Complete nucleotide sequence and gene rearrangement of the mitochondrial genome of Occidozyga martensii

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• 作者：EN LI (1)
  XIAOQIANG LI (1)
  XIAOBING WU (1)
  GE FENG (1)
  MAN ZHANG (1)
  HAITAO SHI (2)
  LIJUN WANG (2)
  JIANPING JIANG (3)
  
  1. College of Life Sciences ; Anhui Province Key Laboratory for Conservation and Exploitation of Biological Resource ; Anhui Normal University ; Wuhu ; 241000 ; People鈥檚 Republic of China
  2. College of Life Sciences ; Hainan Normal University ; Haikou ; 571158 ; People鈥檚 Republic of China
  3. Chengdu Institute of Biology ; Chinese Academy of Sciences ; Chengdu ; 610041 ; People鈥檚 Republic of China
  
• 关键词：mitochondrial genome ; novel gene rearrangement ; phylogenetic relationships ; Occidozyga martensii
• 刊名：Journal of Genetics
• 出版年：2014
• 出版时间：December 2014
• 年：2014
• 卷：93
• 期：3
• 页码：631-641
• 全文大小：1,196 KB
• 参考文献：1. Alam M. S., Kurabayashi A., Hayashi Y., Sano N., Khan M. M. R., Fujii T., / et al. 2010 Complete mitochondrial genomes and novel gene rearrangements in two dicroglossid frogs, / Hoplobatrachus tigerinus and / Euphlyctis hexadactylus, from Bangladesh. / Genes Genet. Syst. 85, 219鈥?32. CrossRef
  2. Boore J. L. 1999 Animal mitochondrial genomes. / Nucleic Acids Res. 27, 1767鈥?780. CrossRef
  3. Boore J. L. 2001 Complete mitochondrial genome sequence of the polychaete annelid / Platynereis dumerilii. / Mol. Biol. Evol. 18, 1413鈥?416. CrossRef
  4. Boore J. L. and Brown W. M. 1998 Big trees from little genomes: mitochondrial gene order as a phylogenetic tool. / Curr. Opin. Genet. Dev. 8, 668鈥?74. CrossRef
  5. Castresana J. 2000 Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. / Mol. Biol. Evol. 17, 540鈥?52. CrossRef
  6. Che J., Pang J. F., Zhao H., Wu G. F., Zhao E. M., and Zhang Y. P. 2007 Molecular phylogeny of the Chinese ranids inferred from nuclear and mitochondrial DNA sequences. / Biochem. Syst. Ecol. 35, 29鈥?9. CrossRef
  7. Dubois A. 1992 Notes sur la classification des Ranidae (Amphibiens, Anoures). / Bull. Mens. Soc. Linn. Lyon 61, 305鈥?52.
  8. Dubois A. 2005 / Amphibia Mundi. 1.1. An ergotaxonomy of recent amphibians. / Alytes 23, 1鈥?4.
  9. Duellman W. E. and Trueb L. 1994 / Biology of Amphibians. Johns Hopkins University Press, Baltimore, USA.
  10. Fei L., Ye C Y., and Huang Y. Z. 1990 / Key to Chinese Amphibia. Science and Technology Literature Publishing House, Chongqing, China.
  11. Fei L., Ye C. Y., Jiang J. P., Xie F., and Huang Y. Z. 2005 / An illustrated key to Chinese amphibians. Sichuan Publishing House of Science and Technology, Chengdu, China.
  12. Ford L. S. and Cannatella D. C. 1993 The major clades of frogs. / Herpetol. Monogr. 7, 94鈥?17. CrossRef
  13. Frost D. R. 2010 Amphibian species of the world: an online reference. Version 5.4. (8 April 2010). American Museum of Natural History, New York, USA. Available at: http://research.amnh.org/vz/herpetology/amphibia/index.php.
  14. Frost D. R., Grant T., Faivovich J., Bain R. H., Haas A., and Haddad C. F. B. 2006 The amphibian tree of life. / B. Am. Mus. Nat. Hist. 297, 1鈥?70. CrossRef
  15. Garesse R., Carrodeguas J. A., Santiago J., Perez M. L., Marco R., and Vallejo C. G. 1997 Artemia mitochondrial genome: molecular biology and evolutive considerations. / Comp. Biochem. Phys. B 117, 357鈥?66. CrossRef
  16. Guindon S., Dufayard J. F., Lefort V., Anisimova M., Hordijk W., and Gascuel O. 2010 New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. / Syst. Biol. 59, 307鈥?21. CrossRef
  17. Hay J. M., Ruvinsky I., Hedges S. B. and Maxson L. R. 1995 Phylogenetic relationships of amphibian families inferred from DNA sequences of mitochondrial 12S and 16S ribosomal RNA genes. / Mol. Biol. Evol. 12, 928鈥?37.
