Mitochondrial genome conformation among CW-group chlorophycean algae

Journal of Phycology

Volumn 39, Issue 1, 2003, Pages 213-220

  Laflamme, Mark ^a   Lee, Robert W ^a  

^a DALHOUSIE UNIVERSITY   (Canada)

Author keywords

Chlamydomonas; Chlorophyceae; Gel electrophoresis; Mitochondrial DNA conformation; Phylogeny

Indexed keywords

GENOME; GREEN ALGA; MITOCHONDRIAL DNA; PHYLOGENY;

ALGAE; CHLAMYDOMONAS; CHLAMYDOMONAS MOEWUSII; CHLAMYDOMONAS REINHARDTII; CHLOROPHYCEAE; EUKARYOTA; VOLVOX;

EID: 0037329976     PISSN: 00223646     EISSN: None     Source Type: Journal    
DOI: 10.1046/j.1529-8817.2003.02045.x     Document Type: Article

References (68)

1. Armstrong, M. R., Blok, V. C. & Philips, M. S. 2000. A multipartite mitochondrial genome in the potato cyst nematode Globodera pallida. Genetics 154:181-92.
2. Backert, S., Nielsen, B. L. & Börner, T. 1997. The mystery of the rings: structure and replication of mitochondrial genomes from higher plants. Trends Plant Sci. 2:477-83.
3. Bendich, A. J. 1993. Reaching for the ring: the study of mitochondrial genome structure. Curr. Genet. 24:279-90.
4. Bendich, A. J. 1996. Structural analysis of mitochondrial DNA molecules from fungi and plants using moving pictures and pulsed-field gel electrophoresis. J. Mol. Biol. 255:564-88.
5. Boer, P. H., Bonen, L., Lee, R. W. & Gray, M. W. 1985. Genes for respiratory chain proteins and ribosomal RNAs are present on a 16-kilobase-pair DNA species from Chlamydomonas reinhardtii mitochondria. Proc. Natl. Acad. Sci. USA 82:3340-44.
6. Boer, P. H. & Gray, M. W. 1991. Short dispersed repeats localized in spacer regions of Chlamydomonas reinhardtii mitochondrial DNA. Curr. Genet. 19:309-12.
7. Boudreau, E. & Turmel, M. 1995. Gene rearrangements in Chlamydomonas chloroplast DNAs are accounted for by inversions and by the expansion/contraction of the inverted repeat. Plant Mol. Biol. 27:351-64.
8. Boynton, J. E., Harris, E. H., Burkhart, B. D., Lamerson, P. M. & Gillham, N. W. 1987. Transmission of mitochondrial and chloroplast genomes in crosses of Chlamydomonas. Proc. Natl. Acad. Sci. USA 84:2391-5.
9. Bridge, D., Cunningham, C. W., Schierwater, B., Desalle, R. & Buss, L. W. 1992. Class-level relationships in the phylum Cnidaria: evidence from mitochondrial genome structure. Proc. Natl. Acad. Sci. USA 89:8750-3.
10. Buchheim, M. A. & Chapman, R. L. 1992. Phylogeny of Carteria (Chlorophyceae) inferred from molecular and organismal data. J. Phycol. 28:362-74.
11. Buchheim, M. A., Lemieux, C., Otis, C., Gutell, R. R., Chapman, R. L. & Turmel, M. 1996. Phylogeny of the Chlamydomonadales (Chlorophyceae): a comparison of ribosomal RNA gene sequences from the nucleus and the chloroplast. Mol. Phylogenet. Evol. 5:391-402.
12. Buchheim, M. A., Michalopulos, E. A. & Buchheim, J. A. 2001. Phylogeny of the Chlorophyceae with special reference to the Sphaeropleales: a study of 18S and 26S rDNA data. J. Phycol. 37:819-35.
13. Burger, G., Zhu, Y., Littlejohn, T. G., Greenwood, S. J., Schnare, M. N., Lang, B. F. & Gray, M. W. 2000. Complete sequence of the mitochondrial genome of Tetrahymena pyriformis and comparison with Paramecium aurelia mitochondrial DNA. J. Mol. Biol. 297:365-80.
14. Carle, G. F. & Olsen, M. V. 1987. Orthogonal-field-alteration gel electrophoresis. Methods Enzymol. 155:468-82.
