mol. Biol. Evol. , vol.17 , pp. 1581-1588
    • Singer, G.A.C.1    Hickey, D.A.2
  • 40
    • 21844488409 scopus 로고
    • Ophiuroid phylogeny and higher taxonomy: Morphological, molecular and palaeontological perspectives
    • Smith, A.B., Paterson, G.L.J., Lafay, B., 1995. Ophiuroid phylogeny and higher taxonomy: morphological, molecular and palaeontological perspectives. Zool. J. Linn. Soc. 114, 213-243.
    • (1995) Zool. J. Linn. Soc. , vol.114 , pp. 213-243
    • Smith, A.B.1    Paterson, G.L.J.2    Lafay, B.3
  • 41
    • 0027301017 scopus 로고
    • The phylogeny of echinoderm classes based on mitochondrial gene arrangements
    • Smith, M.J., Arndt, A., Gorski, S., Fajber, E., 1993. The phylogeny of echinoderm classes based on mitochondrial gene arrangements. J. Mol. Evol. 36, 545-554.
    • (1993) J. Mol. Evol. , vol.36 , pp. 545-554
    • Smith, M.J.1    Arndt, A.2    Gorski, S.3    Fajber, E.4
  • 42
    • 0024969998 scopus 로고
    • Gene arrangement in sea star mitochondrial DNA demonstrates a major inversion event during echinoderm evolution
    • Smith, M.J., Banfield, D.K., Doteval, K., Gorski, S., Kowbel, D.J., 1989. Gene arrangement in sea star mitochondrial DNA demonstrates a major inversion event during echinoderm evolution. Gene 76, 181-185.
    • (1989) Gene , vol.76 , pp. 181-185
    • Smith, M.J.1    Banfield, D.K.2    Doteval, K.3    Gorski, S.4    Kowbel, D.J.5
  • 43
    • 0025043039 scopus 로고
    • Nucleotide sequence of nine protein-coding genes and 22 tRNAs in the mitochondrial DNA of the sea star Pisaster ochraceus
    • Smith, M.J., Banfield, D.K., Doteval, K., Gorski, S., Kowbel, D.J., 1990. Nucleotide sequence of nine protein-coding genes and 22 tRNAs in the mitochondrial DNA of the sea star Pisaster ochraceus. J. Mol. Evol. 31, 195-204.
    • (1990) J. Mol. Evol. , vol.31 , pp. 195-204
    • Smith, M.J.1    Banfield, D.K.2    Doteval, K.3    Gorski, S.4    Kowbel, D.J.5
  • 45
    • 0032125592 scopus 로고    scopus 로고
    • Complete sequence of the amphioxus (Branchiostoma lanceolatum) mitochondrial genome: Relations to vertebrates
    • Spruyt, N., Delarbre, C. Gachelin, G., Laudet, V., 1998. Complete sequence of the amphioxus (Branchiostoma lanceolatum) mitochondrial genome: relations to vertebrates. Nucleic Acids Res. 26, 3279-3285.
    • (1998) Nucleic Acids Res. , vol.26 , pp. 3279-3285
    • Spruyt, N.1    Delarbre, C.2    Gachelin, G.3    Laudet, V.4
  • 46
    • 0028491474 scopus 로고
    • Structural compensation in atypical mitochondrial tRNAs
    • Steinberg, S., Cedergren, R., 1994. Structural compensation in atypical mitochondrial tRNAs. Struct. Biol. 1, 507-510.
    • (1994) Struct. Biol. , vol.1 , pp. 507-510
    • Steinberg, S.1    Cedergren, R.2
  • 49
    • 0001336205 scopus 로고    scopus 로고
    • Phylogenetic inference
    • Hillis, D.M., Moritz, C., Mable, B.K. (Eds.), Sinauer Associates, Sunderland, MA
    • Swofford, D.L., Olsen, G.J., Waddell, P.J., Hillis, D.M., 1996. Phylogenetic inference. In: Hillis, D.M., Moritz, C., Mable, B.K. (Eds.), Molecular Systematics, second ed. Sinauer Associates, Sunderland, MA, pp. 407-514.
    • (1996) Molecular Systematics, Second Ed. , pp. 407-514
    • Swofford, D.L.1    Olsen, G.J.2    Waddell, P.J.3    Hillis, D.M.4
  • 50
    • 0032906462 scopus 로고    scopus 로고
    • Correct and incorrect vertebrate phylogenies obtained by the entire mitochondrial DNA sequences
    • Takezaki, N., Gojobori, T., 1999. Correct and incorrect vertebrate phylogenies obtained by the entire mitochondrial DNA sequences. Mol. Biol. Evol. 16, 590-601.
    • (1999) Mol. Biol. Evol. , vol.16 , pp. 590-601
    • Takezaki, N.1    Gojobori, T.2
  • 51
    • 0029100727 scopus 로고
    • Phylogenetic test of the molecular clock and linearized trees
    • Takezaki, N., Rzhetsky, A., Nei, M., 1995. Phylogenetic test of the molecular clock and linearized trees. Mol. Biol. Evol. 12, 823-833.
    • (1995) Mol. Biol. Evol. , vol.12 , pp. 823-833
    • Takezaki, N.1    Rzhetsky, A.2    Nei, M.3
  • 52
    • 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., 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


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