메뉴 건너뛰기




Volumn 32, Issue 4, 2013, Pages 59-65

The complete mitochondrial genome of the grey bamboo shark (Chiloscyllium griseum) (Orectolobiformes: Hemiscylliidae): Genomic characterization and phylogenetic application

Author keywords

carpet shark; Chiloscyllium griseum; Chondrichthyes; Galeomorphii; mitochondrial genome; phylogeny

Indexed keywords


EID: 84880534309     PISSN: 0253505X     EISSN: None     Source Type: Journal    
DOI: 10.1007/s13131-013-0298-0     Document Type: Article
Times cited : (39)

References (41)
  • 2
    • 0033561361 scopus 로고    scopus 로고
    • Animal mitochondrial genomes
    • DOI 10.1093/nar/27.8.1767
    • Boore J L. 1999. Animal mitochondrial genomes. Nucleic Acids Res, 27: 1767-1780 (Pubitemid 29209617)
    • (1999) Nucleic Acids Research , vol.27 , Issue.8 , pp. 1767-1780
    • Boore, J.L.1
  • 3
    • 19944400426 scopus 로고    scopus 로고
    • Sequencing and comparing whole mitochondrial genomes of animals
    • DOI 10.1016/S0076-6879(05)95019-2, PII S0076687905950192, Molecular Evolution: Producing the Biochemical Data
    • Boore J L, Macey J R, Medina M. 2005. Sequencing and comparing whole mitochondrial genomes of animals. Methods Enzymol, 395: 311-348 (Pubitemid 40754376)
    • (2005) Methods in Enzymology , vol.395 , pp. 311-348
    • Boore, J.L.1    Macey, J.R.2    Medina, M.3
  • 4
    • 0036566781 scopus 로고    scopus 로고
    • Release of replication termination controls mitochondrial DNA copy number after depletion with 2′,3′-dideoxycytidine
    • Brown T A, Clayton D A. 2002. Release of replication termination controls mitochondrial DNA copy number after depletion with 2′, 3′-dideoxycytidine. Nucleic Acids Res, 30: 2004-2010 (Pubitemid 34537597)
    • (2002) Nucleic Acids Research , vol.30 , Issue.9 , pp. 2004-2010
    • Brown, T.A.1    Clayton, D.A.2
  • 5
    • 0031741694 scopus 로고    scopus 로고
    • The complete mitochondrial DNA sequence of the shark Mustelus manazo: Evaluating rooting contradictions to living bony vertebrates
    • Cao Y, Waddell P J, Okada N, et al. 1998. The complete mitochondrial DNA sequence of the shark Mustelus manazo: Evaluating rooting contradictions to living bony vertebrates. Mol Biol Evol, 15: 1637-1646 (Pubitemid 28550988)
    • (1998) Molecular Biology and Evolution , vol.15 , Issue.12 , pp. 1637-1646
    • Cao, Y.1    Waddell, P.J.2    Okada, N.3    Hasegawa, M.4
  • 6
    • 0034043778 scopus 로고    scopus 로고
    • Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis
    • Castresana J. 2000. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol, 17: 540-552 (Pubitemid 30210700)
    • (2000) Molecular Biology and Evolution , vol.17 , Issue.4 , pp. 540-552
    • Castresana, J.1
  • 7
    • 0019978703 scopus 로고
    • Replication of animal mitochondrial DNA
    • Clayton D A. 1982. Replication of animal mitochondrial DNA. Cell, 28: 693-705 (Pubitemid 12084326)
    • (1982) Cell , vol.28 , Issue.4 , pp. 693-705
    • Clayton, D.A.1
  • 8
    • 0003075061 scopus 로고
    • Interrelationships of living elasmobranchs
    • Compagno L J V. 1973. Interrelationships of living elasmobranchs. Zool J Linn Soc, 53: 15-61
    • (1973) Zool J Linn Soc , vol.53 , pp. 15-61
    • Compagno, L.J.V.1
  • 9
    • 0000313357 scopus 로고
    • FAO Species Catalogue. v 4. Sharks of the world. An annotated and illustrated catalogue of shark species known to date
