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The first complete mitochondrial genome from Bostrychus genus (Bostrychus sinensis) and partitioned Bayesian analysis of Eleotridae fish phylogeny

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Abstract

To understand the phylogenetic position of Bostrychus sinensis in Eleotridae and the phylogenetic relationships of the family, we determined the nucleotide sequence of the mitochondrial (mt) genome of Bostrychus sinensis. It is the first complete mitochondrial genome sequence of Bostrychus genus. The entire mtDNA sequence was 16508 bp in length with a standard set of 13 protein-coding genes, 22 transfer RNA genes (tRNAs), two ribosomal RNA genes (rRNAs) and a noncoding control region. The mitochondrial genome of B. sinensis had common features with those of other bony fishes with respect to gene arrangement, base composition, and tRNA structures. Phylogenetic hypotheses within Eleotridae fish have been controversial at the genus level. We used the mitochondrial cytochrome b (cytb) gene sequence to examine phylogenetic relationships of Eleotridae by using partitioned Bayesian method. When the specific models and parameter estimates were presumed for partitioning the total data, the harmonic mean –lnL was improved. The phylogenetic analysis supported the monophyly of Hypseleotris and Gobiomorphs. In addition, the Bostrychus were most closely related to Ophiocara, and the Philypnodon is also the sister to Microphlypnus, based on the current datasets. Further, extensive taxonomic sampling and more molecular information are needed to confirm the phylogenetic relationships in Eleotridae.

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References

  • Akihito Iwata A., Kobayashi T., Ikeo K., Imanishi T., Ono H., Umehara Y. et al. 2000 Evolutionary aspects of gobioid fishes based upon a phylogenetic analysis of mitochondrial cytochrome b genes. Gene 259, 5–15.

    Article  PubMed  Google Scholar 

  • Arnason E. and Rand D. M. 1992 Heteroplasmy of short tandem repeats in mitochondrial DNA of Atlantic cod, Gadus morhua. Genetics 132, 211–220.

    PubMed  CAS  Google Scholar 

  • Bachtrog D. 2007 Reduced selection for codon usage bias in Drosophila Miranda. J. Mol. Evol. 64, 586–690.

    Article  PubMed  CAS  Google Scholar 

  • Brandley M. C., Schmitz A. and Teeder T. W. 2005 Partitioned Bayesian Analyses, Partition Choice and the Phylogenetic Relationships of Scincid Lizards. Syst. Biol. 54, 373–390.

    Article  PubMed  Google Scholar 

  • Brown J. M. and Lemmon A. R. 2007 The importance of data partitioning and the utility of Bayes factors in Bayesian phylogenetics. Syst. Biol. 56, 643–655.

    Article  PubMed  Google Scholar 

  • Cheng Y. Z., Xu T. J., Shi G. and Wang R. X. 2010 Complete mitochondrial genome of the miiuy croaker Miichthys miiuy (Perciforms, Scienidae) with phylogenetic consideration. Mar. Genomic 3, 201–209.

    Article  Google Scholar 

  • Cheng Y. Z., Wang R. X. and Xu T. J. 2011 The mitochondrial genome of the spinyhead croaker Collchthys lucida: Genome organization and phylogenetic consideration. Mar. Genomic 4, 17–23.

    Article  Google Scholar 

  • Cheng Y. Z., Wang R. X., Sun Y. N. and Xu T. J. 2012 The complete mitochondrial genome of the small yellow croaker and partitioned Bayesian analysis of Sciaenidae fish phylogeny. Genet. Mol. Biol. 35, 191–199.

    Article  PubMed  Google Scholar 

  • Clayton D. A. 1991 Nuclear gadgets in mitochondrial DNA replication and transcription. Trends Biochem. Sci. 16, 107–111.

    Article  PubMed  CAS  Google Scholar 

  • Cui Z. X., Liu Y., Li C. P., You F. and Chu K. H. 2009 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 432, 33–43.

    Article  PubMed  CAS  Google Scholar 

  • Desjardins P. and Morais R. 1990 Sequence and gene organization of the chicken mitochondrial genome. A novle gene order in higher vertebrates. J. Mol. Biol. 212, 599–634.

    Article  PubMed  CAS  Google Scholar 

  • Gutell R. R., Gray M. W. and Schnare M. N. 1993 A compilation of large subunit (23S and 23S-like) ribosomal RNA structures. Nucleic Acids Res. 21, 3055–3074.

    Article  PubMed  CAS  Google Scholar 

  • He S. P., Mayden R. L., Wang X. Z., Wang W., Tang W., Tang K. L. et al. 2008 Molecular phylogenetics of the family Cyprindae (Actinopterygii: Cypriniforms) as evidenced by sequence variation in the first intron of S7 ribosomal protein-coding gene: Further evidence from a nuclear gene of the systematic chaos in the family. Mol. Phylogenet. Evol. 46, 818–829.

