The mitochondrial genome of spotted green pufferfish Tetraodon nigroviridis (Teleostei: Tetraodontiformes) and divergence time estimation among model organisms in fishes

Genes and Genetic Systems

Volumn 81, Issue 1, 2006, Pages 29-39

  Yamanoue, Yusuke ^a   Miya, Masaki ^b   Inoue, Jun G ^a,d   Matsuura, Keiichi ^c   Nishida, Mutsumi ^a  

^a UNIVERSITY OF TOKYO   (Japan)

^b NATURAL HISTORY MUSEUM AND INSTITUTE   (Japan)

^c DEPARTMENT OF BOTANY   (Japan)

^d FLORIDA STATE UNIVERSITY   (United States)

Author keywords

Fugu; Mitochondrial genome; Partitioned Bayesian analysis; Takifugu rubripes

Indexed keywords

RIBOSOME RNA; TRANSFER RNA;

AMINO ACID SEQUENCE; ARTICLE; BAYES THEOREM; CODON; GENE SEQUENCE; GENE TRANSFER; GENETIC LINE; GENOME; MITOCHONDRIAL GENETICS; NONHUMAN; NUCLEOTIDE SEQUENCE; ORYZIAS; PHYLOGENY; PUFFER FISH; TELEOST; TETRAODONTIFORMES; TIME PERCEPTION; VERTEBRATE; ZEBRA FISH;

ANIMALS; DNA, MITOCHONDRIAL; EVOLUTION, MOLECULAR; GENOME; MITOCHONDRIA; PHYLOGENY; TETRAODONTIFORMES;

DANIO RERIO; GASTEROSTEUS ACULEATUS; ORYZIAS; PISCES; TAKIFUGU; TAKIFUGU RUBRIPES; TELEOSTEI; TETRAODON FLUVIATILIS; TETRAODON NIGROVIRIDIS; TETRAODONTIDAE; TETRAODONTIFORMES; VERTEBRATA;

EID: 33645772189     PISSN: 13417568     EISSN: 13417568     Source Type: Journal    
DOI: 10.1266/ggs.81.29     Document Type: Article

References (49)

