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PMID: 3148747 Published · ppublish English Comparative Study Journal Article Research Support, Non-U.S. Gov't Review

The evolutionary relationships among known life forms.

Journal of molecular evolution ·Vol. 28 ·No. 1-2 ·1988-00-00 ·Pages 98-112

Cedergren R, Gray MW, Abel Y, Sankoff D

Abstract

Sequences of small subunit (SSU) and large subunit (LSU) ribosomal RNA genes from archaebacteria, eubacteria, and the nucleus, chloroplasts, and mitochondria of eukaryotes have been compared in order to identify the most conservative positions. Aligned sets of these positions for both SSU and LSU rRNA have been used to generate tree diagrams relating the source organisms/organelles. Branching patterns were evaluated using the statistical bootstrapping technique. The resulting SSU and LSU trees are remarkably congruent and show a high degree of similarity with those based on alternative data sets and/or generated by different techniques. In addition to providing insights into the evolution of prokaryotic and eukaryotic (nuclear) lineages, the analysis reported here provides, for the first time, an extensive phylogeny of the mitochondrial lineage.

MeSH Terms
Base Sequence Biological Evolution DNA, Ribosomal/genetics Information Systems Models, Genetic Nucleic Acid Conformation Phylogeny RNA, Ribosomal/genetics Sequence Homology, Nucleic Acid
Chemicals
DNA, Ribosomal RNA, Ribosomal
Authors & Affiliations
4 authors, click to expand affiliations / ORCID
Cedergren R
Department de biochimie, Université de Montréal, Québec, Canada.
Gray M W
Abel Y
Sankoff D
References (83)
83 references, click to expand
  1. Construction of phylogenetic trees.
    Science. 1967 Jan 20;155(3760):279-84 PMID: 5334057
  2. Complete DNA sequence coding for the large ribosomal RNA of yeast mitochondria.
    Nucleic Acids Res. 1983 Jan 25;11(2):339-48 PMID: 6298722
  3. Nucleotide sequence of Aspergillus nidulans mitochondrial genes coding for ATPase subunit 6, cytochrome oxidase subunit 3, seven unidentified proteins, four tRNAs and L-rRNA.
    Nucleic Acids Res. 1982 Aug 11;10(15):4783-94 PMID: 6290989
  4. Are rRNA sequence comparisons the Rosetta stone of phylogenetics?
    Cell. 1986 Dec 5;47(5):640 PMID: 3779840
  5. Dinoflagellate 17S rRNA sequence inferred from the gene sequence: Evolutionary implications.
    Proc Natl Acad Sci U S A. 1986 Nov;83(22):8644-8 PMID: 16578795
  6. Sequence analysis of 28S ribosomal DNA from the amphibian Xenopus laevis.
    Nucleic Acids Res. 1983 Nov 25;11(22):7795-817 PMID: 6359063
  7. Gram-positive bacteria: possible photosynthetic ancestry.
    Science. 1985;229:762-5 PMID: 11539659
  8. Molecular phylogeny of the animal kingdom.
    Science. 1988 Feb 12;239(4841 Pt 1):748-53 PMID: 3277277
  9. The evolving tRNA molecule.
    CRC Crit Rev Biochem. 1981;11(1):35-104 PMID: 7030617
  10. The structure of the yeast ribosomal RNA genes. 4. Complete sequence of the 25 S rRNA gene from Saccharomyces cerevisae.
    Nucleic Acids Res. 1981 Dec 21;9(24):6953-8 PMID: 6460984
  11. Nucleotide sequence of the soybean mitochondrial 18S rRNA gene: evidence for a slow rate of divergence in the plant mitochondrial genome.