    Article  PubMed  CAS  Google Scholar 

  • Hixson J. E., Wong T. W. and Clayton D. A. 1986 Both the conserved and divergent 5’-flanking sequences are required for initiation at the human mitochondrial origin of light strand replication. J. Biol. Chem. 261, 2384–2390.

    PubMed  CAS  Google Scholar 

  • Huelsenbeck J. P. and Ronquist F. 2001 MRBAYES: Bayesian inference of phylogeny. Bioinformatics 17, 754–755.

    Article  PubMed  CAS  Google Scholar 

  • Hurst C. D., Bartlett S. E., Davidson W. S. and Bruce I. J. 1999 The complete mitochondrial DNA sequence of the Atlantic salmon, Salmo salar. Gene 239, 237–242.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    Article  CAS  Google Scholar 

  • Ip Y. K., Chew S F., Leong I. A. W., Jin Y., Lim C. B. and Wu R. S. S. 2001 The sleeper Bostrichthys sinensis (Family Eleotridae) stores glutamine and reduces ammonia production during aerial exposure. J. Comp. Physiol. B 171, 357–367.

    Article  PubMed  CAS  Google Scholar 

  • Ishiguro N., Miya M. and Nishida M. 2001 Complete mitochondrial DNA sequence of ayu Pleoglossus altivelis. Fish Sci. 67, 474–481.

    Article  CAS  Google Scholar 

  • Kass R. E. and Raftery A. E. 1995 Bayes factors. J. Am. Stat. Assoc. 90, 773–735.

    Google Scholar 

  • Kumar S., Dudley J., Nei M. and Tamura K. 2008 MEGA: a biologist-centric software for evolutionary analysis of DNA and protein sequences. Brief Bioinform. 9, 299–306.

    Article  PubMed  CAS  Google Scholar 

  • Lee W. J. and Kocher T. D. 1995 Complete sequence of a sea lamprey (Petromyzon marinus) mitochondrial genome: early establishment of the vertebrate genome organization. Genetics 139, 873–887.

    PubMed  CAS  Google Scholar 

  • Lee W. J., Conroy J., Howell W. H. and Kocher T. D. 1995 Structure and Evolution of Teleost Mitochondrial Control Regions. J. Mol. Evol. 41, 54–66.

    Article  PubMed  CAS  Google Scholar 

  • 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. 11, 1993–2009.

    Article  Google Scholar 

  • Miya M., Takeshima H., Endo H., Isihiguro N. B., Inoue J. G., Mukai T. et al. 2003 Major patterns of higher teleostean phylogenies; a new perspective based on 100 complete mitochondrial DNA sequences. Mol. Phylogenet. Evol. 26, 121–138.

    Article  PubMed  CAS  Google Scholar 

  • Nylander J. A. A., Ronquist F., Huelsenbeck J. P. and Nieves-Aldrey J. L. 2004 Bayesian phylogenetic analysis of combined data. Syst. Biol. 53, 47–67.

    Article  PubMed  Google Scholar 

  • Oh D. J., Kim J. Y., Lee J. A., Yoon W. J., Park S. Y. and Jung Y. H. 2007 Complete mitochondrial genome of the rock bream Oplegnathus fasciatus (Perciformes, Oplegnathidae) with phylogenetic considerations. Gene 392, 174–180.

    Article  PubMed  CAS  Google Scholar 

  • Oh D. J., Kim S. J. and Jung Y. H. 2008 Comparison of the mitochondrial genomes of East Asian Pseudolabrus fishes. Mitochondrial DNA 19, 453–460.

    Article  PubMed  CAS  Google Scholar 

  • Ojala D., Montoya J. and Attardi G. 1981 tRNA punctuation model of RNA processing in human mitochondria. Nature 290, 470–474.

    Article  PubMed  CAS  Google Scholar 

  • Peng Z., Wang J. and He S. 2006 The complete mitochondrial genome of the helmet catfish Cranoglanis bouderius (Siluriformes: Cranoglanididae) and the phylogeny of otophysan fishes. Gene 376, 290–297.

    Article  PubMed  CAS  Google Scholar 

  • Posada D. 2008 jModelTest: phylogenetic model averaging. Mol. Biol. Evol. 25, 1253–1256.

    Article  PubMed  CAS  Google Scholar 

  • Quan X. Q., Jin X. X., Wang R. X., Xu T.J. and Shi G. 2012 Complete mitochondrial genome of the Walking goby Scartelaos histophorus (Perceformes, Gobiidae). Mitochondrial DNA 23, 298–300.

    Article  PubMed  CAS  Google Scholar 

  • Sambrook J. and Russell D. W. 2001 Molecular cloning: a laboratory manual, 3rd edition. Cold Spring Harbor Laboratory Press, New York, NY.

