Journal of Molecular Evolution

, Volume 58, Issue 4, pp 376–389 | Cite as

Complete mtDNA of Ciona intestinalis Reveals Extensive Gene Rearrangement and the Presence of an atp8 and an Extra trnM Gene in Ascidians



The complete mitochondrial genome (mtDNA) of the model organism Ciona intestinalis (Urochordata, Ascidiacea) has been amplified by long-PCR using specific primers designed on putative mitochondrial transcripts identified from publicly available mitochondrial-like expressed sequence tags. The C. intestinalis mtDNA encodes 39 genes: 2 rRNAs, 13 subunits of the respiratory complexes, including ATPase subunit 8 (atp8), and 24 tRNAs, including 2 tRNA-Met with anticodons 5′-UAU-3′and 5′-CAU-3′, respectively. All genes are transcribed from the same strand. This gene content seems to be a common feature of ascidian mtDNAs, as we have verified the presence of a previously undetected atp8 and of two trnM genes in the two other sequenced ascidian mtDNAs. Extensive gene rearrangement has been found in C. intestinalis with respect not only to the common Vertebrata/Cephalochordata/Hemichordata gene organization but also to other ascidian mtDNAs, including the cogeneric Ciona savignyi. Other features such as the absence of long noncoding regions, the shortness of rRNA genes, the low GC content (21.4%), and the absence of asymmetric base distribution between the two strands suggest that this genome is more similar to those of some protostomes than to deuterostomes.


ATP synthase subunit 8 Gene duplication Genome organization Gene rearrangement Mitochondrial genome Tunicates tRNA 


