Skip to main content
NCBI home page
Genetics logoLink to Genetics
. 1999 Dec;153(4):1851–1862. doi: 10.1093/genetics/153.4.1851

Complete DNA sequence of the mitochondrial genome of the ascidian Halocynthia roretzi (Chordata, Urochordata).

S i Yokobori 1, T Ueda 1, G Feldmaier-Fuchs 1, S Pääbo 1, R Ueshima 1, A Kondow 1, K Nishikawa 1, K Watanabe 1
PMCID: PMC1460873  PMID: 10581290

Abstract

The complete nucleotide sequence of the 14,771-bp-long mitochondrial (mt) DNA of a urochordate (Chordata)-the ascidian Halocynthia roretzi-was determined. All the Halocynthia mt-genes were found to be located on a single strand, which is rich in T and G rather than in A and C. Like nematode and Mytilus edulis mtDNAs, that of Halocynthia encodes no ATP synthetase subunit 8 gene. However, it does encode an additional tRNA gene for glycine (anticodon TCT) that enables Halocynthia mitochondria to use AGA and AGG codons for glycine. The mtDNA carries an unusual tRNA(Met) gene with a TAT anticodon instead of the usual tRNA(Met)(CAT) gene. As in other metazoan mtDNAs, there is not any long noncoding region. The gene order of Halocynthia mtDNA is completely different from that of vertebrate mtDNAs except for tRNA(His)-tRNA(Ser)(GCU), suggesting that evolutionary change in the mt-gene structure is much accelerated in the urochordate line compared with that in vertebrates. The amino acid sequences of Halocynthia mt-proteins deduced from their gene sequences are quite different from those in other metazoans, indicating that the substitution rate in Halocynthia mt-protein genes is also accelerated.

Full Text

The Full Text of this article is available as a PDF (180.4 KB).

