Abstract
The complete nucleotide sequence of the urochordate Ciona savignyi (Ascidiacea, Enterogona) mitochondrial (mt) genome (14,737 bp) was determined. The Ciona mt genome does not encode a gene for ATP synthetase subunit 8 but encodes an additional tRNAGly gene (anticodon UCU), as is the case in another urochordate, Halocynthia roretzi (Ascidiacea, Pleurogona), mt genome. In addition, the Ciona mt genome encodes two tRNAMet genes; anticodon CAT and anticodon TAT. The tRNACys gene is thought to lack base pairs at the D-stem. Thus, the Ciona mt genome encodes 12 protein, 2 rRNA, and 24 tRNA genes. The gene arrangement of the Ciona mt genome differs greatly from those of any other metazoan mt genomes reported to date. Only three gene boundaries are shared between the Halocynthia and the Ciona mt genomes. Molecular phylogenetic analyses based on amino acid sequences of mt protein genes failed to demonstrate the monophyly of the chordates.




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References
J Adachi M Hasegawa (1996) MOLPHY 2.3b. Institute of Statistical Mathematics Tokyo
S Anderson AT Bankier BG Barrell MH de Bruijn AR Coulson J Drouin IC Eperon DP Nierlich BA Roe F Sanger PH Schreier AJ Smith R Staden IG Young (1981) ArticleTitleSequence and organization of the human mitochondrial genome. Nature 290 457–465 Occurrence Handle1:CAS:528:DyaL3MXlt1OlsL8%3D Occurrence Handle7219534 Occurrence Handle10.1038/290457a0
S Asakawa H Himeno K Miura K Watanabe (1995) ArticleTitleNucleotide sequence and gene organization of the starfish Asterina pectinifera mitochondrial genome. Genetics 140 1047–1060 Occurrence Handle1:CAS:528:DyaK28Xht1Gjtbs%3D Occurrence Handle7672576 Occurrence Handle1206660 Occurrence Handle10.1093/genetics/140.3.1047
WM Barnes (1994) ArticleTitlePCR amplification of up to 35-kb DNA with high fidelity and high yield from lambda bacteriophage templates. Proc Natl Acad Sci USA 91 2216–2220 Occurrence Handle1:CAS:528:DyaK2cXivFSqsL8%3D Occurrence Handle8134376 Occurrence Handle43341 Occurrence Handle10.1073/pnas.91.6.2216
CT Beagley R Okimoto DR Wolstenholme (1998) ArticleTitleThe mitochondrial genome of the sea anemone Metridium senile (Cnidaria): Introns, a paucity of tRNA genes, and a near-standard genetic code. Genetics 148 1091–1108 Occurrence Handle1:CAS:528:DyaK1cXks1eit7o%3D Occurrence Handle9539427 Occurrence Handle1460033 Occurrence Handle10.1093/genetics/148.3.1091
JL Boore (1999) ArticleTitleAnimal mitochondrial genomes. Nucleic Acids Res 27 1767–1780 Occurrence Handle1:CAS:528:DyaK1MXivVersbo%3D Occurrence Handle10101183 Occurrence Handle148383 Occurrence Handle10.1093/nar/27.8.1767
Boore JL (2001) Mitochondrial gene arrangement source guide, version 6 (http://www.jgi.doe.gov/programs/comparative/Mito_top_level.html )
JL Boore WM Brown (1994) ArticleTitleComplete DNA sequence of the mitochondrial genome of the black chiton, Katharina tunicata. Genetics 138 423–443 Occurrence Handle1:CAS:528:DyaK2MXmtFaqsrg%3D Occurrence Handle7828825 Occurrence Handle1206160 Occurrence Handle10.1093/genetics/138.2.423
JL Boore LL Daehler WM Brown (1999) ArticleTitleComplete sequence, gene arrangement, and genetic code of mitochondrial DNA of the cephalochordate Branchiostomafloridae (Amphioxus). Mol Biol Evol 16 410–418 Occurrence Handle1:CAS:528:DyaK1MXhvVOqtLc%3D Occurrence Handle10331267 Occurrence Handle10.1093/oxfordjournals.molbev.a026122