  1. 1.
    Aguinaldo, AM, Turbeville, JM, Linford, LS, Rivera, MC, Garey, JR, Raff, RA, Lake, JA 1997Evidence for a clade of nematodes, arthropods and other moulting animals.Nature387489493PubMedGoogle Scholar
  2. 2.
    Beagley, CT, Okimoto, R, Wolstenholme, DR 1999Mytilus mitochondrial DNA contains a functional gene for a tRNASer(UCN) with a dihydrouridine arm-replacement loop and a pseudo-tRNASer(UCN) gene.Genetics152641652PubMedGoogle Scholar
  3. 3.
    Benson, G 1999Tandem repeats finder: A program to analyze DNA sequences.Nucleic Acids Res27573580PubMedGoogle Scholar
  4. 4.
    Blanchette, M, Kunisawa, T, Sankoff, D 1999Gene order breakpoint evidence in animal mitochondrial phylogeny.J Mol Evol49193203PubMedGoogle Scholar
  5. 5.
    Boore, JL 1999Animal mitochondrial genomes.Nucleic Acids Res2717671780CrossRefPubMedGoogle Scholar
  6. 6.
    Boore, JL 2001Complete mitochondrial genome sequence of the polychaete annelid Platynereis dumerilii.Mol Biol Evol1814131416PubMedGoogle Scholar
  7. 7.
    Boore, JL, Daehler, LL, Brown, WM 1999Complete sequence, gene arrangement, and genetic code of mitochondrial DNA of the cephalochordate Branchiostoma floridae (Amphioxus).Mol Biol Evol16410418PubMedGoogle Scholar
  8. 8.
    Cameron, CB, Garey, JR, Swalla, BJ 2000Evolution of the chordate body plan: new insights from phylogenetic analyses of deuterostome phyla.Proc Natl Acad Sci USA9744694474PubMedGoogle Scholar
  9. 9.
    Cannone, JJ, Subramanian, S, Schnare, MN, Collett, JR, D’Souza, LM, Du, Y, Feng, B, Lin, N, Madabusi, LV, Muller, KM, Pande, N, Shang, Z, Yu, N, Gutell, RR 2002The Comparative RNA Web (CRW) site: An online database of comparative sequence and structure information for ribosomal, intron, and other RNAs: Correction.BMC Bioinform315CrossRefGoogle Scholar
  10. 10.
    Cantatore, P, Gadaleta, MN, Roberti, M, Saccone, C, Wilson, AC 1987Duplication and remoulding of tRNA genes during the evolutionary rearrangement of mitochondrial genomes.Nature329853855CrossRefPubMedGoogle Scholar
  11. 11.
    Christianson, TW, Clayton, DA 1986In vitro transcription of human mitochondrial DNA: Accurate termination.Proc Natl Acad Sci USA8362776281PubMedGoogle Scholar
  12. 12.
    Copello, M, Devos, L, Lafargue, F 1981Ciona edwardsi (Roule, 1886) espèce littorale de méditerranée distincte de Ciona intestinalis Linné, 1767.Vie Milieu31243253Google Scholar
  13. 13.
    Cserzo, M, Wallin, E, Simon, I, von Heijne, G, Elofsson, A 1997Prediction of transmembrane alpha-helices in procariotic membrane proteins: The dense alignment surface method.Prot Eng10673676CrossRefGoogle Scholar
  14. 14.
    Dehal, P, Satou, Y, Campbell, RK, Chapman, J, Degnan, B, De Tomaso, A, Davidson, B, Di Gregorio, A, Gelpke, M, Goodstein, DM, Harafuji, N, Hastings, KE, Ho, I, Hotta, K, Huang, W, Kawashima, T, Lemaire, P, Martinez, D, Meinertzhagen, IA, Necula, S, Nonaka, M, Putnam, N, Rash, S, Saiga, H, Satake, M, Terry, A, Yamada, L, Wang, HG, Awazu, S, Azumi, K, Boore, J, Branno, M, Chin-Bow, S, DeSantis, R, Doyle, S, Francino, P, Keys, DN, Haga, S, Hayashi, H, Hino, K, Imai, KS, Inaba, K, Kano, S, Kobayashi, K, Kobayashi, M, Lee, BI, Makabe, KW, Manohar, C, Matassi, G, Medina, M, Mochizuki, Y, Mount, S, Morishita, T, Miura, S, Nakayama, A, Nishizaka, S, Nomoto, H, Ohta, F, Oishi, K, Rigoutsos, I, Sano, M, Sasaki, A, Sasakura, Y, Shoguchi, E, Shin-i, T, Spagnuolo, A, Stainier, D, Suzuki, MM, Tassy, O, Takatori, N, Tokuoka, M, Yagi, K, Yoshizaki, F, Wada, S, Zhang, C, Hyatt, PD, Larimer, F, Detter, C, Doggett, N, Glavina, T, Hawkins, T, Richardson, P, Lucas, S, Kohara, Y, Levine, M, Satoh, N, Rokhsar, DS 2002The draft genome of Ciona intestinalis: insights into chordate and vertebrate origins.Science29821572167CrossRefPubMedGoogle Scholar
  15. 15.
    Devenish, RJ, Papakonstantinou, T, Galanis, M, Law, RH, Linnane, AW, Nagley, P 1992Structure/function analysis of yeast mitochondrial ATP synthase subunit 8.Ann NY Acad Sci671403414PubMedGoogle Scholar
  16. 16.
    Durrheim, GA, Corfield, VA, Harley, EH, Ricketts, MH 1993Nucleotide sequence of cytochrome oxidase (subunit III) from the mitochondrion of the tunicate Pyura stolonifera: Evidence that AGR encodes glycine.Nucleic Acids Res2135873588PubMedGoogle Scholar
  17. 17.
    Fearnley, IM, Walker, JE 1986Two overlapping genes in bovine mitochondrial DNA encode membrane components of ATP synthase.EMBO J520032008PubMedGoogle Scholar
  18. 18.
    Foury, F, Roganti, T, Lecrenier, N, Purnelle, B 1998The complete sequence of the mitochondrial genome of Saccharomyces cerevisiae.FEBS Lett440325313PubMedGoogle Scholar
  19. 19.
    Gissi, C, Pesole, G 2003Transcript mapping and genome annotation of ascidian mtDNA using EST data.Genome Res1322032212CrossRefPubMedGoogle Scholar
  20. 20.
    Gray, MW, Lang, BF, Cedergren, R, Golding, GB, Lemieux, C, Sankoff, D, Turmel, M, Brossard, N, Delage, E, Littlejohn, TG, Plante, I, Rioux, P, Saint-Louis, D, Zhu, Y, Burger, G 1998Genome structure and gene content in protist mitochondrial DNAs.Nucleic Acids Res26865878PubMedGoogle Scholar
  21. 21.
    Grillo, G, Attimonelli, M, Liuni, S, Pesole, G 1996CLEANUP: A fast computer program for removing redundancies from nucleotide.Comput Appl Biosci1218PubMedGoogle Scholar
  22. 22.
    Hixson, JE, Wong, TW, Clayton, DA 1986Both 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 Chem26123842093PubMedGoogle Scholar
  23. 23.
    Hoffmann, RJ, Boore, JL, Brown, WM 1992A novel mitochondrial genome organization for the blue mussel, Mytilus edulis.Genetics131397412PubMedGoogle Scholar
  24. 24.
    Holland, PWH, Garcia-Fernàndez, J, Williams, NA, Sidow, A 1994Gene duplications and the origins of vertebrate development.Development1994125133Google Scholar
  25. 25.
    Hoshino, Z, Nishikawa, T 1985Taxonomic studies of Ciona intestinalis (L.) and its allies.Publ Seto Mar Biol Lab106179Google Scholar
  26. 26.
    Hu, M, Chilton, NB, Gasser, RB 2002The mitochondrial genomes of the human hookworms, Ancylostoma duodenale and Necator americanus (Nematoda: Secernentea).Int J Parasitol32145158CrossRefPubMedGoogle Scholar
  27. 27.
    Jacobs, HT, Balfe, P, Cohen, B, Farquharson, A, Comito, L 1988