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Anderson S., Bankier A. T., Barrell B. G., de Bruijn M. H., Coulson A. R., Drouin J., Eperon I. C., Nierlich D. P., Roe B. A., Sanger F. Sequence and organization of the human mitochondrial genome. Nature. 1981 Apr 9;290(5806):457–465. doi: 10.1038/290457a0. [DOI] [PubMed] [Google Scholar]
  2. Asakawa S., Himeno H., Miura K., Watanabe K. Nucleotide sequence and gene organization of the starfish Asterina pectinifera mitochondrial genome. Genetics. 1995 Jul;140(3):1047–1060. doi: 10.1093/genetics/140.3.1047. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Asakawa S., Kumazawa Y., Araki T., Himeno H., Miura K., Watanabe K. Strand-specific nucleotide composition bias in echinoderm and vertebrate mitochondrial genomes. J Mol Evol. 1991 Jun;32(6):511–520. doi: 10.1007/BF02102653. [DOI] [PubMed] [Google Scholar]
  4. Attardi G. Animal mitochondrial DNA: an extreme example of genetic economy. Int Rev Cytol. 1985;93:93–145. doi: 10.1016/s0074-7696(08)61373-x. [DOI] [PubMed] [Google Scholar]
  5. Boore J. L., Brown W. M. Complete DNA sequence of the mitochondrial genome of the black chiton, Katharina tunicata. Genetics. 1994 Oct;138(2):423–443. doi: 10.1093/genetics/138.2.423. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Boore J. L., Collins T. M., Stanton D., Daehler L. L., Brown W. M. Deducing the pattern of arthropod phylogeny from mitochondrial DNA rearrangements. Nature. 1995 Jul 13;376(6536):163–165. doi: 10.1038/376163a0. [DOI] [PubMed] [Google Scholar]
  7. Börner G. V., Mörl M., Janke A., Päbo S. RNA editing changes the identity of a mitochondrial tRNA in marsupials. EMBO J. 1996 Nov 1;15(21):5949–5957. [PMC free article] [PubMed] [Google Scholar]
  8. Cantatore P., Gadaleta M. N., Roberti M., Saccone C., Wilson A. C. Duplication and remoulding of tRNA genes during the evolutionary rearrangement of mitochondrial genomes. 1987 Oct 29-Nov 4Nature. 329(6142):853–855. doi: 10.1038/329853a0. [DOI] [PubMed] [Google Scholar]
  9. Cantatore P., Roberti M., Rainaldi G., Gadaleta M. N., Saccone C. The complete nucleotide sequence, gene organization, and genetic code of the mitochondrial genome of Paracentrotus lividus. J Biol Chem. 1989 Jul 5;264(19):10965–10975. [PubMed] [Google Scholar]
  10. Clary D. O., Wolstenholme D. R. The mitochondrial DNA molecular of Drosophila yakuba: nucleotide sequence, gene organization, and genetic code. J Mol Evol. 1985;22(3):252–271. doi: 10.1007/BF02099755. [DOI] [PubMed] [Google Scholar]
  11. Clayton D. A. Transcription and replication of animal mitochondrial DNAs. Int Rev Cytol. 1992;141:217–232. doi: 10.1016/s0074-7696(08)62067-7. [DOI] [PubMed] [Google Scholar]
  12. Crozier R. H., Crozier Y. C. The mitochondrial genome of the honeybee Apis mellifera: complete sequence and genome organization. Genetics. 1993 Jan;133(1):97–117. doi: 10.1093/genetics/133.1.97. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. De Giorgi C., Martiradonna A., Lanave C., Saccone C. Complete sequence of the mitochondrial DNA in the sea urchin Arbacia lixula: conserved features of the echinoid mitochondrial genome. Mol Phylogenet Evol. 1996 Apr;5(2):323–332. doi: 10.1006/mpev.1996.0027. [DOI] [PubMed] [Google Scholar]
  14. Desjardins P., Morais R. Sequence and gene organization of the chicken mitochondrial genome. A novel gene order in higher vertebrates. J Mol Biol. 1990 Apr 20;212(4):599–634. doi: 10.1016/0022-2836(90)90225-B. [DOI] [PubMed] [Google Scholar]
  15. Durrheim G. A., Corfield V. A., Harley E. H., Ricketts M. H. Nucleotide sequence of cytochrome oxidase (subunit III) from the mitochondrion of the tunicate Pyura stolonifera: evidence that AGR encodes glycine. Nucleic Acids Res. 1993 Jul 25;21(15):3587–3588. doi: 10.1093/nar/21.15.3587. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Flook P. K., Rowell C. H., Gellissen G. The sequence, organization, and evolution of the Locusta migratoria mitochondrial genome. J Mol Evol. 1995 Dec;41(6):928–941. doi: 10.1007/BF00173173. [DOI] [PubMed] [Google Scholar]
