Complete sequence of the mitochondrial DNA in the sea urchin Arbacia lixula: Conserved features of the echinoid mitochondrial genome

Molecular Phylogenetics and Evolution

Volumn 5, Issue 2, 1996, Pages 323-332

  De Giorgi, Carla ^a   Martiradonna, Antonia ^a   Lanave, Cecilia ^b   Saccone, Cecilia ^b  

^a UNIVERSITY OF BARI   (Italy)

^b CNR   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

ARBACIA LIXULA; ECHINODERMATA; ECHINOIDEA; PARACENTROTUS LIVIDUS; STRONGYLOCENTROTUS PURPURATUS;

MITOCHONDRIAL DNA;

AMINO ACID SEQUENCE; ANIMAL; ARTICLE; CHEMISTRY; CLASSIFICATION; CODON; COMPARATIVE STUDY; CONFORMATION; FISH; GENETICS; MAMMAL; MITOCHONDRION; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PHYLOGENY; PROMOTER REGION; SEA URCHIN; SEQUENCE HOMOLOGY; SPECIES DIFFERENCE;

AMINO ACID SEQUENCE; ANIMALS; BASE SEQUENCE; CODON; CONSERVED SEQUENCE; DNA, MITOCHONDRIAL; FISHES; MAMMALS; MITOCHONDRIA; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; PHYLOGENY; PROMOTER REGIONS (GENETICS); SEA URCHINS; SEQUENCE HOMOLOGY, NUCLEIC ACID; SPECIES SPECIFICITY;

EID: 0030122559     PISSN: 10557903     EISSN: None     Source Type: Journal    
DOI: 10.1006/mpev.1996.0027     Document Type: Article

References (51)