1. Aparicio, S., Chapman, J., Stupka, E., Putnam, N., Chia, J. M., et al. (2002) Whole-genome shotgun assembly and analysis of the genome of Fugu rubripes. Science 297, 1301-1310.
2. Benton, M. J. (1993) The fossil record, vol. 2, pp 845, Chapman & Hall, London.
3. Benton, M. J. (2005) Vertebrate palaeontology, 3rd ed., pp. 455, Blackwell, Malden.
4. Broughton, R. E., Milam, J. E., and Roe, B. A. (2001) The complete sequence of the zebrafish (Danio rerio) mitochondrial genome and evolutionary patterns in vertebrate mitochondrial DNA. Genome Res. 11, 1958-1967.
5. Cantatore, P., Roberti, M., Pesole, G., Ludovico, A., Milella, F., Gadaleta, M. N., and Saccone, C. (1994) Evolutionary analysis of cytochrome b sequences in some Perciformes: evidence for a slower rate of evolution than in mammals. J. Mol. Evol. 39, 589-597.
6. Chang, Y. S., Huang, F. L., and Lo, T. B. (1994) The complete nucleotide sequence and gene organization of carp (Cyprinus carpio) mitochondrial genome. J. Mol. Evol. 38, 138-155.
7. Chen, W. -J., Orti, G., and Meyer, A. (2004) Novel evolutionary relationship among four fish model systems. Trends Genet. 20, 424-431.
8. Cheng, S., Higuchi, R., and Stoneking, M. (1994) Complete mitochondrial genome amplification. Nat. Genet. 7, 350-351.
9. Crnogorac-Jurcevic, T., Brown, J. R., Lehrach, H., and Schalkwyk, L. C. (1997) Tetraodon fluviatilis, a new puffer model for genome studies. Genomics 41, 177-184.
10. Delarbre, C., Spruyt, N., Delmarre, C., Gallut, C., Barriel, V., Janvier, P., Laudet, V., and Gachelin, G. (1998) The complete nucleotide sequence of the mitochondrial DNA of the dogfish, Scyliorhinus canicula. Genetics 150, 331-344.
11. Doda, J. N., Wright, C. T., and Clayton, D. A. (1981) Elongation of displacement-loop strands in human and mouse mitochondrial DNA is arrested near specific template sequences. Proc. Natl. Acad. Sci. USA 78, 6116-6120.
12. Gutell, R. R., Gray, M. W., and Schnare, M. N. (1993) A compilation of large subunit (23S and 23S-like) ribosome RNA structures. Nucleic Acids Res. 21, 3055-3074.
13. Hasegawa, M., Kishino, H., and Yano, T. A. (1985) Dating of the human ape splitting by a molecular clock of mitochondrial DNA. J. Mol. Evol. 22, 160-174.
14. Hedges, S. B., and Kumar, S. (2003) Genomic clocks and evolutionary timescales. Trends Genet. 19, 200-206.
15. Hixson, J. E., Wong, T. W., and Clayton, D. A. (1986) Both the conserved stem loop and divergent 5′ -flanking sequences are required for initiation at the human mitochondrial origin of light-strand DNA replication. J. Biol. Chem. 261, 2384-2390.
16. Inoue, J. G., Miya, M., Tsukamoto, K., and Nishida, M. (2000) Complete mitochondrial DNA sequence of the Japanese sardine Sardinops melanostictus. Fish. Sci. 66, 924-932.
17. Inoue, J. G., Miya, M., Tsukamoto, K., and Nishida, M. (2003) Basal actinopterygian relationships: a mitogenomic perspective on the phylogeny of the "ancient fish." Mol. Phylogenet. Evol. 26, 110-120.
18. Inoue, J. G., Miya, M., Venkatesh, B., and Nishida, M. (2005) The mitochondrial genome of Indonesian coelacanth Latimeria menadoensis (Sarcopterygii: Coelacanthiformes) and divergence time estimation between the two coelacanths. Gene 349, 227-235.
19. Ishiguro, N. B., Miya, M., and Nishida, M. (2003) Basal euteleostean relationships: a mitogenomic perspective on the phylogenetic reality of the "Protacanthopterygii." Mol. Phylogenet. Evol. 27, 476-488.
20. Jaillon, O., Aury, J. -M., Brunet, F., Petit, J. -L., Stange-Thomann, N., et al. (2004) Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype. Nature 431, 946-957.
21. Johansen, S., and Bakke, I. (1996) The complete mitochondrial DNA sequence of Atlantic cod (Gadus morhua): relevance to taxonomic studies among codfishes. Mol. Mar. Biol. Biotechnol. 5, 203-214.
22. Kumazawa, Y., Azuma, Y., and Nishida, M. (2004) Tempo of mitochondrial gene evolution: can mitochondrial DNA be used to data old divergences? Endocytobiosis Cell Res. 15, 136-142.
23. Kumazawa, Y., and Nishida, M. (1993) Sequence evolution of mitochondrial tRNA genes and deep-branch animal phylogenetics. J. Mol. Evol. 37, 380-398.
24. Kumazawa, Y., and Nishida, M. (2000) Molecular phylogeny of osteoglossoids: a new model for Gondwanian origin and plate tectonic transportation of the Asian arowana. Mol. Biol. Evol. 17, 1869-1878.
25. Kumazawa, Y., Yamaguchi, M., and Nishida, M. (1999) Mitochondrial molecular clocks and the origin of euteleostean biodiversity: familial radiation of perciforms may have predated the Cretaceous/Tertiary boundary. In: The biology of biodiversity (ed. M. Kato), pp. 35-52. Springer-Verlag, Tokyo.