  17. Green R., Noller H. F. Ribosomes and translation. Annu Rev Biochem. 1997;66:679–716. doi: 10.1146/annurev.biochem.66.1.679. [DOI] [PubMed] [Google Scholar]
  18. Hatzoglou E., Rodakis G. C., Lecanidou R. Complete sequence and gene organization of the mitochondrial genome of the land snail Albinaria coerulea. Genetics. 1995 Aug;140(4):1353–1366. doi: 10.1093/genetics/140.4.1353. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Himeno H., Masaki H., Kawai T., Ohta T., Kumagai I., Miura K., Watanabe K. Unusual genetic codes and a novel gene structure for tRNA(AGYSer) in starfish mitochondrial DNA. Gene. 1987;56(2-3):219–230. doi: 10.1016/0378-1119(87)90139-9. [DOI] [PubMed] [Google Scholar]
  20. Hoffmann R. J., Boore J. L., Brown W. M. A novel mitochondrial genome organization for the blue mussel, Mytilus edulis. Genetics. 1992 Jun;131(2):397–412. doi: 10.1093/genetics/131.2.397. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Jacobs H. T., Elliott D. J., Math V. B., Farquharson A. Nucleotide sequence and gene organization of sea urchin mitochondrial DNA. J Mol Biol. 1988 Jul 20;202(2):185–217. doi: 10.1016/0022-2836(88)90452-4. [DOI] [PubMed] [Google Scholar]
  22. Janke A., Feldmaier-Fuchs G., Thomas W. K., von Haeseler A., Päbo S. The marsupial mitochondrial genome and the evolution of placental mammals. Genetics. 1994 May;137(1):243–256. doi: 10.1093/genetics/137.1.243. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Janke A., Gemmell N. J., Feldmaier-Fuchs G., von Haeseler A., Päbo S. The mitochondrial genome of a monotreme--the platypus (Ornithorhynchus anatinus). J Mol Evol. 1996 Feb;42(2):153–159. doi: 10.1007/BF02198841. [DOI] [PubMed] [Google Scholar]
  24. Janke A., Päbo S. Editing of a tRNA anticodon in marsupial mitochondria changes its codon recognition. Nucleic Acids Res. 1993 Apr 11;21(7):1523–1525. doi: 10.1093/nar/21.7.1523. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Kondow A., Yokobori S., Ueda T., Watanabe K. Ascidian mitochondrial tRNA(Met) possessing unique structural characteristics. Nucleosides Nucleotides. 1998 Jan-Mar;17(1-3):531–539. [PubMed] [Google Scholar]
  26. Kumazawa Y., Yokogawa T., Hasegawa E., Miura K., Watanabe K. The aminoacylation of structurally variant phenylalanine tRNAs from mitochondria and various nonmitochondrial sources by bovine mitochondrial phenylalanyl-tRNA synthetase. J Biol Chem. 1989 Aug 5;264(22):13005–13011. [PubMed] [Google Scholar]
  27. Kyte J., Doolittle R. F. A simple method for displaying the hydropathic character of a protein. J Mol Biol. 1982 May 5;157(1):105–132. doi: 10.1016/0022-2836(82)90515-0. [DOI] [PubMed] [Google Scholar]
  28. Mörl M., Dörner M., Päbo S. C to U editing and modifications during the maturation of the mitochondrial tRNA(Asp) in marsupials. Nucleic Acids Res. 1995 Sep 11;23(17):3380–3384. doi: 10.1093/nar/23.17.3380. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Ojala D., Montoya J., Attardi G. tRNA punctuation model of RNA processing in human mitochondria. Nature. 1981 Apr 9;290(5806):470–474. doi: 10.1038/290470a0. [DOI] [PubMed] [Google Scholar]
  30. Okimoto R., Chamberlin H. M., Macfarlane J. L., Wolstenholme D. R. Repeated sequence sets in mitochondrial DNA molecules of root knot nematodes (Meloidogyne): nucleotide sequences, genome location and potential for host-race identification. Nucleic Acids Res. 1991 Apr 11;19(7):1619–1626. doi: 10.1093/nar/19.7.1619. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Okimoto R., Macfarlane J. L., Wolstenholme D. R. The mitochondrial ribosomal RNA genes of the nematodes Caenorhabditis elegans and Ascaris suum: consensus secondary-structure models and conserved nucleotide sets for phylogenetic analysis. J Mol Evol. 1994 Dec;39(6):598–613. doi: 10.1007/BF00160405. [DOI] [PubMed] [Google Scholar]