J Castresana (2000) ArticleTitleSelection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol 17 540–552 Occurrence Handle1:CAS:528:DC%2BD3cXisVSgt7g%3D Occurrence Handle10742046 Occurrence Handle10.1093/oxfordjournals.molbev.a026334
J Castresana G Feldmaier-Fuchs S Yokobori N Satoh S Pääbo (1998) ArticleTitleThe mitochondrial genome of the hemichordate Balanoglossus carnosus and the evolution of deuterostome mitochondria. Genetics 150 1115–1123 Occurrence Handle1:CAS:528:DyaK1cXnsFCntLo%3D Occurrence Handle9799263 Occurrence Handle1460392 Occurrence Handle10.1093/genetics/150.3.1115
DO Clary DR Wolstenholme (1985) ArticleTitleThe mitochondrial DNA molecular of Drosophila yakuba: Nucleotide sequence, gene organization, and genetic code. J Mol Evol 22 252–271 Occurrence Handle1:CAS:528:DyaL28Xht1eqtb4%3D Occurrence Handle3001325 Occurrence Handle10.1007/BF02099755
M Dörner M Altmann S Pääbo M Mörl (2001) ArticleTitleEvidence for import of a lysyl-tRNA into marsupial mitochondria. Mol Biol Cell 12 2688–2698 Occurrence Handle11553708 Occurrence Handle59704 Occurrence Handle10.1091/mbc.12.9.2688
GA Durrheim VA Corfield EH Harley MH Ricketts (1993) ArticleTitleNucleotide sequence of cytochrome oxidase (subunit III) from the mitochondrion of the tunicate Pyurastolonifera: Evidence that AGR encodes glycine. Nucleic Acids Res 21 3587–3588 Occurrence Handle1:CAS:528:DyaK3sXmtFyktb8%3D Occurrence Handle8393993 Occurrence Handle331473 Occurrence Handle10.1093/nar/21.15.3587
KG Helfenbein WM Brown JL Boore (2001) ArticleTitleThe complete mitochondrial genome of the articulate brachiopod Terebratalia transversa. Mol Biol Evol 18 1734–1744 Occurrence Handle1:CAS:528:DC%2BD3MXmt12hsro%3D Occurrence Handle11504853 Occurrence Handle10.1093/oxfordjournals.molbev.a003961
RJ Hoffmann JL Boore WM Brown (1992) ArticleTitleA novel mitochondrial genome organization for the blue mussel, Mytilus edulis. Genetics 131 397–412 Occurrence Handle1:CAS:528:DyaK2cXis1anurk%3D Occurrence Handle1386586 Occurrence Handle1205014 Occurrence Handle10.1093/genetics/131.2.397
EM Keddie T Higazi TR Unnasch (1998) ArticleTitleThe mitochondrial genome of Onchocercavolvulus: Sequence, structure and phylogenetic analysis. Mol Biochem Parasitol 95 111–127 Occurrence Handle1:CAS:528:DyaK1cXls1yjs7k%3D Occurrence Handle9763293 Occurrence Handle10.1016/S0166-6851(98)00102-9
A Kondow S Yokobori T Ueda K Watanabe (1998) ArticleTitleAscidian mitochondrial tRNAMet possessing unique structural characteristics. Nucleosides Nucleotides 17 531–539 Occurrence Handle1:CAS:528:DyaK1cXhvFeju74%3D Occurrence Handle9708361 Occurrence Handle10.1080/07328319808005196
A Kondow T Suzuki S Yokobori T Ueda K Watanabe (1999) ArticleTitleAn extra tRNA GlyU*CU found in ascidian mitochondria responsible for decoding non-universal codons AGA/AGG as glycine. Nucleic Acids Res 27 2554–2559 Occurrence Handle1:CAS:528:DyaK1MXktFWqu7o%3D Occurrence Handle10352185 Occurrence Handle148460 Occurrence Handle10.1093/nar/27.12.2554
WJ Lee TD Kocher (1995) ArticleTitleComplete sequence of a sea lamprey (Petromyzon marinus) mitochondrial genome: Early establishment of the vertebrate genome organization. Genetics 139 873–887 Occurrence Handle1:CAS:528:DyaK28XhsFWgt7w%3D Occurrence Handle7713438 Occurrence Handle1206387 Occurrence Handle10.1093/genetics/139.2.873