    • Compagno L J V. 1984. FAO Species Catalogue. v 4. Sharks of the world. An annotated and illustrated catalogue of shark species known to date. Part 1-Hexanchiformes to Lamniformes FAO Fish Synop, 125: 1-249
    • (1984) Part 1-Hexanchiformes to Lamniformes FAO Fish Synop , vol.125 , pp. 1-249
    • Compagno, L.J.V.1
  • 10
    • 1642527654 scopus 로고    scopus 로고
    • Sharks of the world. An annotated and illustrated catalogue of shark species known to date. v 2. Bullhead, mackerel and carpet sharks (Heterodontiformes, Lamniformes and Orectolobiformes)
    • FAO Rome
    • Compagno L J V. 2001. Sharks of the world. An annotated and illustrated catalogue of shark species known to date. v 2. Bullhead, mackerel and carpet sharks (Heterodontiformes, Lamniformes and Orectolobiformes). FAO Species Catalogue for Fishery Purposes. No. 1, Vol. 2. Rome: FAO, 269
    • (2001) FAO Species Catalogue for Fishery Purposes. No. 1, Vol. 2 , pp. 269
    • Compagno, L.J.V.1
  • 11
    • 0002013551 scopus 로고    scopus 로고
    • Higher-level elasmobranch phylogeny, basal squaleans, and paraphyly
    • M. L J Stassny L. R Parenti G. D Johnson (eds) Academic Press San Diego 10.1016/B978-012670950-6/50004-7
    • de Carvalho M R. 1996. Higher-level elasmobranch phylogeny, basal squaleans, and paraphyly. In: Stassny M L J, Parenti L R, Johnson G D, eds. Interrelationships of Fishes. San Diego: Academic Press, 35-62
    • (1996) Interrelationships of Fishes , pp. 35-62
    • De Carvalho, M.R.1
  • 12
    • 0037331934 scopus 로고    scopus 로고
    • Molecular phylogenetic evidence refuting the hypothesis of Batoidea (rays and skates) as derived sharks
    • DOI 10.1016/S1055-7903(02)00333-0, PII S1055790302003330
    • Douady C J, Dosay M, Shivji M S, et al. 2003. Molecular phylogenetic evidence refuting the hypothesis of Batoidea (rays and skates) as derived sharks. Phylogenet, 26: 215-221 (Pubitemid 36264253)
    • (2003) Molecular Phylogenetics and Evolution , vol.26 , Issue.2 , pp. 215-221
    • Douady, C.J.1    Dosay, M.2    Shivji, M.S.3    Stanhope, M.J.4
  • 13
    • 0025344222 scopus 로고
    • A sensitive genetic assay for the detection of cytosine deamination: Determination of rate constants and the activation energy
    • Frederico L A, Kunkel T A, Shaw B R. 1990. A sensitive genetic assay for the detection of cytosine deamination: determination of rate constants and the activation energy. Biochemistry, 29: 2532-2537 (Pubitemid 20100849)
    • (1990) Biochemistry , vol.29 , Issue.10 , pp. 2532-2537
    • Frederico, L.A.1    Kunkel, T.A.2    Ramsay Shaw, B.3
  • 14
    • 77950806408 scopus 로고    scopus 로고
    • New algorithms and methods to estimate maximum-likelihood phylogenies: Assessing the performance of PhyML 3.0
    • 10.1093/sysbio/syq010
    • Guindon S, Dufayard J F, Lefort V, et al. 2010. New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst Biol, 59: 307-321
    • (2010) Syst Biol , vol.59 , pp. 307-321
    • Guindon, S.1    Dufayard, J.F.2    Lefort, V.3
  • 15
    • 77958122162 scopus 로고    scopus 로고
    • Cartilaginous fishes (Chondrichthyes)
    • S. B Hedges S. Kumar (eds) Oxford University Press New York
    • Heinicke M P, Naylor G J P, Hedges S B. 2009. Cartilaginous fishes (Chondrichthyes). In: Hedges S B, Kumar S, eds. The Timetree of Life. New York: Oxford University Press, 320-327