  32. Perna N. T., Kocher T. D. Patterns of nucleotide composition at fourfold degenerate sites of animal mitochondrial genomes. J Mol Evol. 1995 Sep;41(3):353–358. doi: 10.1007/BF00186547. [DOI] [PubMed] [Google Scholar]
  33. Ramón Valverde J., Batuecas B., Moratilla C., Marco R., Garesse R. The complete mitochondrial DNA sequence of the crustacean Artemia franciscana. J Mol Evol. 1994 Oct;39(4):400–408. doi: 10.1007/BF00160272. [DOI] [PubMed] [Google Scholar]
  34. Roe B. A., Ma D. P., Wilson R. K., Wong J. F. The complete nucleotide sequence of the Xenopus laevis mitochondrial genome. J Biol Chem. 1985 Aug 15;260(17):9759–9774. [PubMed] [Google Scholar]
  35. Saiki R. K., Gelfand D. H., Stoffel S., Scharf S. J., Higuchi R., Horn G. T., Mullis K. B., Erlich H. A. Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase. Science. 1988 Jan 29;239(4839):487–491. doi: 10.1126/science.2448875. [DOI] [PubMed] [Google Scholar]
  36. Saitou N., Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol. 1987 Jul;4(4):406–425. doi: 10.1093/oxfordjournals.molbev.a040454. [DOI] [PubMed] [Google Scholar]
  37. Sasuga J., Yokobori S., Kaifu M., Ueda T., Nishikawa K., Watanabe K. Gene contents and organization of a mitochondrial DNA segment of the squid Loligo bleekeri. J Mol Evol. 1999 Jun;48(6):692–702. doi: 10.1007/pl00006513. [DOI] [PubMed] [Google Scholar]
  38. Steinberg S., Gautheret D., Cedergren R. Fitting the structurally diverse animal mitochondrial tRNAs(Ser) to common three-dimensional constraints. J Mol Biol. 1994 Mar 4;236(4):982–989. doi: 10.1016/0022-2836(94)90004-3. [DOI] [PubMed] [Google Scholar]
  39. Terrett J. A., Miles S., Thomas R. H. Complete DNA sequence of the mitochondrial genome of Cepaea nemoralis (Gastropoda: Pulmonata). J Mol Evol. 1996 Feb;42(2):160–168. doi: 10.1007/BF02198842. [DOI] [PubMed] [Google Scholar]
  40. 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 Dec 15;25(24):4876–4882. doi: 10.1093/nar/25.24.4876. [DOI] [PMC free article] [PubMed] [Google Scholar]
  41. Thompson J. D., Higgins D. G., Gibson T. J. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 1994 Nov 11;22(22):4673–4680. doi: 10.1093/nar/22.22.4673. [DOI] [PMC free article] [PubMed] [Google Scholar]
  42. Wada H., Satoh N. Details of the evolutionary history from invertebrates to vertebrates, as deduced from the sequences of 18S rDNA. Proc Natl Acad Sci U S A. 1994 Mar 1;91(5):1801–1804. doi: 10.1073/pnas.91.5.1801. [DOI] [PMC free article] [PubMed] [Google Scholar]
  43. Wakita K., Watanabe Y., Yokogawa T., Kumazawa Y., Nakamura S., Ueda T., Watanabe K., Nishikawa K. Higher-order structure of bovine mitochondrial tRNA(Phe) lacking the 'conserved' GG and T psi CG sequences as inferred by enzymatic and chemical probing. Nucleic Acids Res. 1994 Feb 11;22(3):347–353. doi: 10.1093/nar/22.3.347. [DOI] [PMC free article] [PubMed] [Google Scholar]
  44. Watanabe Y., Tsurui H., Ueda T., Furushima R., Takamiya S., Kita K., Nishikawa K., Watanabe K. Primary and higher order structures of nematode (Ascaris suum) mitochondrial tRNAs lacking either the T or D stem. J Biol Chem. 1994 Sep 9;269(36):22902–22906. [PubMed] [Google Scholar]
  45. Yamazaki N., Ueshima R., Terrett J. A., Yokobori S., Kaifu M., Segawa R., Kobayashi T., Numachi K., Ueda T., Nishikawa K. Evolution of pulmonate gastropod mitochondrial genomes: comparisons of gene organizations of Euhadra, Cepaea and Albinaria and implications of unusual tRNA secondary structures. Genetics. 1997 Mar;145(3):749–758. doi: 10.1093/genetics/145.3.749. [DOI] [PMC free article] [PubMed] [Google Scholar]
  46. Yokogawa T., Watanabe Y., Kumazawa Y., Ueda T., Hirao I., Miura K., Watanabe K. A novel cloverleaf structure found in mammalian mitochondrial tRNA(Ser) (UCN). Nucleic Acids Res. 1991 Nov 25;19(22):6101–6105. doi: 10.1093/nar/19.22.6101. [DOI] [PMC free article] [PubMed] [Google Scholar]

Articles from Genetics are provided here courtesy of Oxford University Press

RESOURCES