    Phylogenetic implications of genome rearrangement and sequence evolution in echinoderm mitochondrial DNA.

    Paul, CRCSmith, AB eds. Echinoderm phylogeny and evolutionary biology.Clarendon PressOxford121137
    Google Scholar
  28. 28.
    Kakuda, T 2001

    Mitochondrial DNA analysis of Boltenia echinata ibuki (OKA, 1934).

    Sawada, HYokosawa, HLambert, CC eds. The biology of ascidians.Springer-VerlagTokyo283289
    Google Scholar
  29. 29.
    Kondow, A, Yokobori, S, Ueda, T, Watanabe, K 1998Ascidian mitochondrial tRNA(Met) possessing unique structural characteristics.Nucleosides Nucleotides17531539PubMedGoogle Scholar
  30. 30.
    Kumazawa, Y, Nishida, M 1993Sequence evolution of mitochondrial tRNA genes and deep-branch animal phylogenetics.J Mol Evol37380398PubMedGoogle Scholar
  31. 31.
    Lambert, C, Lafargue, F, Lambert, G 1990Preliminary note on the genetic isolation of Ciona species (Ascidiacea, Urochordata).Vie Milieu40293295Google Scholar
  32. 32.
    Lambert, G 2001

    A global overview os ascidian introductions and their possible impact on the endemic fauna.

