Complete mitochondrial genome of the miiuy croaker Miichthys miiuy (Perciformes, Sciaenidae) with phylogenetic consideration

Marine Genomics

Volumn 3, Issue 3-4, 2010, Pages 201-209

  Cheng, Yuanzhi ^a   Xu, Tianjun ^a   Shi, Ge ^a   Wang, Rixin ^a  

^a ZHEJIANG OCEAN UNIVERSITY   (China)

Author keywords

Light strand replication origin; Miichthys miiuy; Mitochondrial genome; Sciaenidae

Indexed keywords

COLLICHTHYS; COLLICHTHYS NIVEATUS; LARIMICHTHYS; LARIMICHTHYS POLYACTIS; MIICHTHYS MIIUY; OSTEICHTHYES; PERCIFORMES; PISCES; SCIAENIDAE; VERTEBRATA;

EID: 78649528984     PISSN: 18747787     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.margen.2010.10.003     Document Type: Article

References (40)

1. Avise J.C. Mitochondrial DNA and evolutionary genetics of higher animals. Philos. Trans. R. Soc. Lond. 1986, 312:325-342.
2. Billington N., Hebert P.D.N. Mitochondrial DNA variation in Great Lakes walleye (Stizostedion vitreum) populations. Can. J. Fish. Aquat. Sci. 1988, 45:643-654.
3. Brought R.E., Dowling T.E. Length variation in mitochondrial DNA of the minnow Cyprinella spiloptera. Genetics 1994, 138:179-190.
4. Broughton R.E., Milam J.E., Roe B.A. The complete sequence of the zebrafish (Danio rerio) mitochondrial genome and evolutionary patterns in vertebrate mitochondrial DNA. Genome Res. 2001, 11:1958-1967.
5. Chen Q.M. Molecular Phylogeny of the Sciaenidae in China 2007, Jinan University, GuangZhou, (in Chinese with an English abstract).
6. Choi Y., Kim J.H., Park J.Y. Marine Fishes of Korea 2002, Kyohaksa Publ Co Ltd, Seoul.
7. Clayton D.A. Nuclear gadgets in mitochondrial DNA replication and transcription. Trends Biochem. Sci. 1991, 16:107-111.
8. Cui Z.X., Liu Y., Li C.P., You F., Chu K.H. The complete mitochondrial genome of the large yellow croaker, Larimichthys cracea (Perciformes, Sciaenidae): unusual features of its control region and the phylogenetic position of the Sciaenidae. Gene 2009, 432:33-43.
9. Desjardins P., Morais R. Sequence and gene organization of the chicken mitochondrial genome. A novle gene order in higher vertebrates. J. Mol. Biol. 1990, 212:599-634.
10. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985, 39:783-791.
11. Groves P., Shields G.F. Phylogenetics of the Caprinae on cytochrome b sequence. Mol. Phylogenet. Evol. 1996, 5:467-476.
12. Guindon S., Gascuel O. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst. Biol. 2003, 52:696-704.
13. Hixson J.E., Wong T.W., Clayton D.A. Both the conserved and divergent 5'- flanking sequences are required for initiation at the human mitochondrial origin of light strand replication. J. Biol. Chem. 1986, 261:2384-2390.
14. Hurst C.D., Bartlett S.E., Davidson W.S., Bruce I.J. The complete mitochondrial DNA sequence of the Atlantic salmon, Salmo salar. Gene 1999, 239:237-242.
15. Johansen S., Guddal P.H., Johansen T. Organization of the mitochondrial genome of atlantic cod, Gadus morhua. Nucleic Acids Res. 1990, 18:411-419.
16. Kim I.C., Lee J.S. The complete mitochondrial genome of the rockfish Sebastes schlegeli (Scorpaeniformes, Scorpaenidae). Mol. Cells 2004, 17:322-328.
17. Kim I.C., Kweon H.S., Kim Y.J., Kim C.B., Gye M.C., Lee W.O., Lee Y.S., Lee J.S. The complete mitochondrial genome of the javeline goby (Acanthogobius hasta) (Perciformes, Gobiidae) and phylogenetic considerations. Gene 2004, 336:147-153.
18. Li C., Orti G., Zhang G., Lu G. A practical approach to phylogenomics: the phylogeny of ray-finned fish (Actinopterygii) as a case study. BMC Evol. Biol. 2007, 7:44.