26. Miya, M., Kawaguchi, A., and Nishida, M. (2001) Mitogenomic exploration of higher teleostean phylogenies: a case study for moderate-scale evolutionary genomics with 38 newly determined complete mitochondrial DNA sequences. Mol. Biol. Evol. 18, 1993-2009.
27. Miya, M., and Nishida, M. (1999) Organization of the mitochondrial genome of a deep-sea fish Gonostoma gracile (Teleostei: Stomiiformes): first example of transfer RNA gene rearrangements in bony fishes. Mar. Biotechnol. 1, 416-426.
28. Miya, M., and Nishida, M. (2000) Use of mitogenomic information in teleostean molecular phylogenetics: a tree-based exploration under the maximum-parsimony optimality criterion. Mol. Phylogenet. Evol. 17, 437-455.
29. Miya, M., Takeshima, H., Endo, H., Ishiguro, N. B., Inoue, J. G., Mukai, T., Satoh, T. P., Yamaguchi, M., Kawaguchi, A., Mabuchi, K., Shirai, S. M., and Nishida, M. (2003) Major patterns of higher teleostean phylogenies: a new perspective based on 100 complete mitochondrial DNA sequences. Mol. Phylogenet. Evol. 26, 121-138.
30. Nei, M., and Glazko, G. V. (2002) Estimation of divergence times for a few mammalian and several primate species. J. Heredity 93, 157-164.
31. Ojala, D., Montoya, J., and Attardi, G. (1981) tRNA punctuation model of RNA processing in human mitochondria. Nature 290, 470-474.
32. Ronquist, F., and Huelsenbeck, J. P. (2003) MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19, 1572-1574.
33. Saitoh, K., Hayashizaki, K., Yokoyama, Y., Asahida, T., Toyohara, H., and Yamashita, Y. (2000) Complete nucleotide sequence of Japanese flounder (Paralichthys olivaceus) mitochondrial genome structural properties and cue for resolving teleostean relationships. J. Heredity 91, 271-278.
34. Schrago, C. G., and Russo, C. A. M. (2003) Timing the origin of new world monkeys. Mol. Biol. Evol. 20, 1620-1625.
35. Springer, M. S., Murphy, W. J., Eizirik, E., and OíBrien, S. J. (2003) Placental mammal diversification and the Cretaceous-Tertiary boundary. Proc. Natl. Acad. Sci. U.S.A. 100, 1056-1061.
36. Takezaki, N., Rzhetsky, A., and Nei, M. (1995) Phylogenetic test of the molecular clock and linearized trees. Mol. Biol. Evol. 12, 823-833.
37. Thompson, J. D., Gibson, T. J., Plewniak, F., Jeanmougin, F., and Higgins, D. G. (1997) The Clustal X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 25, 4876-4882.
38. Thorne, J. L., and Kishino, H. (2002) Divergence time and evolutionary rate estimation with multilocus data. Syst. Biol. 51, 689-702.
39. Tyler, J. C., and Bannikov, A. F. (1992) A remarkable new genus of tetraodontiform fish with features of both balistids and ostraciids from the Eocene of Turkmenistan. Smiths. Contrib. Paleobiol. 72, 1-14.
40. Tyler, J. C., and Sorbini, L. (1996) New superfamily and three new families of tetraodontiform fishes from the Upper Cretaceous: the earliest and most morphologically primitive plectognaths. Smiths. Contrib. Paleobiol. 82, 1-59.
41. Venter, J. C., Adams, M. D., Myers, E. W., Li, P. W., Mural, R. J., et al. (2001) The sequence of the human genome. Science 291, 1304-1351.
42. Volff, J. N., Bouneau, L., Ozouf-Costaz, C., and Fischer, C. (2003) Diversity of retrotransposable elements in compact puffer genomes. Trends Genet. 19, 674-678.
43. Walberg, M. W., and Clayton, D. A. (1981) Sequence and properties of the human KB cell and mouse L cell D-loop regions of mitochondrial DNA. Nucleic Acids Res. 9, 5411-5421.
44. Wang, H. Y., and Lee, S. C. (2002) Secondary structure of mitochondrial 12S rRNA among fish and its phylogenetic applications. Mol. Biol. Evol. 19, 138-148.
45. Yang, Z. (1994) Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: approximate methods. J. Mol. Evol. 39, 306-314.
46. Yang, Z. (1997) PAML: a program package for phylogenetic analysis by maximum likelihood. Comp. App. Biosci. 13, 555-556.
47. Yang, Z., Nielsen, R., and Hasegawa, M. (1998) Models of amino acid substitution and applications to mitochondrial protein evolution. Mol. Biol. Evol. 15, 1600-1611.
48. Zardoya, R., Garrido-Pertierra, A., and Bautista, J. M. (1995) The complete nucleotide sequence of the mitochondrial DNA genome of the rainbow trout, Oncorhynchus mykiss. J. Mol. Evol. 41, 942-951.
49. Zardoya, R., and Meyer, A. (1997) The complete DNA sequence of the mitochondrial genome of a "living fossil," the coelacanth (Latimeria chalumnae). Genetics 146, 995-1010.