    Sawada, HYokosawa, HLambert, CC eds. The biology of ascidians.Springer-VerlagTokyo249257
    Google Scholar
  33. 33.
    Lavrov, DV, Brown, WM 2001Trichinella spiralis mtDNA: A nematode mitochondrial genome that encodes a putative ATP8 and normally structured tRNAS and has a gene arrangement relatable to those of coelomate metazoans.Genetics157621637PubMedGoogle Scholar
  34. 34.
    Le, TH, Blair, D, Agatsuma, T, Humair, P-F, Campbell, NJH, Iwagami, M, Littlewood, DT, Peacock, B, Johnston, DA, Bartley, J, Rollinson, D, Herniou, EA, Zarlenga, DS, McManus, DP 2000Phylogenies inferred from mitochondrial gene orders-a cautionary tale from.Mol Biol Evol1711231125PubMedGoogle Scholar
  35. 35.
    Lowe, TM, Eddy, SR 1997tRNAscan-SE: A program for improved detection of transfer RNA genes in genomic sequence.Nucleic Acids Res25955964PubMedGoogle Scholar
  36. 36.
    Macey, JR, Schulte, JA, 2n, Larson, A, Tuniyev, BS, Orlov, N, Papenfuss, TJ 1999Molecular phylogenetics, tRNA evolution, and historical biogeography in anguid lizards and related taxonomic families.Mol Phylogenet Evol12250227CrossRefPubMedGoogle Scholar
  37. 37.
    Ohno, S 1970Evolution by gene duplication.George Allen and UnwinLondonGoogle Scholar
  38. 38.
    Papakonstantinou, T, Galanis, M, Nagley, P, Devenish, RJ 1993Each of three positively-charged amino acids in the C-terminal region of yeast mitochondrial ATP synthase subunit 8 is required for assembly.Biochim Biophys Acta11442232CrossRefPubMedGoogle Scholar
  39. 39.
    Papakonstantinou, T, Law, RH, Nagley, P, Devenish, RJ 1996aNon-functional variants of yeast mitochondrial ATP synthase subunit 8 that assemble into the complex.Biochem Mol Biol Int39253260Google Scholar
  40. 40.
    Papakonstantinou, T, Law, RH, Nesbitt, WS, Nagley, P, Devenish, RJ 1996bMolecular genetic analysis of the central hydrophobic domain of subunit 8 of yeast mitochondrial ATP synthase.Curr Genet301218CrossRefGoogle Scholar
  41. 41.
    Perna, NT, Kocher, TD 1995Patterns of nucleotide composition at fourfold degenerate sites of animal mitochondrial genomes.J Mol Evol41353358PubMedGoogle Scholar
  42. 42.
    Pesole, G, Attimonelli, M, Saccone, C 1996Linguistic analysis of nucleotide sequences: Algorithms for pattern recognition and analysis of codon strategy.Methods Enzymol266281294PubMedGoogle Scholar
  43. 43.
    Pesole, G, Liuni, S, D’Souza, M 2000PatSearch: A pattern matcher software that finds functional elements in nucleotide and protein sequences and assesses their statistical significance.Bioinformatics16439450Google Scholar
  44. 44.
    Peterson, KJ, Eernisse, DJ 2001Animal phylogeny and the ancestry of bilaterians: Inferences from morphology and 18S rDNA gene sequences.Evol Dev3170205CrossRefPubMedGoogle Scholar
  45. 45.
    Rajbhandary, U, Chow, MC 1995

    Initiator tRNAs and initiation of protein synthesis.

    Soll, DRajbhandary, U eds. tRNA structure, biosynthesis and function.American Society of MicrobiologyWashington, DC511528
    Google Scholar
  46. 46.
    Reyes, A, Gissi, C, Pesole, G, Saccone, C 1998Evolution of asymmetric base composition in the mitochondrial genome of mammals.Mol Biol Evol15957966PubMedGoogle Scholar
  47. 47.
    Saccone, C, Sbisà, E 1994

    The evolution of the mitochondrial genome.

    Bittar, EE eds. Principles of medical biology.JAI PressGreenwich, CT3972
    Google Scholar
  48. 48.
    Saccone, C, De Giorgi, C, Gissi, C, Pesole, G, Reyes, A 1999Evolutionary genomics in Metazoa: The mitochondrial DNA as model system.Gene238195209CrossRefPubMedGoogle Scholar
  49. 49.
    Satoh, N 1994Developmental biology of ascidians.Cambridge University PressNew YorkGoogle Scholar
  50. 50.
    Satou, Y, Takatori, N, Fujiwara, S, Nishikata, T, Saiga, H, Kusakabe, T, Shin-i, T, Kohara, Y, Satoh, N 2002Ciona intestinalis cDNA projects: Expressed sequence tag analyses and gene expression profiles during embryogenesis.Gene2878396PubMedGoogle Scholar
  51. 51.
    Seutin, G, Lang, BF, Mindell, DP, Morais, R 1994Evolution of the WANCY region in amniote mitochondrial DNA.Mol Biol Evol11329340PubMedGoogle Scholar
  52. 52.
    Shu, DG, Chen, L, Han, J, Zhang, XL 2001An Early Cambrian tunicate from China.Nature411472473CrossRefPubMedGoogle Scholar
  53. 53.
    Sprinzl, M, Horn, C, Brown, M, Ioudovitch, A, Steinberg, S 1998Compilation of tRNA sequences and sequences of tRNA genes.Nucleic Acids Res26148153PubMedGoogle Scholar
  54. 54.
    Spruyt, N, Delarbre, C, Gachelin, G, Laudet, V 1998Complete sequence of the amphioxus (Branchiostoma lanceolatum) mitochondrial genome: relations to vertebrates.Nucleic Acids Res2632793285CrossRefPubMedGoogle Scholar
  55. 55.
    Stach, T, Turbeville, JM 2002Phylogeny of Tunicata inferred from molecular and morphological characters.Mol Phylogenet Evol25408428CrossRefPubMedGoogle Scholar
  56. 56.
    Stephens, AN, Khan, MA, Roucou, X, Nagley, P, Devenish, RJ 2003The molecular neighborhood of subunit 8 of yeast mitochondrial F1F0-ATP synthase probed by cysteine scanning mutagenesis and chemical modification.J Biol Chem2781786717875CrossRefPubMedGoogle Scholar
  57. 57.
    Swalla, B 2001