    Google Scholar 

  • Shadel G. S. and Clayton D. A. 1997 Mitochondrial DNA maintenance in vertebrates. Annu. Rev. Biochem. 66, 409–435.

    Article  PubMed  CAS  Google Scholar 

  • Shi G., Jin X. X., Zhao S. L., Xu T. J. and Wang R. X. 2012 Complete mitochondrial genome of Trypauchen vagina (Perciformes, Gobioidei). Mitochondrial DNA 23, 151–153.

    Article  PubMed  CAS  Google Scholar 

  • Thacker C. E. 2003 Molecular phylogeny of gobioid fishes (Teleostei: Perciformes: Gobioidei). Mol. Phylogenet. Evol. 26, 354–368.

    Article  PubMed  CAS  Google Scholar 

  • Thacker C. E. and Hardman M. A. 2005 Molecular phylogeny of basal gobioid fishes: Rhyacichthyidae, Odontobutidae, Xenisthmidae, Eleotridae. Mol. Phylogenet. Evol. 37, 858–875.

    Article  PubMed  CAS  Google Scholar 

  • Thompson J. D., Higgins D. G. and Gibson T. J. 1994 CLUSTALW: improving the sensitivity of progresssive multiple sequence alignment through sequence weighting, position-specil gap penalties and weight matrix choice. Nulcleic Acid Res. 22, 4673–4680.

    Article  CAS  Google Scholar 

  • Tzeng C. S., Hui S. F., Shen S. C. and Huang P. C. 1992 The complete nucleotide sequence to the Crossostoma lacustre mitochondrial genome: conservation and variations among vertebrates. Nucleic Acids Res. 20, 4853–4858.

    Article  PubMed  CAS  Google Scholar 

  • Waldbieser G. C., Bilodeau A. L. and Nonneman D. J. 2003 Complete sequence and characterization of the channel catfish mitochondrial genome. Mitochondrial DNA 14, 265–277.

    CAS  Google Scholar 

  • Wang H. Y., Tsai M. P., Dean J. and Lee S. C. 2001 Molecular phylogeny of gobioid fishes (Perciformes: Gobioider) based on mitochondrial 12S rRNA sequences. Mol. Phylogenet. Evol. 20, 390–408.

    Article  PubMed  CAS  Google Scholar 

  • Wang X. Z., Wang J., He S. P. and Mayden R. L. 2007 The complete mitochondrial genome of the Chinese hook snout carp Opsariichthys bidens (Actinopterygii: Cypriniformes) and an alternative pattern of mitogenomic evolution in vertebrate. Gene 399, 11–19.

    Article  PubMed  CAS  Google Scholar 

  • Wyman S. K., Jansen R. K. and Boore J. L. 2004 Automatic annotation of organellar genomes with DOGMA. Bioinformatics 20, 3252–3255.

    Article  PubMed  CAS  Google Scholar 

  • Xia J., Xia K., Gong J. and Jiang S. 2007 Complete mitochondrial DNA sequence, gene organization and genetic variation of control regions in Parargyrops edita. Fish Sci. 73, 1042–1049.

    Article  CAS  Google Scholar 

  • Xu T. J., Cheng Y. Z., Sun Y. N., Shi G. and Wang R. X. 2011 The complete mitochondrial genome of bighead croaker, Collichthys niveatus (Perciforms, Sciaenidae): structure of control region and phylogenetic considerations. Mol. Biol. Rep. 38, 4673– 4685.

    Article  PubMed  CAS  Google Scholar 

  • Yang Z. 1996 Maximum likelihood models for combined analyses of multiple sequence data. J. Mol. Evol. 42, 587–596.

    Article  PubMed  CAS  Google Scholar 

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Acknowledgements

This study was supported by National Natural Science Foundation of China (31272661). We thank Prof. Shenglong Zhao for the help of fish sampled and identified by morphology.

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Authors and Affiliations

  1. Laboratory for Marine Living Resources and Molecular Engineering, College of Marine Science, Zhejiang Ocean University, 316000, Zhoushan, People’s Republic of China

    TAO WEI, XIAO XIAO JIN & TIAN JUN XU

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  1. TAO WEI
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  2. XIAO XIAO JIN
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  3. TIAN JUN XU
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Correspondence to TIAN JUN XU.

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[Wei T., Jin X. X. and Xu T. J. 2013 The first complete mitochondrial genome from Bostrychus genus (Bostrychus sinensis) and partitioned Bayesian analysis of Eleotridae fish phylogeny. J. Genet. 92, xx–xx]

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WEI, T., JIN, X.X. & XU, T.J. The first complete mitochondrial genome from Bostrychus genus (Bostrychus sinensis) and partitioned Bayesian analysis of Eleotridae fish phylogeny. J Genet 92, 247–257 (2013). https://doi.org/10.1007/s12041-013-0259-6

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  • DOI: https://doi.org/10.1007/s12041-013-0259-6

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