    • (2009) The Timetree of Life , pp. 320-327
    • Heinicke, M.P.1    Naylor, G.J.P.2    Hedges, S.B.3
  • 16
    • 0019949369 scopus 로고
    • Correlation between the abundance of yeast transfer RNAs and the occurrence of the respective codons in protein genes. Differences in synonymous codon choice patterns of yeast and Escherichia coli with reference to the abundance of isoaccepting transfer RNAs
    • DOI 10.1016/0022-2836(82)90250-9
    • Ikemura T. 1982. Correlation between the abundance of yeast transfer RNAs and occurrence of respective codons in protein genes: differences in synonymous codon choice patterns of yeast and Escherichia coli with reference to the abundance of isoaccepting transfer RNAs. JMol Evol, 158: 573-597 (Pubitemid 12044688)
    • (1982) Journal of Molecular Biology , vol.158 , Issue.4 , pp. 573-597
    • Ikemura, T.1
  • 17
    • 13744252890 scopus 로고    scopus 로고
    • MAFFT version 5: Improvement in accuracy of multiple sequence alignment
    • DOI 10.1093/nar/gki198
    • Katoh K, Kuma K, Toh H, et al. 2005. MAFFT version 5: improvement in accuracy of multiple sequence alignment. Nucleic Acids Research, 33: 511-518 (Pubitemid 40360980)
    • (2005) Nucleic Acids Research , vol.33 , Issue.2 , pp. 511-518
    • Katoh, K.1    Kuma, K.-I.2    Toh, H.3    Miyata, T.4
  • 18
    • 0013469077 scopus 로고    scopus 로고
    • Molecular Phylogeny of the Sharks and Rays of Superorder Squalea Based on Mitochondrial Cytochrome b Gene
    • Kitamura T, Takemura A, Watabe S, et al. 1996. Molecular phylogeny of the sharks and rays of superorder squalea based on mitochondrial Cytochrome b gene. Fisheries Science, 62: 340-343 (Pubitemid 126419675)
    • (1996) Fisheries Science , vol.62 , Issue.3 , pp. 340-343
    • Kitamura, T.1    Takemura, A.2    Watabe, S.3    Taniuchi, T.4    Shimizu, M.5
  • 19
    • 63849199927 scopus 로고    scopus 로고
    • Diversification trajectories and evolutionary life-history traits in early sharks and batoids
    • 10.1098/rspb.2008.1441
    • Kriwet J, Kiessling W, Klug S. 2009. Diversification trajectories and evolutionary life-history traits in early sharks and batoids. Proc Biol Sci, 276: 945-951
    • (2009) Proc Biol Sci , vol.276 , pp. 945-951
    • Kriwet, J.1    Kiessling, W.2    Klug, S.3
  • 20
    • 65649117685 scopus 로고    scopus 로고
    • DnaSP v5: A software for comprehensive analysis of DNA polymorphism data
    • 10.1093/bioinformatics/btp187
    • Librado P, Rozas J. 2009. DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics, 25: 1451-1452
    • (2009) Bioinformatics , vol.25 , pp. 1451-1452
    • Librado, P.1    Rozas, J.2
  • 21
    • 0027278557 scopus 로고
    • Instability and decay of the primary structure of DNA
    • DOI 10.1038/362709a0
    • Lindahl T. 1993. Instability and decay of the primary structure of DNA. Nature, 362: 709-715 (Pubitemid 23125973)
    • (1993) Nature , vol.362 , Issue.6422 , pp. 709-715
    • Lindahl, T.1
  • 22
    • 36048989002 scopus 로고    scopus 로고
    • OrganellarGenomeDRAW (OGDRAW): A tool for the easy generation of high-quality custom graphical maps of plastid and mitochondrial genomes
    • DOI 10.1007/s00294-007-0161-y
    • Lohse M, Drechsel O, Bock R. 2007. OrganellarGenomeDRAW (OGDRAW): a tool for the easy generation of high-quality custom graphical maps of plastid and mitochondrial genomes. Curr Genet, 52: 267-274 (Pubitemid 350090630)