15. Coleman, A. 1999. Phylogenetic analysis of "Volvocacae" for comparative genetic studies. Proc. Natl. Acad. Sci. USA 96:13892-7.
16. Denovan-Wright, E. M. & Lee, R. W. 1992. Comparative analysis of the mitochondrial genomes of Chlamydomonas eugametos and Chlamydomonas moewusii. Curr. Genet. 21:197-202.
17. Denovan-Wright, E. M., Nedelcu, A. M. & Lee, R. W. 1998. Complete sequence of the mitochondrial DNA of Chlamydomonas eugametos. Plant Mol. Biol. 36:285-95.
18. Drissi, R., Sor, F., Nosek, J. & Fukuhara, H. 1994. Genes of the linear mitochondrial DNA of Williopsis mrakii: coding sequences for a maturase-like protein, a ribosomal protein VAR1 homologue, cytochrome oxidase subunit 2 and methionyl tRNA. Yeast 10:391-8.
19. Duby, F., Cardol, P., Matagne, R. F. & Remacle, C. 2001. Structure of the telomeric ends of the mtDNA, transcriptional analysis and complex I assembly in the dum24 mitochondrial mutant of Chlamydomonas reinhardtii. Mol. Genet. Genom. 266:109-14.
20. Fan, J. & Lee, R. W. 2002. Mitochondrial genome of the colorless green alga Polytomella parva: two linear DNA molecules with homologous inverted repeat termini. Mol. Biol. Evol. 19:999-1007.
21. Feagin, J. E. 1995. The extrachromosomal DNAs of apicomplexan parasites. Annu. Rev. Microbiol. 48:81-104.
22. Friedl, T. 1995. Inferring taxonomic positions and testing genus level assignments in coccoid green lichen algae: a phylogenetic analysis of 18S ribosomal RNA sequences from Dictyochloropsis reticulata and from members of the genus Myrmecia (Chlorophyta, Trebouxiophyceae cl. Nov.). J. Phycol. 31:632-9.
23. Friedl, T. 1997. The evolution of the green algae. Plant Syst. Evol. 11:87-101.
24. Fukuhara, H., Sor, F., Drissi, R., Dinouël, N., Miyakawa, I., Rousset, S. & Viola, A.-M. 1993. Linear mitochondrial DNAs of yeasts: frequency of occurrence and general features. Mol. Cell Biol. 13:2309-14.
25. Grant, D. & Chiang, K. 1980. Physical mapping and characterization of Chlamydomonas mitochondrial DNA molecules: their unique ends, sequence homogeneity and conservation. Plasmid 4:82-96.
26. Gray, M. W. 1999. Evolution of organellar genomes. Curr. Opin. Genet. Dev. 9:678-87.
27. Gray, M. W., Burger, G. & Lang, B. F. 1999. Mitochondrial evolution. Science 283:1476-81.
28. Hepperle, D., Nozaki, H., Hohenberger, S., Huss, V. A. R., Morita, E. & Krientz, L. 1998. Phylogenetic position of the Phacotaceae within the Chlamydophyceae as revealed by analysis of 18S rDNA and rbcl sequences. J. Mol. Evol. 47:420-30.
29. Johnson, P. H. & Grossman, L. I. 1977. Electrophoresis of DNA in agarose gels. Optimizing separations of conformational isomers of double- and single-stranded DNAs. Biochemistry 16:4217-25.
30. Kessler, U. & Zetsche, K. 1995. Physical map and gene organization of the mitochondrial genome from the unicellular green alga Platymonas (Tetraselmis) subcordiformis. Plant Mol. Biol. 29:1081-6.
31. Kroymann, J. & Zetsche, K. 1998. The mitochondrial genome of Chlorogonium elongatum inferred from the complete sequence. J. Mol. Evol. 47:431-40.
32. Kück, U., Jekosch, K. & Holzamer, P. 2000. DNA sequence analysis of the complete mitochondrial genome of the green alga Scenedesmus obliquus: evidence for UAG being a leucine, and UCA being a non-sense codon. Gene 253:13-8.
33. Lang, B. F., Burger, G., O'Kelly, C. J., Cedergren, R., Golding, G. B., Lemieux, C., Sankoff, D., Turmel, M. & Gray, M. W. 1999a An ancestral mitochondrial DNA resembling a eubacterial genome in miniature. Nature 387:493-7.