SJ Mudge JH Williams HJ Eyre GR Sutherland PJ Cowan DA Power (1998) ArticleTitleComplex organisation of the 5′-end of the human glycine tRNA synthetase gene. Gene 209 45–50 Occurrence Handle1:CAS:528:DyaK1cXhvFeru74%3D Occurrence Handle9524218 Occurrence Handle10.1016/S0378-1119(98)00007-9
T Muramatsu K Nishikawa F Nemoto Y Kuchino S Nishimura T Miyazawa S Yokoyama (1988) ArticleTitleCodon and amino-acid specificities of a transfer RNA are both converted by a single post-transcriptional modification. Nature 336 179–181 Occurrence Handle1:CAS:528:DyaL1MXjsFCqtQ%3D%3D Occurrence Handle3054566 Occurrence Handle10.1038/336179a0
S Nada PK Chang JD Dignam (1993) ArticleTitlePrimary structure of the gene for glycyl-tRNA synthetase from Bombyx mori. J Biol Chem 268 7660–7667 Occurrence Handle1:CAS:528:DyaK3sXks1CmsLc%3D Occurrence Handle8463296 Occurrence Handle10.1016/S0021-9258(18)53008-8
N Nameki K Tamura H Asahara T Hasegawa (1997) ArticleTitleRecognition of tRNAGly by three widely diverged glycyl-tRNA synthetases: Evolution of tRNA recognition. Nucleic Acids Symp Ser 37 123–124 Occurrence Handle1:CAS:528:DyaK1cXivFCgsb0%3D
Y Noguchi K Endo F Tajima R Ueshima (2000) ArticleTitleThe mitochondrial genome of the brachiopod Laqueus rubellus. Genetics 155 245–259 Occurrence Handle1:CAS:528:DC%2BD3cXjslKht7k%3D Occurrence Handle10790399 Occurrence Handle1461069 Occurrence Handle10.1093/genetics/155.1.245
R Okimoto DR Wolstenholme (1990) ArticleTitleA set of tRNAs that lack either the TΨC arm or the dihydrouridine arm: Towards a minimal tRNA adaptor. EMBO J 9 3405–3411 Occurrence Handle1:CAS:528:DyaK3MXjsl2hsA%3D%3D Occurrence Handle2209550 Occurrence Handle552080 Occurrence Handle10.1002/j.1460-2075.1990.tb07542.x
R Okimoto JL Macfarlane DO Clary DR Wolstenholme (1992) ArticleTitleThe mitochondrial genomes of two nematodes, Caenorhabditis elegans and Ascaris suum. Genetics 130 471–498 Occurrence Handle1:CAS:528:DyaK3sXhs1aju7g%3D Occurrence Handle1551572 Occurrence Handle1204866 Occurrence Handle10.1093/genetics/130.3.471
UL RajBhandary CM Chow (1995) Initiator tRNAs and initiation of protein synthesis. D Chow UL Söll, (Eds) tRNA: Structure, biosynthesis, and function. AMS Press Washington, DC 511–528
AS Reichert M Mörl (2000) ArticleTitleRepair of tRNAs in metazoan mitochondria. Nucleic Acids Res 28 2043–2048 Occurrence Handle1:CAS:528:DC%2BD3cXktFSrur4%3D Occurrence Handle10773071 Occurrence Handle105380 Occurrence Handle10.1093/nar/28.10.2043
A Reichert U Rothbauer M Mörl (1998) ArticleTitleProcessing and editing of overlapping tRNAs in human mitochondria. J Biol Chem 273 31977–31984 Occurrence Handle1:CAS:528:DyaK1cXnvVelt7w%3D Occurrence Handle9822669 Occurrence Handle10.1074/jbc.273.48.31977
W Rossmanith (1997) ArticleTitleProcessing of human mitochondrial tRNASer(AGY) GCU: A novel pathway in tRNA biosynthesis. J Mol Biol 265 365–371 Occurrence Handle1:CAS:528:DyaK2sXht1ansbk%3D Occurrence Handle9034356 Occurrence Handle10.1006/jmbi.1996.0750
W Rossmanith A Tullo T Potuschak R Karwan E Sbisa (1995) ArticleTitleHuman mitochondrial tRNA processing. J Biol Chem 270 12885–12891 Occurrence Handle1:CAS:528:DyaK2MXlvFOhsLw%3D Occurrence Handle7759547 Occurrence Handle10.1074/jbc.270.21.12885
