Detection of seven major evolutionary lineages in cyanobacteria based on the 16S rRNA gene sequence analysis with new sequences of five marine Synechococcus strains

Journal of Molecular Evolution

Volumn 48, Issue 6, 1999, Pages 723-739

  Honda, Daiske ^a   Yokota, Akira ^a   Sugiyama, Junta ^a  

^a UNIVERSITY OF TOKYO   (Japan)

Author keywords

Cyanobacteria; Maximum likelihood method; Neighbor joining method; Phylogeny; Rate homo and heterogeneous models; Ribosomal RNA; Synechococcus

Indexed keywords

RNA 16S;

ARTICLE; CYANOBACTERIUM; GENETIC PROCEDURES; MOLECULAR EVOLUTION; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; RNA SEQUENCE; SEQUENCE ANALYSIS; STRAIN DIFFERENCE; TAXONOMY;

CYANOBACTERIA; EVOLUTION; MODELS, GENETIC; MOLECULAR SEQUENCE DATA; OCEANS AND SEAS; PHYLOGENY; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA; WATER MICROBIOLOGY;

EID: 0032999983     PISSN: 00222844     EISSN: None     Source Type: Journal    
DOI: 10.1007/PL00006517     Document Type: Article

References (89)

1. Adachi J, Hasegawa M (1995) Improved dating of the human/ chimpanzee separation in the mitochondrial DNA tree: Heterogeneity among amino acid sites. J Mol Evol 40:622-628
2. Adachi J, Hasegawa M (1996) Computer science monographs, No. 28. MOLPHY version 2.3. - Programs for molecular phylogenetics based on maximum likelihood. Institute of Statistical Mathematics, Tokyo
3. Anagnostidis K, Komárek J (1988) Modern approach to the classification system of cyanophytes. 3 - Oscillatoriales. Arch Hydrobiol (Suppl 80) Algol Stud 50/53:327-472
4. Bhattacharya D, Medlin L (1995) The phylogeny of plastids: a review based on comparisons of small-subunit ribosomal RNA coding regions. J Phycol 31:489-498
5. Bryant DA (1994) The molecular biology of cyanobacteria. Kluwer Academic, Dordrecht, The Netherlands, p 881
6. Castenholz RW (1989a) Subsection III. Order Oscillatoriales. In: Staley JT, Bryant MP, Pfennig N, Holt JG (eds) Bergey's manual of systematic bacteriology, Vol 3. Williams and Wilkins, Baltimore, pp 1771-1780
7. Castenholz RW (1989b) Subsection IV. Order Nostocales. In: Staley JT, Bryant MP, Pfennig N, Holt JG (eds) Bergey's manual of systematic bacteriology, Vol 3. Williams and Wilkins, Baltimore, pp 1780-1793
8. Castenholz RW (1989c) Subsection V. Order Stigonematales. In: Staley JT, Bryant MP, Pfennig N, Holt JG (eds) Bergey's manual of systematic bacteriology, Vol 3. Williams and Wilkins, Baltimore, pp 1794-1799
9. Castenholz RW, Waterbury JB (1989a) Preface. In: Staley JT, Bryant MP, Pfennig N, Holt JG (eds) Bergey's manual of systematic bacteriology, Vol 3. Williams and Wilkins, Baltimore, pp 1710-1727
10. Castenholz RW, Waterbury JB (1989b) Taxa of the Cyanobacteria. In: Staley JT, Bryant MP, Pfennig N, Holt JG (eds) Bergey's manual of systematic bacteriology, Vol 3. Williams and Wilkins, Baltimore, pp 1727-1728
11. Chisholm SW, Olson RJ, Zettler ER, Goericke R, Waterbury JB, Welschmeyer NA (1988) A novel free-living prochlorophyte abundant in the oceanic euphotic zone. Nature 334:340-343
12. De Ley J, Mannheim W, Segers P, Lievens A, Denijn M, Vanhoucke M Gillis M (1987) Ribosomal ribonucleic acid cistron similarities and taxonomic neighborhood of Brucella and CDC group Vd. Int J Syst Bacteriol 37:35-42
13. Delwiche CF, Palmer JD (1996) Rampant horizontal transfer and duplication of rubisco genes in cubacteria and plastids. Mol Biol Evol 13:873-882
14. Delwiche CF, Kunsel M, Palmer JD (1995) Phylogenetic analysis of tufA sequences indicates a cyanobacterial origin of all plastids. Mol Phylogen Evol 4:110-128
15. Douglas SE, Murphy CA (1994) Structural, transcriptional, and phylogenetic analyses of the atpB gene cluster from the plastid of Cryptomonas Φ (Cryptophyceae). J Phycol 30:329-340
16. Dyer DL, Gafford RD (1961) Some characteristics of a thermophilic blue-green alga. Science 134:616-617
