A molecular test of cyanobacterial phylogeny: inferences from constraint analyses

Hydrobiologia - Tập 468 - Trang 135-145 - 2002
M. K. Litvaitis1
1Department of Zoology and Center for Marine Biology, University of New Hampshire, Durham, U.S.A.

Tóm tắt

Parsimony and neighbor-joining analyses of 16S rDNA nucleotide sequences of 68 species and strains of cyanobacteria and prochlorophytes supported a monophyletic Nostocales, a monophyletic Stigonematales, three independent lineages of prochlorophytes within the cyanobacteria, and a paraphyletic Chroococcales (p<0.0001) and Oscillatoriales (p = 0.0147). Within the Oscillatoriales, the genus Oscillatoria formed an unnatural taxon (p<0.0001) and needs major revisions. Using constraint analysis, the genus Microcystis was found to be monophyletic and the paraphyletic positions of Microcystis elabens and M. holsatica are probably due to long-branch attraction. Further, a separation of Chroococcales based on varying levels of polyunsaturated fatty acids is more consistent with nucleotide-based phylogenies than with existing morphological groupings. It is proposed that Chroococcales be redefined to exclude the genus Microcystis, and that a new order be erected for Microcystis. Finally, it is more parsimonious to assume a common cyanobacterial/prochlorophyte ancestor, than to evoke de novo synthesis of chlb in each prochlorophyte lineage plus in the lineage leading to green chloroplasts. This common ancestor is proposed to have contained both chlorophyll a and b plus phycobilins. Subsequent multiple losses of chlb in cyanobacteria and the loss of chla and phycobilins in prochlorophytes, led to the currently observed pigment distribution. It is therefore, recommended that Prochlorales be reclassified as cyanobacteria.