1. Aloni, Y., and Attardi, G. (1971). Expression of the mitochondrial genome in HeLa cells. II. Evidence for complete transcription of mitochondrial DNA. J. Mol. Biol. 55: 251-270.
2. Anderson, S., Bankier, A. T., Barrel, B. G., De Bruijn, M. H. L., Coulson, A. R., Drouin, J., Eperon, I. C., Nierlich, D. P., Roe, B. A., Sanger, F., Schreier, P. H., Smith, A. J. H., Staden, R., and Young, I. G. (1981). Sequence and organization of the human mitochondrial genome. Nature 290: 457-465.
3. Anderson, S., De Bruijn, M. H. L., Coulson, A. R., Eperon, I. C., Sanger, F., and Young, I. G. (1982). Complete sequence of bovine mitochondrial DNA. Conserved features of the mammalian mitochondrial genome. J. Mol. Biol. 156: 683-717.
4. Asakawa, S., Kumazawa, Y., Araki, T., Himeno, H., Miura, K., and Watanabe, K. (1991). Strand-specific nucleotide composition bias in echinoderm and vertebrate mitochondrial genomes. J. Mol. Evol. 32: 511-520.
5. Avise, J. C., Bowen, B. W., Lamb, T., Meylan, A. B., and Bermingham, E. (1992). Mitochondrial DNA evolution at a turtle's pace: Evidence for low genetic variability and reduced microevolutionary rate in the Testudines. Mol. Biol. Evol. 9: 457-473.
6. Busslinger, M., Rusconi, S., and Birnstiel, M. L. (1982). An unusual evolutionary behaviour of a sea urchin histone gene cluster. EMBO J. 1: 27-33.
7. Cantatore, P., Roberti, M., Rainaldi, G., Gadaleta, M. N., and Saccone, C. (1989). The complete nucleotide sequence, gene organization, and genetic code of the mitochondrial genome of Paracentrotus lividus. J. Biol. Chem. 264: 10965-10975.
8. Cantatore, P., Roberti, M., Pesole, G., Ludovico, A., Milella, F., Gadaleta, M. N., and Saccone, C. (1994). Evolutionary analysis of cytochrome b sequences in some Perciformes. Evidences for a slower rate of evolution than in mammals. J Mol. Evol. 39: 589-597.
9. Crozier, R. H., and Crozier, Y. C. (1993). The mitochondrial genome of the Honeybee Apis mellifera: Complete sequence and genome organization. Genetics 133: 97-117.
10. De Giorgi, C., (1988). Mitochondrial DNA polymorphism in the eggs of the sea urchin Arbacia lixula. Cell. Biol. Int. Rep. 12: 407-412.
11. De Giorgi, C., Lanave, C., Musci, M. D., and Saccone, C. (1991). Mitochondrial DNA in the sea urchin Arbacia lixula: Evolutionary inferences from nucleotide sequence analysis. Mol. Biol. Evol. 8: 515-529.
12. Desjardins, P., and Morais, R. (1990). Sequence and gene organization of the chicken mitochondrial genome: A novel gene order in higher vertebrates. J. Mol. Biol. 212: 599-634.
13. Felsenstein, J. (1993). PHYLIP (Phylogeny Inference Package) v. 3.5, Department of Genetics, University of Washington, Seattle.
14. Hall, T. J., Grula, J. W., Davidson, E. H., and Britten, R. J. (1980). Evolution of sea urchin non-repetitive DNA. J. Mol. Evol. 16: 95-110.
15. Ser AGY in starfish mitochondrial DNA. Gene 56: 219-230.
16. Hixson, J. E., and Brown, W. M. (1986). A comparison of the small ribosomal RNA genes from the mitochondrial DNA of the great apes and humans: Sequence, structure, evolution, and phylogenetic implications. Mol. Biol. Evol. 3: 1-18.
17. Jacobs, H. T., Herbert, E. R., and Rankine, J. (1989a). Sea urchin egg mitochondrial DNA contains a short displacement loop (D-loop) in the replication origin region. Nucleic Acids Res. 17: 8949-8965.
18. Jacobs, H. T., Elliott, D. J., Math, V. B., and Farquharson, A. (1988). Nucleotide sequence and gene organization of sea urchin mitochondrial DNA. J. Mol. Biol. 202: 185-217.
19. Jacobs, H. T., Asakawa, S., Araki, T., Miura, K., Smith, M. J., and Watanabe, K. (1989b). Conserved tRNA gene cluster in starfish mitochondrial DNA. Curr. Genet. 15: 193-206.
20. Kier, P. M. (1977). The poor fossil record of the regular echinoid. Paleobiology 3: 168-174.
21. Kumazawa, Y., Yokogawa, T., Hasegawa, E., Miura, K., and Watanabe, K. (1989). The aminoacylation of structurally variant phenylalanine tRNAs from mitochondria and various non mitochondrial sources by bovine mitochondrial phenylalanyl-tRNA synthetase. J. Biol. Chem. 264: 13005-13011.
22. Moritz, C., and Brown, W. M. (1986). Tandem duplication of D-loop and ribosomal RNA sequences in lizard mitochondrial DNA. Science 233: 1425-1427.
23. Ojala, D., Montoya, J., and Attardi, G. (1981). tRNA punctation model of RNA processing in human mitochondria. Nature 290: 470-474.
24. Okimoto, R., Chamberlin, H. M., Macfarlane, J. L., and Wolstenholme, D. R. (1991). Repeated sequence sets in mitochondrial DNA molecules of root knot nematodes (Meloidogyne): Nucleotide sequences, genome location and potential far host-race identification. Nucleic Acids Res. 19: 1619-1626.