34. Lang, B. F., Gray, M. W., Burger, G. 1999b. Mitochondrial genome evolution and the origin of eukaryotes. Annu. Rev. Genet. 33:351-97.
35. Lee, R. W., Dumas, C., Lemieux, C. & Turmel, M. 1991. Cloning and characterization of the Chlamydomonas moewusii mitochondrial genome. Mol. Gen. Genet. 231:53-8.
36. Lemieux, C., Turmel, M. & Lee, R. W. 1980. Characterization of chloroplast DNA in Chlamydomonas eugametos and C. moewusii and its inheritance in hybrid progeny. Curr. Genet. 2:139-47.
37. Lewis, L. A., Wilcox, L. W., Fuerst, P. A. & Floyd, G. L. 1992. Concordance of molecular and ultrastructural data in the study of zoosporic Chlorococcalean green algae. J. Phycol. 28:375-80.
38. Ma, D.-P., King, Y.-T., Kim, Y., Luckett, W. S., Boyle, J. A. & Chang, Y.-F. 1992. Amplification and characterization of an inverted repeat from the Chlamydomonas reinhardtii mitochondrial genome. Gene 119:253-7.
39. Maleszka, R. 1993. Single-stranded regions in yeast mitochondrial DNA revealed by pulsed-field gel electrophoresis. Appl. Theor. Electroph. 3:259-63.
40. Maleszka, R. & Clark-Walker, G. 1992. In vivo conformation of mitochondrial DNA in fungi and zoosporic moulds. Curr. Genet. 22:341-4.
41. Maleszka, R., Skelly, P. & Clark-Walker, G. 1991. Rolling circle replication of DNA in yeast mitochondria. EMBO J. 10:3923-9.
42. Mattox, K. R. & Stewart, K. D. 1984. Classification of the green algae: a concept based on comparative cytology. In Irvine, D. E. G. & John, D. M. [Eds.] Systematics of the Green Algae. Academic Press, London, pp. 29-72.
43. Michaelis, G., Vahrenholz, C. & Pratje, E. 1990. Mitochondrial DNA of Chlamydomonas reinhardtii: the gene for apocytochrome b and the complete functional map of the 15.8 kb DNA. Mol. Gen. Genet. 223:211-6.
44. Moestrup, Ø. 1991. Further studies of the presumably primitive green algae, including the description of the Pedinophyceae class. nov. and Resultor gen. nov. J. Phycol. 27:119-33.
45. Moore, L. J. & Coleman, A. W. 1989. The linear 20 kb mitochondrial genome of Pandorina morum (Volvocaceae, Chlorophyta). Plant Mol. Biol. 13:459-65.
46. Moritz, C., Dowling, T. E. & Brown, W. M. 1987 Evolution of animal mitochondrial DNA: relevance for population biology and systematics. Annu. Rev. Ecol. Syst. 18:269-92.
47. Nakayama, T., Watanabe, S., Mitsui, K., Uchida, H. & Inouye, I. 1996. The phylogenetic relationship between the Chlamydomonadales and Chlorococcales inferred from 18SrDNA sequence data. Phycol. Res. 44:47-55.
48. Nedelcu, A., Lee, R., Lemieux, C., Gray, M. & Burger, G. 2000. The complete mitochondrial DNA sequence of Scenedesmus obliquus reflects an intermediate stage in the evolution of the green algal mitochondrial genome. Genome Res. 10:819-31.
49. Nedelcu, A. M. & Lee, R. W. 1998a. Modes and tempos of mitochondrial and chloroplast genome evolution in Chlamydomonas: a comparative analysis. In Rochaix, J. D., Goldschmidt-Clermont, M. & Merchant, S. [Eds.] The Molecular Biology of Chloroplast and Mitochondria in Chlamydomonas. Kluwer Academic Publishers, The Netherlands, pp. 63-91.
50. Nedelcu, A. M. & Lee, R. W. 1998b. Short repetitive sequences in green algal mitochondrial genomes: potential roles in mitochondrial genome evolution. Mol. Biol. Evol. 15:690-701.