Tài liệu tham khảo

Anagnostidis, K. & J. Komárek, 1985. Modern approach to the classification system of cyanophytes. 1. Introduction. Arch. Hydrobiol., Suppl. 71, Algol. Studies 38/39: 291–302. Anagnostidis, K. & J. Komárek, 1988. Modern approach to the classification system of cyanophytes. 3. Oscillatoriales. Arch. Hydrobiol., Suppl. 80, Algol. Studies 50/53: 327–472. Anagnostidis, K. & J. Komárek, 1990. Modern approach to the classification system of cyanophytes. 5. Stigonematales. Arch. Hydrobiol., Suppl. 86, Algol. Studies 59: 1–73. Burger‐Wiersma, T., M. Veenhuis, H. J. Korthals, C. C. M. Van de Wiel & L. R. Mur, 1986. A new prokaryote containing Chlsa and b. Nature 320: 262–264. Castenholz, R. W. & J. B. Waterbury, 1989. Oxygenic photosynthetic bacteria sect 19., Group I. Cyanobacteria. In Staley, J. T., M. P. Bryant, N. Pfennig & J. G. Holt (eds), Bergey's Manual of Systematic Bacteriology. Vol 3. Williams and Wilkins Co, Baltimore: 1710–1728. Chisholm, S. W., R. J. Olson, E. R. Zettler, R. Goericke, J. B. Waterbury & N. A. Welschmeyer, 1988. A novel free-living prochlorophyte abundant in the oceanic euphotic zone. Nature 334: 340–343. Delwiche, C. F. & J. D. Palmer, 1996. Rampant horizontal transfer and duplication of Rubisco genes in eubacteria and plastids. Mol. Biol. Evol. 13: 873–882. Desikachary, T., 1973. Status of classical taxonomy. In Carr, N. G. & B. A. Whitton (eds), The Biology of Blue-Green Algae. University of California Press, Berkeley: 473–486. Drouet, F., 1981. Summary of the classification of blue-green algae. Beihefte Nova Hedwigia 66: 135–209. Felsenstein, J., 1978. Cases in which parsimony or compatibility methods will be positively misleading. Syst. Zool. 40: 366–375. Florenzano, G., W. Balloni & R. Materassi, 1986. Nomenclature of Prochloron didemni (Lewin, 1977) sp. n., nom. rev., Prochloron (Lewin, 1976) gen. n., nom. rev., Prochloraceae fam. n., Prochlorales ord. n., nom. rev. in the class Photobacteria Gibbons and Murray 1978. Internat. J. Syst. Bacteriol. 36: 351–353. Garcia‐Pichel, F., U. Nubel & G. Muyzer, 1998. The phylogeny of unicellular, extremely halotolerant cyanobacteria. Arch. Microbiol. 169: 469–482. Geitler, L., 1925. Synoptische Darstellung der Cyanophyceen in morphologischer und systematischer Hinsicht. Beih. Bot. Centralbl. 2: 163–324. Geitler, L., 1932. Cyanophyceae. In Kolkwitz, R. (ed.), Rabenhorst's Kryptogamenflora von Deutschland, österreich und der Schweiz. Vol XIV. Akadem. Verlagsgesellsch., Leipzig. Reprinted 1971, Johnson, New York: 1–1196. Holton, R. W., H. H. Blecker & T. S. Stevens, 1968. Fatty acids in the blue-green algae: possible relation to phylogenetic position. Science 160: 545–547. Honda, D., A. Yokota & J. Sugiyama, 1999. Detection of seven major evolutionary lineages in cyanobacteria based on 16S rRNA gene sequence analysis with new sequences of five marine Synechococcus strains. J. Mol. Evol. 48: 723–739. Higgins, D. G., A. J. Bleasby & R. Fuchs, 1992. CLUSTAL V: improved software for multiple sequence alignment. Comp. Appl. Biosci. 8: 189–191. Johns, R. B., P. D. Nichols, F. T. Gillian, G. J. Perry & J. K. Volkman, 1981. Lipid composition of the symbiotic prochlorophyte in relation to the host. Comp. Biochem. Physiol. 69B: 843–849. Kenyon, C. N., 1972. Fatty acid composition of unicellular strains of blue-green algae. J. Bacteriol. 109: 827–834. Kenyon, C. N., R. Rippka & R. Y. Stanier, 1972. Fatty acid composition and physiological properties of some filamentous blue-green algae. Arch. Microbiol. 83: 216–236. Komárek, J. & K. Anagnostidis, 1986. Modern approach to the classification system of cyanophytes. 2. Chroococcales. Arch. Hydrobiol., Suppl. 73, Algol. Studies 43: 157–226. Komárek, J. & K. Anagnostidis, 1989. Modern approach to the classification system of cyanophytes. 4. Nostocales. Arch. Hydrobiol., Suppl. 82, Algol. Studies 56: 247–345. Kondo, R., M. Komura, S. Hiroishi & Y. Hata, 1998. Detection and 16S rDNA sequence analysis of a bloom-forming cyanobacterial genus Microcystis. Fish. Sci. 64: 840–841. Lachance, M.