  18. Hedges S. B. and Maxson L. R. 1993 A molecular perspective on lissamphibian phylogeny. / Herpetol. Monogr. 7, 27鈥?2. CrossRef
  19. Hixson J. E., Wong T. W., and Clayton D. A. 1986 Both the conserved stem-loop and divergent 5<sup>鈥?/sup>-flanking sequences are required for initiation at the human mitochondrial origin of light-strand replication. / J. Biol. Chem. 261, 2384鈥?2390.
  20. Hoegg S., Vences M., Brinkmann H. and Meyer A. 2004 Phylogeny and comparative substitution rates of frogs inferred from sequences of three nuclear genes. / Mol. Biol. Evol. 21, 1188鈥?200.
  21. Igawa T., Kurabayashi A., Usuki C., Fujii T., and Sumida M. 2008 Complete mitochondrial genomes of three neobatrachian anurans: A case study of divergence time estimation using different data and calibration settings. / Gene 407, 116鈥?29. CrossRef
  22. Inger R. F. 1996 Commentary on a proposed classification of the family Ranidae. / Herpetologica 52, 241鈥?46.
  23. Irisarri I., San Mauro D., Green D M., and Zardoya R. 2010 The complete mitochondrial genome of the relict frog / Leiopelma archeyi: insights into the root of the frog tree of life. / Mitochondrial DNA 21, 173鈥?82. CrossRef
  24. Jeanmougin F., Thompson J. D., Gouy M., Higgins D. G., and Gibson T. J. 1998 Multiple sequence alignment with Clustal X. / Trends Biochem. Sci. 23, 403鈥?05. CrossRef
  25. Jiang J. P. and Zhou K. Y. 2005 Phylogenetic relationships among Chinese ranids inferred from sequence data set of 12S and 16S rDNA. / Herpetol. J. 15, 1鈥?.
  26. Kumazawa Y. and Nishida M. 1995 Variations in mitochondrial tRNA gene organization of reptiles as phylogenetic markers. / Mol. Biol. Evol. 12, 759鈥?72.
  27. Kurabayashi A. and Ueshima R. 2000 Complete sequence of the mitochondrial DNA of the primitive opisthobranch gastropod, / Pupa strigosa: systematic implication of the genome organization. / Mol. Biol. Evol. 17, 266鈥?77.
  28. Kurabayashi A., Usuki C., Mikami N., Fujii T., Yonekawa H., Sumida M. / et al. 2006 Complete nucleotide sequence of the mitochondrial genome of a Malagasy poison frog, / Mantella madagascariensis: evolutionary implications on mitochondrial genomes of higher anuran groups. / Mol. Phylogenet. Evol. 39, 223鈥?36.
  29. Larson P. M. 2005 Ontogeny, phylogeny, and morphology in anuran larvae: morphometric analysis of cranial development and evolution in / Rana tadpoles (Anura: Ranidae). / J. Morphol. 264, 34鈥?2. CrossRef
  30. Liu Z. Q., Wang Y. Q., and Su B. 2005 The mitochondrial genome organization of the rice frog, / Fejervarya limnocharis (Amphibia: Anura): a new gene order in the vertebrate mtDNA. / Gene 346, 145鈥?51. CrossRef
  31. Macey J. R., Larson A., Ananjeva N. B., Fang Z. and 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鈥?04.
  32. Macey J. R., Schulte I. J. A., Larson A., and Papenfuss T. J. 1998 Tandem duplication via light-strand synthesis may provide a precursor for mitochondrial genome rearrangement. / Mol. Biol. Evol. 15, 71鈥?5. CrossRef
  33. Meyer A. and Zardoya R. 2003 Recent advances in the (molecular) phylogeny of vertebrates. / Annu. Rev. Ecol. Evol. S. 34, 311鈥?338. CrossRef
  34. Moritz C. and Brown W. M. 1987 Tandem duplications in animal mitochondrial DNAs: variation in incidence and gene content among lizards. / Proc. Natl. Acad. Sci. USA 84, 7183鈥?187. CrossRef
  35. P盲盲bo S., Thomas W. K., Whitfield K. M., Kumazawa Y., and Wilson A. C. 1991 Rearrangements of mitochondrial transfer RNA genes in marsupials. / J. Mol. Evol. 33, 426鈥?30. CrossRef
  36. Pabijan M., Spolsky C., Uzzell T. and Szymura J. M. 2008 Comparative analysis of mitochondrial genomes in Bombina (Anura; Bombinatoridae). / J. Mol. Evol. 67, 246鈥?56.