17. Felsenstein J (1981) Evolutionary trees from DNA sequences: A maximum likelihood approach. J Mol Evol 17:368-376
18. Felsenstein J (1985) Confidence limits on phylogenies: An approach using the bootstrap. Evolution 39:783-791
19. Geitler L (1932) Cyanophyceae. Rabenhorst's Kryptogamenflora von Deutschland, Österreich und der Schweiz 14:1-1196. Akad Verslagsges, Leipzig (Reprinted 1971, Johnson, New York)
20. Giovannoni SJ, Turner S, Olsen GJ, Barns S, Lane DJ, Pace NR (1988) Evolutionary relationships among cyanobacteria and green chloroplasts. J Bacteriol 170:3584-3592
21. Golden SS, Nalty MS, Cho D-SC (1989) Genetic relationship of two highly studied Synechococcus strains designated Anacystis nidulans. J Bacteriol 171:24-29
22. Goodfellow M, O'Donnell AG (1993) Roots of bacterial systematics. In: Goodfellow M, O'Donnell AG (eds) Handbook of new bacterial systematics. Academic Press, London, pp 3-54
23. Guglielmi G, Cohen-Bazire G (1982a) Structure et distribution des pores et des perforations de l'enveloppe de peptidoglycane chez quelques cyanobactéries. Protistologica 18:151-165
24. Guglielmi G, Cohen-Bazire G (1982b) Étude comparée de la structure et de la distribution des filament extracellulaires ou fimbriae chez quelques cyanobactéries. Protistologica 18:167-177
25. Hasegawa M, Hashimoto T (1993) Ribosomal RNA trees misleading? Nature 361:23
26. Hasegawa M, Kishino H (1994) Accuracies of the simple methods for estimating the bootstrap probability of a maximum-likelihood tree. Mol Biol Evol 11:142-145
27. Hasegawa M, Kishino H, Yano T (1985) Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. J Mol Evol 22:160-174
28. Hess WR, Weihe A, Loiseaux-de Goër S, Partensky F, Vaulot D (1995) Characterization of the single psbA gene of Prochlorococcus marinus CCMP 1375 (Prochlorophyta). Plant Mol Biol 27:1189-1196
29. Hills DM, Huelsenbeck JP, Swofford DL (1994) Hobgoblin of phylogenetics? Nature 369:363-364
30. Ishida T, Yokota A, Sugiyama J (1997) Phylogenetic relationships of filamentous cyanobacterial taxa inferred from 16S rRNA sequence divergence. J Gen Appl Microbiol 43:237-241
31. Johnson PW, Sieburth JMcN (1979) Chroococcoid cyanobacteria in the sea: A ubiquitous and diverse phototrophic biomass. Limnol Oceanogr 24:928-935
32. Kishino H, Hasegawa M (1989) Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data, and the branching order in Hominoidea. J Mol Evol 29:170-179
33. Kishino H, Miyata T, Hasegawa M (1990) Maximum likelihood inference of protein phylogeny and the origin of chloroplasts. J Mol Evol 31:151-160
34. La Roche J, van der Staay GWM, Partensky F, Ducret A, Aebersold R, Li R, Golden SS, Hiller RG, Wrench PM, Larkum AWD, Green BR (1996) Independent evolution of the prochlorophyte and green plant chlorophyll a/b light-harvesting proteins. Proc Natl Acad Sci USA 93:15244-15248
35. Lane DJ (1991) 16S/23S rRNA sequencing. In: Stackebrandt E, Goodfellow M (eds) Nucleic acid techniques in bacterial systematics. John Wiley & Sons, Chichester, pp 115-174
36. Lewin RA (1977) Prochloron, a type genus of the Prochlorophyta. Phycologia 16:216
37. Lewin RA (1989) Group II. Order Prochlorales Lewin 1977. In: Staley JT, Bryant MP, Pfennig N, Holt JG (eds) Bergey's manual of systematic bacteriology. Vol 3. Williams and Wilkins, Baltimore, pp 1799-1806
38. Lockhart PJ, Penny D, Hendy MD, Howe CJ, Beanland TJ, Larkum AWD (1992) Controversy on chloroplast origins. FEBS Lett 301: 127-131
39. Madigan MT, Martinko JM, Parker J (1996) Brock biology of microorganisms, 8th ed. Prentice-Hall, Englewood Cliffs, NJ p 986
40. Maidak BL, Larsen N, McCaughey MJ, Overbeek R, Olsen GJ, Fogel K, Blandy J, Woese CW (1994) The Ribosomal Database project. Nucleic Acids Res 22:3485-3487
41. Masui R, Wada K, Matsubara H, Rogers LJ (1988) Properties and amino acid sequence of the ferredoxin from the unicellular cyanobacterium Synechococcus 6307. Phytochemistry 27:2821-2826
42. Miyadoh S (1997) Atlas of actinomycetes. Asakura, Tokyo, p 223