-A., 1981. Genetic relatedness of heterocystous cyanobacteria by deoxyribonucleic acid-deoxyribonucleic acid reassociation. Int. J. Syst. Bact. 31: 139–147. Larson, A., 1994. The comparison of morphological and molecular data in phylogenetic systematics. In Schierwater, B., B. Streit, G. B. Wagner & R. DeSalle (eds), Molecular Ecology and Evolution: Approaches and Applications. Birkhäuser Verlag, Basel: 371–390. Lewin, R. A., 1976. Prochlorophyta as a proposed new division of algae. Nature 261: 697–698. Lewin, R. A., 1977. Prochloron, type genus of the Prochlorophyta. Phycologia 16: 217. Lewin, R. A., 1981. Prochloron and the theory of symbiogenesis. Ann. New York Acad. Sci. 361: 325–329. Lewin, R. A., 1984. Prochloron — a status report. Phycologia 23: 203–204. Lockhart, P. J., M. A. Steel, M. D. Hendy & D. Penny, 1994. Recovering evolutionary trees under a more realistic model of sequence evolution. Mol. Biol. Evol. 11: 605–621. Matthijs, H. C. P., G. W. M. Van der Staay & L. R. Mur, 1994. Prochlorophytes: The 'other’ cyanobacteria? In Bryant, D. A. (ed.), The Molecular Biology of Cyanobacteria. Kluwer Academic Publishers, Dordrecht, The Netherlands: 49–64. Mazel, D., J. Houmard, A. M. Castets & N. Tabdeau de Marsac, 1990. Highly repetitive DNA sequences in cyanobacterial genomes. J. Bacteriol. 172: 2755–2761. Morden, C. W. & S. S. Golden, 1989. psbA genes indicate common ancestry of prochlorophytes and chloroplasts. Nature 337: 383–385. Miller, K. R. & J. S. Jacob, 1989. On Prochlorothrix. Nature 338: 303–304. Neilan, B., D. Jacobs, T. Del Dot, L. Blackall, P. R. Hawkins, P. T. Cox & A. E. Goodman, 1997. rRNA sequences and evolutionary relationships among toxic and non-toxic cyanobacteria of the genus Microcystis. Internat. J. Syst. Bacteriol. 47: 693–697. Nelissen, B., R. De Baere, A. Wilmotte & R. De Wachter, 1996. Phylogenetic relationships of nonaxenic filamentous cyanobacterial strains based on 16S rDNA sequence analysis. J. Mol. Evol. 42: 194–200. Palenik, B. & R. Haselkorn, 1992. Multiple evolutionary origins of prochlorophytes, the chlorophyll b-containing prokaryotes. Nature 355: 265–267. Pearson, J. E. & J.M. Kingsbury, 1966. Culturally induced variation in four morphologically diverse blue-green algae. Am. J. Bot. 53: 192–200. Rippka, R. & M. Herdman, 1992. Pasteur Culture Collection of Cyanobacteria. Catalogue and Taxonomic Handbook. Vol I: Catalogue of Strains. Institute Pasteur, Paris: 103 pp. Rippka, R., J. Deruelles, J. B. Waterbury, M. Herdman & R. Y. Stanier, 1979. Generic assignments, strain histories and properties of pure cultures of cyanobacteria. J. Gen. Microbiol. 111: 1–61. Rudi, K., O. M. Skulberg & K. S. Jakobsen, 1998. Evolution of cyanobacteria by exchange of genetic material among phyletically related strains. J. Bacteriol. 180: 3453–3461. Saitou, N. & M. Nei, 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4: 406–425. Stam, W. T., 1980. Relationships between a number of filamentous blue-green algal strains Cyanophyceae. revealed by DNA-DNA hybridization. Arch. Hydrobiol., Suppl. 56, Algol. Studies 25: 351–374. Stam, W. T. & G. Venema, 1975. The use of DNA-DNA hybridization for determination of the relationship between some blue-green algae Cyanophyceae. Acta Bot. Neerland. 26: 327–342. Stanier, R. Y., W. R. Sistrom, T. A. Hansen, B. A. Whitton, R. W. Castenholz, N. Pfennig, V. N. Gorlenko, E. N. Kondratieva, K. E. Eimhjellen, R. Whittenbury, R. L. Gherna & H. G. Trüper, 1978. Proposal to place the nomenclature of the cyanobacteria blue-green algae under the rules of the International Code of Nomenclature of Bacteria. International J. Syst. Bacteriol. 28: 335–336. Swofford, D., 1999. PAUP*: Phylogenetic Analysis Using Parsimony (and other methods), vers. 4.0, Sinauer Associates, Sunderland, MA. Tomitani, A., K. Okada, H. Miyashita, H. C. Matthijs, T. Ohno & A. Tanaka, 1999. Chlorophyll b and phycobilins in the common ancestor of cyanobacteria and chloroplasts. Nature 400: 159–162. Turner, S., T. Burger-Wiersma, S. J. Giovannoni, L. R. Murt & N. R. Pace, 1989. The relationship of a prochlorophyte Prochlorothrix hollandica to green chloroplasts. Nature 337: 380–382. Urbach, E., D. L. Robertson & S. W. Chisholm, 1992. Multiple evolutionary origins of prochlorophytes within the cyanobacterial radiation. Nature 355: 267–270. Urbach, E., D. J. Scanlan, D. L. Distel, J. B. Waterbury & S. W. Chisholm, 1998. Rapid diversification of marine phytoplankton with dissimilar light-harvesting structures inferred from sequences of Prochlorococcus and Synechococcus (Cyanobacteria). J. Mol. Evol. 46: 188–201. Ward, D. M., M. M. Bateson, R. Weller & A. L. Ruff‐Roberts, 1992. Ribosomal RNA analysis of microorganisms as they occur in nature. Adv. Microbiol. Ecol. 12: 219–286. Waterbury, J. B. & R. Rippka, 1989. Oxygenic photosynthetic bacteria sect 19., Subsection I. Order Chroococcales. In Staley, J. T., M. P. Bryant, N. Pfennig & J. G. Holt (eds), Bergey's Manual of Systematic Bacteriology. Vol 3. Williams and Wilkins Co, Baltimore: 1729–1746. Wilmotte, A., 1994. Molecular evolution and taxonomy of cyanobacteria. In Bryant, D. A. (ed.), The Molecular Biology of Cyanobacteria. Kluwer Academic Publishers, Dordrecht, The Netherlands: 1–25.