    Plant Mol Biol. 1985 Mar;5(2):119-24 PMID: 24306571
  12. The structure of rat 28S ribosomal ribonucleic acid inferred from the sequence of nucleotides in a gene.
    Nucleic Acids Res. 1983 Nov 25;11(22):7819-31 PMID: 6316273
  13. The rDNA of C. elegans: sequence and structure.
    Nucleic Acids Res. 1986 Mar 11;14(5):2345-64 PMID: 3960722
  14. Structure and evolution of the small subunit ribosomal RNA gene of Crithidia fasciculata.
    Curr Genet. 1986;10(5):405-10 PMID: 2832072
  15. Complete nucleotide sequence of a 23S ribosomal RNA gene from Bacillus stearothermophilus.
    DNA. 1984 Oct;3(5):347-57 PMID: 6096097
  16. An intron in the 23S rRNA gene of the Chlorella chloroplasts: complete nucleotide sequence of the 23S rRNA gene.
    Curr Genet. 1987;11(5):347-52 PMID: 3450409
  17. Complete nucleotide sequence of a 23S ribosomal RNA gene from Escherichia coli.
    Proc Natl Acad Sci U S A. 1980 Jan;77(1):201-4 PMID: 6153795
  18. A rate-independent technique for analysis of nucleic acid sequences: evolutionary parsimony.
    Mol Biol Evol. 1987 Mar;4(2):167-91 PMID: 3447007
  19. 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. 1986 Jan;3(1):1-18 PMID: 3444394
  20. Paramecium mitochondrial genes. II. Large subunit rRNA gene sequence and microevolution.
    J Biol Chem. 1984 Apr 25;259(8):5173-81 PMID: 6715340
  21. Primary structure of the Neurospora crassa small subunit ribosomal RNA coding region.
    Nucleic Acids Res. 1986 Dec 9;14(23):9540 PMID: 2948156
  22. Ribosomal RNA phylogeny and the primary lines of evolutionary descent.
    Cell. 1986 May 9;45(3):325-6 PMID: 3084106
  23. Length variation in eukaryotic rRNAs: small subunit rRNAs from the protists Acanthamoeba castellanii and Euglena gracilis.
    Gene. 1986;44(1):63-70 PMID: 3095190
  24. CONFIDENCE LIMITS ON PHYLOGENIES: AN APPROACH USING THE BOOTSTRAP.
    Evolution. 1985 Jul;39(4):783-791 PMID: 28561359
  25. The ribosomal RNA genes of Drosophila mitochondrial DNA.
    Nucleic Acids Res. 1985 Jun 11;13(11):4029-45 PMID: 2989784
  26. Phylogenetic structure of the prokaryotic domain: the primary kingdoms.
    Proc Natl Acad Sci U S A. 1977 Nov;74(11):5088-90 PMID: 270744
  27. The secondary structures of the Xenopus laevis and human mitochondrial small ribosomal subunit RNA are similar.
    FEBS Lett. 1986 Mar 31;198(2):333-8 PMID: 2420643
  28. Organization and expression of algal (Chlamydomonas reinhardtii) mitochondrial DNA.
    Philos Trans R Soc Lond B Biol Sci. 1988 May 31;319(1193):135-47 PMID: 2901763
  29. Ribosomal RNA sequence suggests microsporidia are extremely ancient eukaryotes.
    Nature. 1987 Mar 26-Apr 1;326(6111):411-4 PMID: 3550472
  30. Variation among human 28S ribosomal RNA genes.
    Proc Natl Acad Sci U S A. 1985 Nov;82(22):7666-70 PMID: 3865188
  31. Origin of the eukaryotic nucleus determined by rate-invariant analysis of rRNA sequences.
    Nature. 1988 Jan 14;331(6152):184-6 PMID: 3340165
  32. What was the first living cell?
    Nature. 1988 Jan 14;331(6152):111-2 PMID: 3340157
  33. Estimates of DNA and protein sequence divergence: an examination of some assumptions.
    Mol Biol Evol. 1983 Dec;1(1):125-42 PMID: 6599960
  34. A common origin of rickettsiae and certain plant pathogens.
    Science. 1985 Nov 1;230(4725):556-8 PMID: 3931222
  35. A discontinuous small subunit ribosomal RNA in Tetrahymena pyriformis mitochondria.
    J Biol Chem. 1986 Apr 15;261(11):5187-93 PMID: 3082879
  36. The small-subunit ribosomal RNA gene sequences from the hypotrichous ciliates Oxytricha nova and Stylonychia pustulata.
    Mol Biol Evol. 1985 Sep;2(5):399-410 PMID: 3939705
  37. Phylogeny and DNA-DNA hybridization.
    Mol Biol Evol. 1986 May;3(3):285-9 PMID: 3444405
  38. Distinctive sequence of human mitochondrial ribosomal RNA genes.
    Nature. 1980 Jul 31;286(5772):460-7 PMID: 6157106
  39. Complete sequence of bovine mitochondrial DNA. Conserved features of the mammalian mitochondrial genome.
    J Mol Biol. 1982 Apr 25;156(4):683-717 PMID: 7120390
  40. Precise localization and nucleotide sequence of the two mouse mitochondrial rRNA genes and three immediately adjacent novel tRNA genes.