    • (2007) Current Genetics , vol.52 , Issue.5-6 , pp. 267-274
    • Lohse, M.1    Drechsel, O.2    Bock, R.3
  • 23
    • 0030854739 scopus 로고    scopus 로고
    • TRNAscan-SE: A program for improved detection of transfer RNA genes in genomic sequence
    • DOI 10.1093/nar/25.5.955
    • Lowe T M, Eddy S R. 1997. tRNAscan-SE: a programfor improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res, 25: 955-964 (Pubitemid 27298263)
    • (1997) Nucleic Acids Research , vol.25 , Issue.5 , pp. 955-964
    • Lowe, T.M.1    Eddy, S.R.2
  • 24
    • 0002941794 scopus 로고
    • Higher elasmobranch phylogeny and biostratigraphy
    • 10.1111/j.1096-3642.1984.tb00534.x
    • Maisey J. 1984. Higher elasmobranch phylogeny and biostratigraphy. Zool J Linn Soc, 82: 33-54
    • (1984) Zool J Linn Soc , vol.82 , pp. 33-54
    • Maisey, J.1
  • 25
    • 34249276761 scopus 로고    scopus 로고
    • Ribosomal RNA genes and deuterostome phylogeny revisited: More cyclostomes, elasmobranchs, reptiles, and a brittle star
    • DOI 10.1016/j.ympev.2006.11.023, PII S1055790306004799
    • Mallatt J, Winchell C J. 2007. Ribosomal RNA genes and deuterostome phylogeny revisited: more cyclostomes, elasmobranchs, reptiles, and a brittle star. Phylogenet, 43: 1005-1022 (Pubitemid 46805075)
    • (2007) Molecular Phylogenetics and Evolution , vol.43 , Issue.3 , pp. 1005-1022
    • Mallatt, J.1    Winchell, C.J.2
  • 26
    • 33745159942 scopus 로고    scopus 로고
    • Phylogenetic relationships among the major lineages of modern elasmobranchs
    • W. C Hamlett B. G M Jamieson (eds) Science Publishers Inc. Enfield, NH
    • Naylor G J P, Ryburn J A, Fedrigo O, et al. 2005. Phylogenetic relationships among the major lineages of modern elasmobranchs. In: Hamlett W C, Jamieson B G M, eds. Reproductive Biology and Phylogeny. v 3. Enfield, NH: Science Publishers Inc., 1-25
    • (2005) Reproductive Biology and Phylogeny. v 3 , pp. 1-25
    • Naylor, G.J.P.1    Ryburn, J.A.2    Fedrigo, O.3
  • 27
    • 0019444843 scopus 로고
    • TRNA punctuation model of RNA processing in human mitochondria
    • DOI 10.1038/290470a0
    • Ojala D, Montoya J, Attardi G. 1981. tRNA punctuation model of RNA processing in human mitochondria. Nature, 290: 470-474 (Pubitemid 11159076)
    • (1981) Nature , vol.290 , Issue.5806 , pp. 470-474
    • Ojala, D.1    Montoya, J.2    Attardi, G.3
  • 28
    • 45849154165 scopus 로고    scopus 로고
    • JModelTest: Phylogenetic model averaging
    • DOI 10.1093/molbev/msn083
    • Posada D. 2008. jModelTest: phylogenetic model averaging. Biol, 25: 1253-1256 (Pubitemid 351882013)
    • (2008) Molecular Biology and Evolution , vol.25 , Issue.7 , pp. 1253-1256
    • Posada, D.1
  • 30
    • 77949447172 scopus 로고    scopus 로고
    • RNAstructure: Software for RNA secondary structure prediction and analysis
    • 10.1186/1471-2105-11-129
    • Reuter J S, Mathews D H. 2010. RNAstructure: software for RNA secondary structure prediction and analysis. BMC Bioinformatics, 11: 129
    • (2010) BMC Bioinformatics , vol.11 , pp. 129
    • Reuter, J.S.1    Mathews, D.H.2
  • 31
    • 0031950474 scopus 로고    scopus 로고
    • Asymmetrical directional mutation pressure in the mitochondrial genome of mammals