19. Macey J.R., Larson A., Ananjeva N.B., Fang Z., Papenfuss T.J. Two novel gene orders and the role of light-strand replication in rearrangements of the vertebrate mitochondrial genome. Mol. Biol. Evol. 1997, 14:91-104.
20. Miya M., Kawaguchi A., Nishida M. 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. 2001, 18:1993-2009.
21. 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., Nishida M. Major patterns of higher teleostean phylogenies: a new perspective based on 100 complete mitochondrial DNA sequences. Mol. Phylogenet. Evol. 2003, 26:121-138.
22. Naylor G.J., Collins T.M., Brown W.M. Hydrophobicity and phylogeny. Nature 1995, 373:555-556.
23. Oh D.J., Kim J.Y., Lee J.A., Yoon W.J., Park S.Y., Jung Y.H. Complete mitochondrial genome of the rock bream Oplegnathus fasciatus (Perciformes, Oplegnathidae) with phylogenetic considerations. Gene 2007, 392:174-180.
24. Oh D.J., Kim S.J., Jung Y.H. Comparison of the mitochondrial genomes of East Asian Pseudolabrus fishes. Mitochondr DNA 2008, 19:453-460.
25. Ohtsuki T., Kawai G., Watanabe K. The minimal tRNA: unique structure of Ascaris suum mitochondrial tRNAser-UCU having a short T arm and lacking the entire D arm. FEBS Lett. 2002, 514:37-43.
26. Ojala D., Montoya J., Attardi G. tRNA punctuation model of RNA processing in human mitochondria. Nature 1981, 290:470-474.
27. Peng Z., Wang J., He S. The complete mitochondrial genome of the helmet catfish Cranoglanis bouderius (Siluriformes: Cranoglanididae) and the phylogeny of otophysan fishes. Gene 2006, 376:290-297.
28. Posada D., Crandall K.A. MODELTEST: testing the model of DNA substitution. Bioinformatics 1998, 14:817-818.
29. Rokas A., Williams B.L., King N., Carroll S.B. Genome-scale approaches to resolving incongruence in molecular phylogenies. Nature 2003, 425:798-804.
30. Shadel G.S., Clayton D.A. Mitochondrial DNA maintenance in vertebrates. Annu. Rev. Biochem. 1997, 66:409-435.
31. Southern S.O., Southern P.J., Dizon A.E. Molecular characterization of a cloned dolphin mitochondrial genome. J. Mol. Evol. 1988, 28:32-40.
32. Taanman J.W. The mitochondrial genome: structure, transcription, translation and replication. Biochim. Biophys. Acta 1999, 1410:103-123.
33. Thompson J.D., Gibson T.J., Plewniak F., Jeanmougin F., Higgins D.G. The CLUSTAL-X Windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 1997, 25:4876-4882.
34. Tzeng C.S., Hui C.F., Shen S.C., Huang P.C. The complete nucleotide sequence of the Crossostoma lacustre mitochondrial genome: conservation and variation among vertebrates. Nucleic Acids Res. 1992, 20:4853-4858.
35. Waldbieser G.C., Bilodeau A.L., Nonneman D.J. Complete sequence and characterization of the channel catfish mitochondrial genome. DNA Seq. 2003, 14:265-277.
36. Wang X.Z., Wang J., He S.P., Mayden R.L. The complete mitochondrial genome of the Chinese hook snout carp Opsariichthys bidens (Actinopterygii: Cypriniformes) and an alternative pattern of mitogenomic evolution in vertebrate. Gene 2007, 399:11-19.
37. Xu T.J., Chen S.L., Ji X.S., Tian Y.S. MHC polymorphism and disease resistance to Vibrio anguillarum in 12 selective Japanese flounder (Paralichthys olivaceus) families. Fish Shellfish Immunol. 2008, 25:213-221.
38. Zardoya R., Meyer A. The complete DNA sequence of the mitochondrial genome of a 'living fossil', the coelacanth (Latimeria chalumnae). Genetics 1997, 146:995-1010.
39. Zardoya R., Garrido-Pertierra A., Bautista J.M. The complete nucleotide sequence of the mitochondrial DNA genome of the rainbow trout, Oncorhynchus mykiss. J. Mol. Evol. 1995, 41:942-951.
40. Zhang Q.Y., Hong W.S. Status and prospects of artificial propagation and breeding technique of marine fish in China in the 1990s. Mod. Fish. Info. 2000, 15:3-6. (in Chinese).