51. Nosek, J., Tomáska, L., Fukuhara, H., Suyama, Y. & Kovác, L. 1998. Linear mitochondrial genomes: 30 years down the line. Trends Genet. 14:184-8.
52. Oldenburg, D. J. & Bendich, A. J. 2001. Mitochondrial DNA from the liverwort Marchantia polymorpha: circularly permuted linear molecules, head-to-tail concatemers, and a 5′ protein. J. Mol. Biol. 310:549-62.
53. Pröschold, T., Marin, B., Schlösser, U. G. & Melkonian, M. 2001. Molecular phylogeny and taxonomic revision of Chlamydomonas (Chlorophyta). I. Emendation of Chlamydomonas Ehrenberg and Chloromonas Gobi, and description of Oogamochlamys gen. nov. and Lobochlamys gen. nov. Protist 151:265-300.
54. Ryan, R., Grant, D., Chiang, K.-S. & Swift, H. 1978. Isolation and characterization of mitochondrial DNA from Chlamydomonas reinhardtii. Proc. Natl. Acad. Sci. USA 75:3268-72.
55. Sambrook, J., Fritsch, E. F. & Maniatis, T. 1989. Molecular Cloning: A Laboratory Manual, 2nd edition. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York, USA, 1659 pp.
56. Schardl, C., Lonsdale, D., Pring, D. & Rose, K. 1984. Linearization of the maize mitochondrial chromosomes by recombination with linear episomes. Nature 310:292-6.
57. Sheeler, P., Cantor, M. & More, J. 1968. Growth characteristics of Polytomella agilis in batch cultures. Life Sci. 7:289-93.
58. Sluiman, H. J. 1985. A cladistic evaluation of the lower and higher green plants (Viridiplantae). Plant Syst. Evol. 149:217-32.
59. Steinkötter, J., Bhattacharya, D., Semmelroth, I., Bibeau, C. & Melkonian, M. 1994. Prasinophytes form independent lineages within the chlorophyta:evidence from ribosomal RNA sequence comparisons. J. Phycol. 30:340-5.
60. Turmel, M., Gutell, R. R., Mercier, J.-P., Otis, C. & Lemieux, C. 1993. Analysis of the chloroplast large subunit ribosomal RNA gene from 17 Chlamydomonas taxa. J. Mol. Biol. 232:446-67.
61. Turmel, M., Lemieux, C., Burger, G., Lang, B., Otis, C., Plante, I. & Gray, M. 1999. The complete mitochondrial DNA sequences of Nephroselmis olivacea and Pedinomonas minor: two radically different evolutionary patterns within green algae. Plant Cell 11:1717-29.
62. Turmel, M., Otis, C. & Lemieux, C. 2002. The complete mitochondrial sequence of Mesostigma viride identifies this green alga as the earliest green plant divergence and predicts a highly compact mitochondrial genome in the ancestor of all green plants. Mol. Biol. Evol. 19:24-38.
63. Vahrenholz, C., Riemen, G., Pratje, E., Dujon, B. & Michaelis, G. 1993. Mitochondrial DNA of Chlamydomonas reinhardtii: the structure of the ends of the linear 15.8 kb genome suggests mechanisms for DNA replication. Curr. Genet. 24:241-7.
64. Waddle, J. A., Schuster, A. M., Lee, K. W. & Meints, R. H. 1990. The mitochondrial genome of an exsymbiotic chlorella-like green alga. Plant Mol. Biol. 14:187-95.
65. Ward, B. L., Anderson, R. S. & Bendich, A. J. 1981. The mitochondrial genome is large and variable in a family of plants (cucurbitaceae). Cell 25:793-803.
66. Whiteway, M. S. & Lee, R. W. 1977. Chloroplast DNA content increases with nuclear ploidy in Chlamydomonas. Mol. Gen. Genet. 157:11-5.
67. Wilson, R. J. & Williamson, D. H. 1997. Extrachromosomal DNA in the apicomplexa. Microbiol. Mol. Biol. Rev. 61:1-16.
68. Wolff, G., Plante, I., Lang, F. B., Kück, U. & Burger, G. 1994. Complete sequence of the mitochondrial DNA of the chlorophyte alga Prototheca wickerhamii: gene content and genome organization. J. Mol. Biol. 237:75-86.