    Cell. 1980 Nov;22(1 Pt 1):157-70 PMID: 7428037
  41. Sequence of the small subunit ribosomal RNA gene from the hypotrichous ciliate Euplotes aediculatus.
    J Protozool. 1986 Feb;33(1):26-9 PMID: 3007752
  42. Eocytes: a new ribosome structure indicates a kingdom with a close relationship to eukaryotes.
    Proc Natl Acad Sci U S A. 1984 Jun;81(12):3786-90 PMID: 6587394
  43. Eubacteria, halobacteria, and the origin of photosynthesis: the photocytes.
    Proc Natl Acad Sci U S A. 1985 Jun;82(11):3716-20 PMID: 3858845
  44. Phylogenetic relationships between chlorophytes, chrysophytes, and oomycetes.
    Proc Natl Acad Sci U S A. 1987 Aug;84(16):5823-7 PMID: 3475703
  45. Progressive sequence alignment as a prerequisite to correct phylogenetic trees.
    J Mol Evol. 1987;25(4):351-60 PMID: 3118049
  46. Primary and secondary structure of 26S ribosomal RNA of Oenothera mitochondria.
    Curr Genet. 1985;9(6):505-15 PMID: 3870932
  47. Bacterial evolution.
    Microbiol Rev. 1987 Jun;51(2):221-71 PMID: 2439888
  48. The complete nucleotide sequence of a 23-S rRNA gene from tobacco chloroplasts.
    Eur J Biochem. 1982 May;124(1):13-9 PMID: 6177532
  49. Sequences of the coding and flanking regions of the large ribosomal subunit RNA gene of mosquito mitochondria.
    Nucleic Acids Res. 1984 Oct 25;12(20):7771-85 PMID: 6093053
  50. Two dimensional polyacrylamide gel electrophoresis analysis of Tetrahymena mitochondrial tRNA.
    Curr Genet. 1986;10(5):411-20 PMID: 3127061
  51. An iterative approach from the standpoint of the additive hypothesis to the dendrogram problem posed by molecular data sets.
    J Theor Biol. 1973 Mar;38(3):423-57 PMID: 4632522
  52. Gene organization and primary structure of a ribosomal RNA operon from Escherichia coli.
    J Mol Biol. 1981 May 15;148(2):107-27 PMID: 7028991
  53. Evolutionary diversity of eukaryotic small-subunit rRNA genes.
    Proc Natl Acad Sci U S A. 1986 Mar;83(5):1383-7 PMID: 2419907
  54. Structure of ribosomal RNA.
    Annu Rev Biochem. 1984;53:119-62 PMID: 6206780
  55. Origin and evolution of organisms as deduced from 5S ribosomal RNA sequences.
    Mol Biol Evol. 1987 Sep;4(5):445-72 PMID: 2452957
  56. On the evolutionary descent of organisms and organelles: a global phylogeny based on a highly conserved structural core in small subunit ribosomal RNA.
    Nucleic Acids Res. 1984 Jul 25;12(14):5837-52 PMID: 6462918
  57. The rRNA operon from Zea mays chloroplasts: nucleotide sequence of 23S rDNA and its homology with E.coli 23S rDNA.
    Nucleic Acids Res. 1981 Jun 25;9(12):2853-69 PMID: 7024906
  58. Probing fungal mitochondrial evolution with tRNA.
    Biosystems. 1985;18(3-4):263-7 PMID: 2417640
  59. A test for nucleotide sequence homology.
    J Mol Biol. 1973 Jun 15;77(1):169-64 PMID: 4203659
  60. Eubacterial origin of chlamydiae.
    J Bacteriol. 1986 Aug;167(2):570-4 PMID: 3525517
  61. Primary structure of the Paramecium tetraurelia small-subunit rRNA coding region: phylogenetic relationships within the Ciliophora.