43. Morden CW, Golden SS (1989) psbA genes indicate common ancestry of prochlorophytes and chloroplasts. Nature 337:382-385
44. Murray MG, Thompson WF (1980) Rapid isolation of high molecular weight plant DNA. Nucleic Acids Res 8:4321-4325
45. Neilan BA, Jacobs D, Del Dot T, Blackall LL, Hawkins PR, Cox PT, Goodman AE (1997) rRNA sequences and evolutionary relationships among toxic and nontoxic cyanobacteria of the genus Microcystis. Int J Syst Bacteriol 47:693-697
46. Nelissen B, De Baere R, Wilmotte A, De Watcher R (1996) Phylogenetic relationships of Nonaxenic filamentous cyanobacterial strains based on 16S rRNA sequence analysis. J Mol Evol 42:194-200
47. Olsen GJ (1988) Phylogenetic analysis using ribosomal RNA. Methods Enzymol 164:793-812
48. Olsen GJ, Matsuda H, Hagstrom R, Overbeek R (1994) FastDNAml: A tool for construction of phylogenetic trees of DNA sequences using maximum likelihood. Comput Appl Biosci 10:41-48
49. Palenik B, Haselkorn R (1992) Multiple evolutionary origins of prochlorophytes, the chlorophyll b-containing prokaryotes. Nature 355:265-267
50. Palenik B, Swift H (1996) Cyanobacterial evolution and prochlorophyte diversity as seen in DNA-dependent RNA polymerase gene sequences. J Phycol 32:638-646
51. Provasoli L (1968) Media and prospects for the cultivation of marine algae. In: Watanabe A, Hattori A (eds) Culture and collection of algae. Proceedings of the U.S. Japan Conference, Hakone, September 1966. Japanese Society of Plant Physiologists, Tokyo, pp 63-75
52. Rippka R, Cohen-Bazire G (1983) The Cyanobacteriales: A legitimate order based on the type strain Cyanobacterium stanieri? Ann Microbiol 134B:21-36
53. Rippka R, Herdman M (1992) Pasteur Culture Collection of cyanobacterial strains in axenic culture. Catalogue and taxonomic handbook. Vol. I. Catalogue of strains. Institut Pasteur, Paris, p 103
54. Rippka R, Waterbury J, Cohen-Bazire G (1974) A cyanobacterium which lacks thylakoids. Arch Microbiol 100:419-436
55. Rippka R, Deruelles J Waterbury JB, Herdman M, Stanier RY (1979) Generic assignments, strain histories and properties of pure cultures of cyanobacteria. J Gen Microbiol 111:1-61
56. Saitou N, Nei M (1987) The neighbor-joining method: A new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406-425
57. Seewaldt E, Stackebrandt E (1982) Partial sequence of 16S ribosomal RNA and the phylogeny of Prochloron. Nature 295:618-620
58. Shimada A, Kanai S, Maruyama T (1995) Partial sequence of ribulose-1,5-bisophosphate carboxylase/oxygenase and the phylogeny of Prochloron and Prochlorococcus (Prochlorales). J Mol Evol 40: 671-677
59. Sonoyama M, Motoki A, Okamoto G, Hirano M, Ishida H, Katoh S (1996) Secondary structure and thermostability of the photosystem II manganese-stabilizing protein of the thermophilic cyanobacterium Synechococcus elongatus. Biochim Biophys Acta 1297:167-170
60. Stackebrandt E, Rainey FA, Ward-Rainey NL (1997) Proposal for a new hierarchic classification system, Actinobacteria classis nov. Int J Syst Bacteriol 47:479-491
61. Stockner JG, Antia NJ (1986) Algal picoplankton from marine and freshwater ecosystems: A multidisciplinary perspective. Can J Fish Aquat Sci 43:2472-2503
62. Strimmer K, von Haeseler A (1996) Quartet puzzling: A quartet maximum-likelihood method for reconstructing tree topologies. Mol Biol Evol 13:964-969
63. Tamura K, Nei M (1993) Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol Biol Evol 10:512-526
64. Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22:4673-4680
65. Turner S (1997) Molecular systematics of oxygenic photosynthetic bacteria. Pl Syst Evol (Suppl)11:13-52
66. Turner S, Burger-Wiersma T, Giovannoni SJ, Mur LR, Pace NR (1989) The relationship of a prochlorophyte Prochlorothrix hollandica to green chloroplasts. Nature 337:380-382
67. Uchino Y, Yokota A, Sugiyama J (1997) Phylogenetic position of the marine subdivision of Agrobacterium species based on 16S rRNA sequence analysis. J Gen Appl Microbiol 43:243-247