  37. Posada D. and Crandall K. A. 1998 Modeltest: testing the model of DNA substitution. / Bioinformatics 14, 817鈥?18. CrossRef
  38. Pugener L. A., Maglia A. M., and Trueb L. 2003 Revisiting the contribution of larval characters to an analysis of phylogenetic relationships of basal anurans. / Zool. J. Linn. Soc. 139, 129鈥?155. CrossRef
  39. Quinn T. W. and Mindell D. P. 1996 Mitochondrial gene order adjacent to the control region in crocodile, turtle, and tuatara. / Mol. Phylogenet. Evol. 5, 344鈥?51. CrossRef
  40. Ren Z. M., Zhu B., Ma E. B., Wen J., Tu T. Y., Cao Y., / et al. 2009 Complete nucleotide sequence and gene arrangement of the mitochondrial genome of the crab-eating frog / Fejervarya cancrivora and evolutionary implications. / Gene 441, 148鈥?55. CrossRef
  41. Roe B. A., Ma D. P., Wilson R. K. and Wong J. F. H. 1985 The complete nucleotide sequence of the / Xenopus laevis mitochondrial genome. / J. Biol. Chem. 260, 9759鈥?774.
  42. Roelants K. and Bossuyt F. 2005 Archaeobatrachian paraphyly and Pangaean diversification of crown-group frogs. / Syst. Biol. 54, 111鈥?26. CrossRef
  43. Roelants K., Jiang J. P., and Bossuyt F. 2004 Endemic ranid (Amphibia: Anura) genera in southern mountain ranges of the Indian subcontinent represent ancient frog lineages: evidence from molecular data. / Mol. Phylogenet. Evol. 31, 730鈥?40. CrossRef
  44. Ronquist F. and Huelsenbeck J. P. 2003 MrBayes 3: Bayesian phylogenetic inference under mixed models. / Bioinformatics 19, 1572鈥?574. CrossRef
  45. Rychlik W. and Rychlik P. 2000 / Oligo primer analysis software, ver. 6.01. Molecular Biology Insights, Cascade, Colorado, USA.
  46. Sambrook J. and Russell D. W. 2001 / Molecular cloning: a laboratory manual, 3rd edition. Cold Spring Harbor Laboratory Press, New York.
  47. San Mauro D., Garcia-Paris M. and Zardoya R. 2004a Phylogenetic relationships of discoglossid frogs (Amphibia: Anura: Discoglossidae) based on complete mitochondrial genomes and nuclear genes. / Gene 343, 357鈥?66.
  48. San Mauro D., Gower D. J., Oommen O. V., Wilkinson M., and Zardoya R. 2004b Phylogeny of caecilian amphibians (Gymnophiona) based on complete mitochondrial genomes and nuclear RAG1. / Mol. Phylogenet. Evol. 33, 413鈥?27. CrossRef
  49. Sano N., Kurabayashi A., Fujii T., Yonekawa H., and Sumida M. 2004 Complete nucleotide sequence and gene rearrangement of the mitochondrial genome of the bell-ring frog, / Buergeria buergeri (family Rhacophoridae). / Genes Genet. Syst. 79, 151鈥?63. CrossRef
  50. Sano N., Kurabayashi A., Fujii T., Yonekawa H. and Sumida M. 2005 Complete nucleotide sequence of the mitochondrial genome of the Schlegel鈥檚 tree frog, / Rhacophorus schlegelii (family Rhacophoridae): duplicated control regions and gene rearrangements. / Genes Genet. Syst. 80, 213鈥?24.