    J Mol Evol. 1986;23(1):53-60 PMID: 3084799
  62. Primary and secondary structure of rat 28 S ribosomal RNA.
    Nucleic Acids Res. 1984 Apr 25;12(8):3677-93 PMID: 6328433
  63. Multiple spacer sequences in the nuclear large subunit ribosomal RNA gene of Crithidia fasciculata.
    EMBO J. 1987 Apr;6(4):1063-71 PMID: 16453755
  64. Molecules as documents of evolutionary history.
    J Theor Biol. 1965 Mar;8(2):357-66 PMID: 5876245
  65. Nucleotide sequence of the Bacillus subtilis ribosomal RNA operon, rrnB.
    Gene. 1985;37(1-3):261-6 PMID: 2414156
  66. Earliest phylogenetic branchings: comparing rRNA-based evolutionary trees inferred with various techniques.
    Cold Spring Harb Symp Quant Biol. 1987;52:825-37 PMID: 3454291
  67. Evolutionary relationships amongst archaebacteria. A comparative study of 23 S ribosomal RNAs of a sulphur-dependent extreme thermophile, an extreme halophile and a thermophilic methanogen.
    J Mol Biol. 1987 May 5;195(1):43-61 PMID: 3116261
  68. The gene for the large (16S) ribosomal RNA from the Locusta migratoria mitochondrial genome.
    Curr Genet. 1987;11(8):631-8 PMID: 3450412
  69. The primary and secondary structure of yeast 26S rRNA.
    Nucleic Acids Res. 1981 Dec 21;9(24):6935-52 PMID: 7335496
  70. Compilation of small ribosomal subunit RNA sequences.
    Nucleic Acids Res. 1986;14 Suppl:r73-118 PMID: 3085068
  71. Complete nucleotide sequence of the 23S rRNA gene of the Cyanobacterium, Anacystis nidulans.
    Nucleic Acids Res. 1984 Apr 11;12(7):3373-86 PMID: 6326060
  72. Mitochondrial origins.
    Proc Natl Acad Sci U S A. 1985 Jul;82(13):4443-7 PMID: 3892535
  73. Comparative anatomy of 16-S-like ribosomal RNA.
    Prog Nucleic Acid Res Mol Biol. 1985;32:155-216 PMID: 3911275
  74. The concept of cellular evolution.
    J Mol Evol. 1977 Sep 20;10(1):1-6 PMID: 903983
  75. The complete nucleotide sequence of mouse 28S rRNA gene. Implications for the process of size increase of the large subunit rRNA in higher eukaryotes.
    Nucleic Acids Res. 1984 Apr 25;12(8):3563-83 PMID: 6328426
  76. Complete nucleotide sequence of the 26S rRNA gene of Physarum polycephalum: its significance in gene evolution.
    Proc Natl Acad Sci U S A. 1983 Jun;80(11):3163-7 PMID: 6304693
  77. The complete nucleotide sequence of a 23S rRNA gene from a blue-green alga, Anacystis nidulans.
    Gene. 1983 Oct;24(2-3):219-25 PMID: 6416928
  78. Primary sequence of wheat mitochondrial 5S ribosomal ribonucleic acid: functional and evolutionary implications.
    Biochemistry. 1981 Jul 7;20(14):4022-9 PMID: 7284306
  79. Sequence of the small subunit ribosomal RNA gene expressed in the bloodstream stages of Plasmodium berghei: evolutionary implications.
    J Protozool. 1986 Nov;33(4):525-9 PMID: 3540280
  80. The mitochondrial genome of the fission yeast, Schizosaccharomyces pombe. Sequence of the large-subunit ribosomal RNA gene, comparison of potential secondary structure in fungal mitochondrial large-subunit rRNAs and evolutionary considerations.
    Eur J Biochem. 1987 Dec 15;169(3):527-37 PMID: 2446871
  81. The complete nucleotide sequence of a rice 25S.rRNA gene.
    Gene. 1985;37(1-3):255-9 PMID: 3902573
  82. Sequence analysis of the maize mitochondrial 26 S rRNA gene and flanking regions.
    Plasmid. 1984 Mar;11(2):141-50 PMID: 6728934
  83. Archaebacterial phylogeny: perspectives on the urkingdoms.
    Syst Appl Microbiol. 1986;7:161-77 PMID: 11542063
Article Info
Journal
Journal of molecular evolution
Abbr.
J Mol Evol
ISSN
0022-2844
Published
1988-00-00
Pages
98-112
Language
English
Region
Germany
NLM ID
0360051
Subset
IM
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