68. Urbach E, Robertson DL, Chisholm SW (1992) Multiple evolutionary origins of prochlorophytes within the cyanobacterial radiation. Nature 355:267-270
69. Urbach E, Scanlan DJ, Distel DL, Waterbury JB, Chisholm SW (1998) Rapid diversification of marine picophytoplankton with dissimilar light-harvesting structures inferred from sequences of Prochlorococcus and Synechococcus (Cyanobacteria). J Mol Evol 46:188-201
70. Uzzell T, Corbin KW (1971) Fitting discrete probability distributions to evolutionary events. Science 172:1089-1096
71. Van de Peer Y, Jansen J, De Rijk P, De Wachter R (1997) Database on the structure of small ribosomal subunit RNA. Nucleic Acids Res 25:111-116
72. Vioque A (1997) The RNase P RNA from cyanobacteria: short tandemly repeated repetitive (STRR) sequences are present within the RNase P RNA gene in heterocyst-forming cyanobacteria. Nucleic Acids Res 25:3471-3477
73. Wakeley J (1993) Substitution rate variation among sites in hypervariable region 1 of human mitochondrial DNA. J Mol Evol 37:613-623
74. Waterbury JB, Rippka R (1989) Subsection I. Order Chroococcales Wettstein 1924, emend. Rippka et al., 1979. In: Staley JT, Bryant MP, Pfennig N, Holt JG (eds) Bergey's manual of systematic bacteriology, Vol 3. Williams and Wilkins, Baltimore, pp 1728-1746
75. Waterbury JB, Watson SW, Guillard RRL, Brand LE (1979) Widespread occurrence of a unicellular, marine, planktonic, cyanobacterium. Nature 277:293-294
76. Watson GMF, Tabita FR (1996) Regulation, unique gene organization, and unusual primary structure of carbon fixation genes from a marine phycoerythrin-containing cyanobacterium. Plant Mol Biol 32:1103-1115
77. Watson GMF, Tabita FR (1997) Microbial ribulose 1,5-bisphosphate carboxylase/oxygenase: a molecule for phylogenetic and enzymological investigation. FEMS Microbiol Lett 146:13-22
78. Whitton BA (1992) Diversity, ecology, and taxonomy of the cyanobacteria. In: Mann NH, Carr NG (eds) Photosynthetic prokaryotes. Plenum Press, New York, pp 1-51
79. Wilmotte A (1991) Taxonomic study of marine oscillatoriacean strains (Cyanophyceae, Cyanobacteria) with narrow trichomes. I. Morphological variability and autecological features. Arch Hydrobiol (Suppl 92) Algol Studies 64:215-248
80. Wilmotte A (1994) Molecular evolution and taxonomy of the Cyanobacteria. In: Bryant DA (ed) The molecular biology of cyanobacteria. Kluwer Academic, Dordrecht, The Netherlands, pp 1-25
81. Wilmotte A, Golubic S (1991) Morphological and genetic criteria in the taxonomy of Cyanophyta/Cyanobacteria. Arch Hydrobiol (Suppl 92) Algol Stud 64:1-24
82. Wilmotte AMR, Stam WT (1984) Genetic relationships among cyanobacterial strains originally designated as 'Anacystis nidulans' and some other Synechococcus strains. J Gen Microbiol 130:2737-2740
83. Wilmotte A, Turner S, Van de Peer Y, Pace NR (1992) Taxonomic study of marine oscillatoriacean strains (cyanobacteria) with narrow trichomes. II. Nucleotide sequence analysis of the 16S ribosomal RNA. J Phycol 28:828-838
84. Woese CR (1987) Bacterial evolution. Microbiol Rev 51:221-271
85. Yamaoka T, Satoh K, Katoh S (1978) Photosynthetic activities of a thermophilic blue-green alga. Plant Cell Physiol 19:943-954
86. Yang Z (1994) Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: Approximate methods. J Mol Evol 39:306-314
87. Yang Z, Kumar S (1996) Approximate methods for estimating the pattern of nucleotide substitution and the variation of substitution rates among sites. Mol Biol Evol 13:650-659
88. Zehr JP, Ohki K, Fujita Y, Landry D (1991) Unique modification of adenine in genomic DNA of the marine cyanobacterium Trichodesmium sp. strain NIBB 1067. J Bacteriol 173:7059-7062
89. Zehr JP, Mellon MT, Hiorns WD (1997) Phylogeny of cyanobacterial nifH genes: Evolutionary implications and potential applications to natural assemblages. Microbiology 143:1443-1450