25. Okimoto, R., Macfarlane, J. L., Clary, D. O., and Wolstenholme, D. R. (1992). The mitochondrial genomes of two nematodes, Caenorhabditis elegans and Ascaris suum. Genetics 130: 471-498.
26. Paabo, 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: 426-430.
27. Prager, E. M., and Wilson, A. C. (1988). Ancient origin of lactalbumin from lysozyme: Analysis of DNA and aminoacid sequences. J. Mol. Evol. 27: 326-335.
28. Saccone, C., and Sbisa', E. (1989). Organization and evolution of mitochondrial DNA in metazoa. In "Organelles in Eukaryotic Cells" (J. M. Tager, A. Azzi, S. Papa, and F. Guerrieri, Eds.), pp. 127-142, Plenum, New York.
29. Saccone, C., Attimonelli, M., De Giorgi, C., Lanave, C., and Sbisa', E. (1990a). The role of tRNA genes in the evolution of animal mitochondrial DNA. In "Structure, Function and Biogenesis of Energy Transfer Systems" (E. Quagliariello, S. Papa, F. Palmieri, and C. Saccone, Eds.), pp. 93-96, Elsevier, Amsterdam.
30. Saccone, C., Lanave, C., Pesole, G., and Preparata, G. (1990b). Influence of base composition on quantitative estimates of gene evolution. Methods Enzymol. 183: 570-583.
31. Saccone, C., Lanave, C., Pesole, G., and Sbisa', E. (1993). Peculiar features and evolution of mitochondrial genome in mammals. In "Mitochondrial DNA in Human Pathology" (S. Di Mauro and D. C. Wallace, Eds.), pp. 27-37, Raven Press, New York.
32. Sampson, J. R., Direnzo, A. B., Behlen, L. S., and Uhlenbeck, O. C. (1989). Nucleotides in yeast tRNAPhe required for the specific recognition by its cognate synthetase. Science 243: 1363-1366.
33. Schulman, L. H., and Pelka, H. (1988). Anticodon switching changes the identity of methionine and valine transfer RNAs. Science 242: 765-768.
34. Simons, E. L. (1989). Human origins. Science 245: 1343-1350.
35. Smith, A. B. (1984). Echinoid palaeobiology. Allen and Unwin, London.
36. Smith, A. B. (1988). Phylogenetic relationship, divergence times, and rates of molecular evolution for Camarodont sea urchins. Mol. Biol. Evol. 5: 345-365.
37. Smith, A. B. (1989). RNA sequence data in phylogenetic reconstruction testing the limits of its resolution. Cladistics 5: 321-344.
38. Smith, A. B., Lafay, B., and Christen, R. (1992). Comparative variation of morphological and molecular evolution through geologic time: 28S ribosomal RNA versus morphology in echinoids. Philos. Trans. R. Soc. London B 338: 365-382.
39. Smith, M. J., Banfield, D. K., Doteval, K., Gorski, S., and Kowbel, D. J. (1990). Nucleotide sequence of nine protein-coding genes and 22 tRNAs in the mitochondrial DNA of the sea star Pisaster ochraceus. J. Mol. Evol. 31: 195-204.
40. Smith, M. J., Arndt, A., Gorski, S., and Fajber, E. (1993). The phylogeny of echinoderm classes based on mitochondrial gene arrangements. J. Mol. Evol. 36: 545-554.
41. Snyder, M., Fraser, A. R., Laroche, J., Gartner-Kepkay, K. E., and Zouros, E. (1987). Atypical mitochondrial DNA from the deep-sea scallop Placopecten magellanicus. Proc. Natl. Acad. Sci. USA 84: 7595-7599.
42. Sprinzl, M., Hartmann, T., Weber, J., Blank, J., and Zeidler, R. (1989). Compilation of tRNA sequences and sequences of tRNA genes. Nucleic Acids Res. 17: r1-r172.
43. Sueoka, N. (1962). On the genetic basis of variation and heterogeneity of DNA base composition. Proc. Natl. Acad. Sci. USA 48: 582-592.
44. Ser(AGY) is a main recognition site for homologous seryl-tRNA synthetase. Nucleic Acids Res. 20: 2217-2222.
45. Valverde, J. R., Batuecas, B., Moratilla, C., Marco, R., and Garesse, R. (1994). The complete mitochondrial DNA sequence of the crustacean Artemia franciscana. J. Mol. Evol. 39: 400-408.
46. Vawter, L., and Brown, W. M. (1986). Nuclear and mitochondrial DNA comparisons reveal extreme rate variation in the molecular clock. Science 234: 194-196.
47. Wada, H., and Satoh, N. (1994). Phylogenetic relationships among extant classes of echinoderms, as inferred from sequences of 18S rDNA, coincide with relationships deduced from the fossil record. J. Mol. Evol. 38: 41-49.
48. Phe lacking the "conserved" GG and TΨCG sequences as inferred by enzymatic and chemical probing. Nucleic Acids Res. 22: 347-353.
49. Wilson, C. I., Ochman, H., and Prager, E. M. (1987). Molecular time scale for evolution. Trends Genet. 3: 241-247.
50. Wolstenholme, D. R. (1992). Animal mitochondrial DNA: Structure and evolution. Int. Rev. Cytol. 141: 173-215.
51. Wolstenholme, D. R., and Clary, D. O. (1985). Sequence evolution of Drosophila mitochondrial DNA. Genetics 109: 725-744.