    • Reyes A, Gissi C, Pesole G, et al. 1998. Asymmetrical directional mutation pressure in the mitochondrial genome of mammals. Biol, 15: 957-966 (Pubitemid 28364449)
    • (1998) Molecular Biology and Evolution , vol.15 , Issue.8 , pp. 957-966
    • Reyes, A.1    Gissi, C.2    Pesole, G.3    Saccone, C.4
  • 32
    • 0041386108 scopus 로고    scopus 로고
    • MrBayes 3: Bayesian phylogenetic inference under mixed models
    • DOI 10.1093/bioinformatics/btg180
    • Ronquist F, Huelsenbeck J P. 2003. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics, 19: 1572-1574 (Pubitemid 37038874)
    • (2003) Bioinformatics , vol.19 , Issue.12 , pp. 1572-1574
    • Ronquist, F.1    Huelsenbeck, J.P.2
  • 34
    • 0002963694 scopus 로고
    • Comments on elasmobranch evolution
    • W. Gilbert R. F Mathewson D. P Rail (eds) Johns Hopkins Press Baltimore
    • Schaeffer B. 1967. Comments on elasmobranch evolution. In: Gilbert PW, Mathewson R F, Rail D P, eds. Sharks, Skates and Rays. Baltimore: Johns Hopkins Press, 3-35
    • (1967) Sharks, Skates and Rays , pp. 3-35
    • Schaeffer, B.1
  • 35
    • 0000124209 scopus 로고
    • Phylogenetic relationships of the angel sharks, with comments on elasmobranch phylogeny (Chondrichthyes, Squatinidae)
    • 10.2307/1446211
    • Shirai S. 1992a. Phylogenetic relationships of the angel sharks, with comments on elasmobranch phylogeny (Chondrichthyes, Squatinidae). Copeia, 2: 505-518
    • (1992) Copeia , vol.2 , pp. 505-518
    • Shirai, S.1
  • 37
    • 0002876005 scopus 로고    scopus 로고
    • Phylogenetic interrelationships of neoselachians (Chondrichthyes: Euselachii)
    • M. L J Stassny L. R Parenti G. D Johnson (eds) Academic Press San Diego 10.1016/B978-012670950-6/50003-5
    • Shirai S. 1996. Phylogenetic interrelationships of neoselachians (Chondrichthyes: Euselachii). In: Stassny M L J, Parenti L R, Johnson G D, eds. Interrelationships of Fishes. San Diego: Academic Press, 9-34
    • (1996) Interrelationships of Fishes , pp. 9-34
    • Shirai, S.1
  • 39
    • 84880558539 scopus 로고
    • Phylogeny and evolutionary ecology of Mesozoic, Neoselachii. News Jahrbuch für Geologie und Palaontologie Monatshefte
    • Thies D, Reif WE. 1985. Phylogeny and evolutionary ecology of Mesozoic, Neoselachii. News Jahrbuch für Geologie und Palaontologie Monatshefte, Abh. Stuttgart, 169: 331-361
    • (1985) Abh. Stuttgart , vol.169 , pp. 331-361
    • Thies, D.1    Reif, W.E.2
  • 40
    • 79951581466 scopus 로고    scopus 로고
    • Shark tales: A molecular species level phylogeny of sharks (Selachimorpha, Chondrichthyes)
    • 10.1016/j.ympev.2010.11.018
    • Vélez-Zuazo X, Agnarsson I. 2011. Shark tales: A molecular species level phylogeny of sharks (Selachimorpha, Chondrichthyes). Phylogenet, 58: 207-217
    • (2011) Phylogenet , vol.58 , pp. 207-217
    • Vélez-Zuazo, X.1    Agnarsson, I.2
  • 41
    • 0028917766 scopus 로고
    • A persistent RNA-DNA hybrid is formed during transcription at a phylogenetically conserved mitochondrial DNA sequence
    • Xu B, Clayton D A. 1995. A persistent RNA-DNA hybrid is formed during transcription at a phylogenetically conserved mitochondrial DNA sequence. Cell Biol, 15: 580-589 (Pubitemid 24379957)
    • (1995) Molecular and Cellular Biology , vol.15 , Issue.1 , pp. 580-589
    • Xu, B.1    Clayton, D.A.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.