J Sambrook EF Fritsch T Maniatis (1989) Molecular cloning: A laboratory manual. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY
J Sasuga S Yokobori M Kaifu T Ueda K Nishikawa K Watanabe (1999) ArticleTitleGene contents and organization of a mitochondrial DNA segment of the squid Loligo bleekeri. J Mol Evol 46 692–702 Occurrence Handle10.1007/PL00006513
HA Schmidt K Strimmer M Vingron A von Haeseler (2002) ArticleTitleTREE-PUZZLE: Maximum likelihood phylogenetic analysis using quartets and parallel computing. Bioinformatics 18 502–504 Occurrence Handle1:CAS:528:DC%2BD38XivFKrsL0%3D Occurrence Handle11934758 Occurrence Handle10.1093/bioinformatics/18.3.502
G Seutin BF Lang DP Mindell R Morais (1994) ArticleTitleEvolution of the WANCY region in amniote mitochondrial DNA. Mol Biol Evol 11 329–340 Occurrence Handle1:CAS:528:DyaK2cXlt1Knt70%3D Occurrence Handle8015429
M Sprinzl C Horn M Brown A Ioudovitch S Steinberg (1998) ArticleTitleCompilation of tRNA sequences and sequences of tRNA genes. Nucleic Acids Res 26 148–153 Occurrence Handle1:CAS:528:DyaK1cXovVansQ%3D%3D Occurrence Handle9399820 Occurrence Handle147216 Occurrence Handle10.1093/nar/26.1.148
N Spruyt C Delarbre G Gachelin V Laudet (1998) ArticleTitleComplete sequence of the amphioxus (Branchiostoma lanceolatum) mitochondrial genome: relations to vertebrates. Nucleic Acids Res 26 3279–3285 Occurrence Handle1:CAS:528:DyaK1cXks1Gjs7w%3D Occurrence Handle9628930 Occurrence Handle147690 Occurrence Handle10.1093/nar/26.13.3279
A Stechmann M Schlegel (1999) ArticleTitleAnalysis of the complete mitochondrial DNA sequence of the brachiopod Terebratulina retusa places Brachiopoda within the protostomes. Proc R Soc Lond B Biol Sci 266 2043–2052 Occurrence Handle1:CAS:528:DyaK1MXnvVShs7c%3D Occurrence Handle10.1098/rspb.1999.0885
K Strimmer A von Haeseler (1996) ArticleTitleQuartet puzzling: A quartet maximum likelihood method for reconstructing tree topologies. Mol Biol Evol 13 964–969 Occurrence Handle1:CAS:528:DyaK28XltlSmsLk%3D Occurrence Handle10.1093/oxfordjournals.molbev.a025664
N Takeuchi L Vial M Panvert E Schmitt K Watanabe Y Mechulam S Blanquet (2001) ArticleTitleRecognition of tRNAs by Methionyl-tRNA transformylase from mammalian mitochondria. J Biol Chem 276 20064–20068 Occurrence Handle1:CAS:528:DC%2BD3MXktlKns70%3D Occurrence Handle11274157 Occurrence Handle10.1074/jbc.M101007200
InstitutionalAuthorNameThe C. elegans Sequencing Consortium (1998) ArticleTitleGenome sequence of the nematode C. elegans: A platform for investigating biology. Science 282 2012–2018 Occurrence Handle10.1126/science.282.5396.2012
InstitutionalAuthorNameThe FlyBase Consortium (2002) ArticleTitleThe FlyBase database of the Drosophila genome projects and community literature. Nucleic Acids Res 30 106–108 Occurrence Handle99082 Occurrence Handle10.1093/nar/30.1.106
JD Thompson TJ Gibson F Plewniak F Jeanmougin DG Higgins (1997) ArticleTitleThe CLUSTAL_X windows interface: Flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25 4876–4882 Occurrence Handle1:CAS:528:DyaK1cXntFyntQ%3D%3D Occurrence Handle9396791 Occurrence Handle147148 Occurrence Handle10.1093/nar/25.24.4876
K Tomita S Yokobori T Oshima T Ueda K Watanabe (2002) ArticleTitleThe cephalopod Loligobleekeri mitochondrial genome: Multiplied noncoding regions and transposition of tRNA genes. J Mol Evol 54 486–500 Occurrence Handle1:CAS:528:DC%2BD38Xjt1Ggurk%3D Occurrence Handle11956687 Occurrence Handle10.1007/s00239-001-0039-4