  51. Su X., Wu X. B., Yan P., Cao S. Y., and Hu Y. L. 2007 Rearrangement of a mitochondrial tRNA gene of the concave-eared torrent frog, / Amolops tormotus. / Gene 394, 25鈥?4. CrossRef
  52. Sumida M., Kanamori Y., Kaneda H., Kato Y., Hasegawa M. and Yonekawa H. 2001 Complete nucleotide sequence and rearrangement of the mitochondrial genome of the Japanese pond frog, / Rana nigromaculata. Genes Genet. Syst. 76 (5), 311鈥?25.
  53. Swofford D. L. 2002 / PAUP*: Phylogenetic analysis using parsimony (*and other methods), version 4.0b10. Sinaucer Associates, Sunderland, USA.
  54. Tamura K., Peterson D., Peterson N., Stecher G., Nei M., and Kumar S. 2011 MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. / Mol. Biol. Evol. 28, 2731鈥?739. CrossRef
  55. Wiens J. J., Sukumaran J., Pyron R. A., and Brown R. M. 2009 Evolutionary and biogeographic origins of high tropical diversity in old world frogs (Ranidae). / Evolution 63, 1217鈥?231. CrossRef
  56. Wolstenholme D. R. 1992 Animal mitochondrial DNA: structure and evolution. In / Mitochondrial genomes (ed. D. R. Wolstenholme and K. W. Jeon), pp.173鈥?16. Academic Press, New York, USA.
  57. Xia X. H. 2013 DAMBE5: a comprehensive software package for data analysis in molecular biology and evolution. / Mol. Biol. Evol. 30, 1720鈥?728.
  58. Yu D. N., Zhang J. Y., Zheng R. Q., and Shao C. 2012 The complete mitochondrial genome of / Hoplobatrachus rugulosus (Anura: Dicroglossidae). / Mitochondrial DNA 23, 336鈥?337. CrossRef
  59. Zhang J. F., Nie L. W., Wang Y., and Hu L. L. 2009 The complete mitochondrial genome of the large-headed frog, / Limnonectes bannaensis (Amphibia: Anura), and a novel gene organization in the vertebrate mtDNA. / Gene 442, 119鈥?27. CrossRef
  60. Zhang P., Liang D., Mao R. L., Hillis D. M., Wake D. B., and Cannatella D. C. 2013 Efficient sequencing of anuran mtDNAs and a mitogenomic exploration of the phylogeny and evolution of frogs. / Mol. Biol. Evol. 30, 1899鈥?915. CrossRef
  61. Zhang P., Zhou H., Chen Y. Q., Liu Y. F., and Qu L. H. 2005a Mitogenomic perspectives on the origin and phylogeny of living amphibians. / Syst. Biol. 54, 391鈥?00. CrossRef
  62. Zhang P., Zhou H., Liang D., Liu Y. F., Chen Y Q., and Qu L. H. 2005b The complete mitochondrial genome of a tree frog, / Polypedates megacephalus (Amphibia: Anura: Rhacophoridae),and a novel gene organization in living amphibians. / Gene 346, 133鈥?43. CrossRef
  63. Zhou Y., Zhang J. Y., Zheng R. Q., Yu B. G., and Yang G. 2009 Complete nucleotide sequence and gene organization of the mitochondrial genome of / Paa spinosa (Anura: Ranoidae). / Gene 447, 86鈥?6. CrossRef</sup>
  
• 刊物主题：Life Sciences, general; Microbial Genetics and Genomics; Plant Genetics & Genomics; Animal Genetics and Genomics; Evolutionary Biology;
• 出版者：Springer India
• ISSN：0973-7731

文摘

In this study, the complete nucleotide sequence (18,321 bp) of the mitochondrial (mt) genome of the round-tongued floating frog, Occidozyga martensii was determined. Although, the base composition and codon usage of O. martensii conformed to the typical vertebrate patterns, this mt genome contained 23 tRNAs (a tandem duplication of tRNA-Met gene). The LTPF tRNA-gene cluster, and the derived position of the ND5 gene downstream of the control region, were present in this mitogenome. Moreover, we found that in the WANCY tRNA-gene cluster, the tRNA-Asn gene was located between the tRNA-Tyr and COI genes instead of between the tRNA-Ala and tRNA-Cys genes which is a novel mtDNA gene rearrangement in vertebrates. Based on the concatenated nucleotide sequences of the 13 protein-coding genes, phylogenetic analysis (BI, ML, MP) was performed to further clarify the phylogenetic relations of this species within anurans.