    Phylogeny of the Urochordates: Implications for Chordata evolution.

    Sawada, HYokosawa, HLambert, CC eds. The biology of ascidians.Springer-VerlagTokyo219224
    Google Scholar
  58. 58.
    Swalla, BJ, Cameron, CB, Corley, LS, Garey, JR 2000Urochordates are monophyletic within the deuterostomes.Syst Biol495264CrossRefPubMedGoogle Scholar
  59. 59.
    Tomita, K, Ueda, T, Ishiwa, S, Crain, PF, McCloskey, JA, Watanabe, K 1999Codon reading patterns in Drosophila melanogaster mitochondria based on their tRNA sequences: A unique wobble rule in animal mitochondria.Nucleic Acids Res2742914297CrossRefPubMedGoogle Scholar
  60. 60.
    Turbeville, JM, Schulz, JR, Raff, RA 1994Deuterostome phylogeny and the sister group of the chordates: Evidence from molecules and morphology.Mol Biol Evol11648655PubMedGoogle Scholar
  61. 61.
    Valverde, JR, Marco, R, Garesse, R 1994A conserved heptamer motif for ribosomal RNA transcription termination in animal mitochondria.Proc Natl Acad Sci USA9153685371PubMedGoogle Scholar
  62. 62.
    Wolstenholme, DR 1992Animal mitochondrial DNA: structure and evolution.Int Rev Cytol141173216PubMedGoogle Scholar
  63. 63.
    Yokobori, S, Ueda, T, Watanabe, K 1993Codons AGA and AGG are read as glycine in ascidian mitochondria.J Mol Evol3618PubMedGoogle Scholar
  64. 64.
    Yokobori, S, Ueda, T, Feldmaier-Fuchs, G, Paabo, S, Ueshima, R, Kondow, A, Nishikawa, K, Watanabe, K 1999Complete DNA sequence of the mitochondrial genome of the ascidian Halocynthia roretzi (Chordata, Urochodata).Genetics15318511862Google Scholar
  65. 65.
    Yokobori, S, Suzuki, T, Watanabe, K 2001Genetic code variations in mitochondria: tRNA as a major determinant of genetic code plasticity.J Mol Evol53314326CrossRefPubMedGoogle Scholar
  66. 66.
    Zardoya, R, Meyer, A 1996The complete nucleotide sequence of the mitochondrial genome of the lungfish (Protopterus dolloi) supports its phylogenetic position as a close relative of land vertebrates.Genetics14212491263PubMedGoogle Scholar
  67. 67.
    Zhang, A 1987Fossil appendicularians in the early Cambrian.Sci Sinica (B)30888896Google Scholar
  68. 68.
    Winchell, CJ, Sullivan, J, Cameron, CB, Swalla, BJ, Mallatt, J 2002Evaluating hypotheses of deuterostome phylogeny and chordate evolution with new LSU and SSU ribosomal DNA data.Mol Biol Evol19762776PubMedGoogle Scholar

Copyright information

© Springer-Verlag New York Inc. 2004

Authors and Affiliations

  • Carmela Gissi
    • 1
  • Fabio Iannelli
    • 1
  • Graziano Pesole
    • 1
  1. 1.Dipartimento di Scienze Biomolecolari e BiotecnologieUniversità di Milano, Via Celoria 26, 20133 MilanoItaly

Personalised recommendations