N Yamazaki R Ueshima JA Terrett S Yokobori M Kaifu R Segawa T Kobayashi K Numachi T Ueda K Nishikawa K Watanabe RH Thomas (1997) ArticleTitleEvolution of pulmonate gastropod mitochondrial genomes: Comparisons of gene organizations of Euhadra, Cepaea and Albinaria and implications of unusual tRNA secondary structures. Genetics 145 749–758 Occurrence Handle1:CAS:528:DyaK2sXmsVaktL0%3D Occurrence Handle9055084 Occurrence Handle1207859 Occurrence Handle10.1093/genetics/145.3.749
Z Yang (1997) ArticleTitlePAML: A program package for phylogenetic analysis by maximum likelihood. Comput Appl Biosci 15 555–556
S Yokobori S Pääbo (1995) ArticleTitleTransfer RNA editing in land snail mitochondria. Proc Natl Acad Sci USA 92 10432–10435 Occurrence Handle1:CAS:528:DyaK2MXovFaltLc%3D Occurrence Handle7479799 Occurrence Handle40811 Occurrence Handle10.1073/pnas.92.22.10432
S Yokobori S Pääbo (1995) ArticleTitletRNA editing in metazoans. Nature 377 490 Occurrence Handle1:STN:280:DyaK28%2FhtlOgug%3D%3D Occurrence Handle7566145 Occurrence Handle10.1038/377490a0
S Yokobori S Pääbo (1997) ArticleTitlePolyadenylation creates the discriminator nucleotide of chicken mitochondrial tRNATyr. J Mol Biol 265 95–99 Occurrence Handle1:CAS:528:DyaK2sXpslGltw%3D%3D Occurrence Handle9020972 Occurrence Handle10.1006/jmbi.1996.0728
S Yokobori T Ueda K Watanabe (1993) ArticleTitleCodons AGA and AGG are read as glycine in ascidian mitochondria. J Mol Evol 36 1–8 Occurrence Handle1:CAS:528:DyaK3sXnsVKjuw%3D%3D Occurrence Handle8381878 Occurrence Handle10.1007/BF02407301
S Yokobori T Ueda G Feldmaier-Fuchs S Pääbo R Ueshima A Kondow K Nishikawa K Watanabe (1999) ArticleTitleComplete DNA sequence of the mitochondrial genome of the ascidian Halocynthia roretzi (Chordata, Urochordata). Genetics 153 1851–1862 Occurrence Handle1:CAS:528:DC%2BD3cXhvV2ktQ%3D%3D Occurrence Handle10581290 Occurrence Handle1460873 Occurrence Handle10.1093/genetics/153.4.1851
S Yokobori T Suzuki K Watanabe (2001) ArticleTitleGenetic code variations in mitochondria: tRNA as a major determinant of genetic code plasticity. J Mol Evol 53 314–326 Occurrence Handle1:CAS:528:DC%2BD3MXotVaiu74%3D Occurrence Handle11675591 Occurrence Handle10.1007/s002390010221
CE Zevering C Moritz A Heideman RA Sturm (1991) ArticleTitleParallel origins of duplications and the formation of pseudogenes in mitochondrial DNA from parthenogenetic lizards (Heteronotia binoei; Gekkonidae). J Mol Evol 3 431–441 Occurrence Handle10.1007/BF02103135
Acknowledgements
We thank Dr. K. Watanabe, University of Tokyo, and Dr. A. Yamagishi, Tokyo University of Pharmacy and Life Science, for their valuable comments on this study. This work was supported by the grants from the Ministry of Education, Culture, Sports, Science and Technology of Japan to S.Y. and T.O.
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Yokobori, Si., Watanabe, Y. & Oshima, T. Mitochondrial Genome of Ciona savignyi (Urochordata, Ascidiacea, Enterogona): Comparison of Gene Arrangement and tRNA Genes with Halocynthia roretzi Mitochondrial Genome. J Mol Evol 57, 574–587 (2003). https://doi.org/10.1007/s00239-003-2511-9
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DOI: https://doi.org/10.1007/s00239-003-2511-9


