Phylogeny of the non-photosynthetic green micro-algal genus Prototheca (Trebouxiophyceae, Chlorophyta) and related taxa inferred from SSU and LSU ribosomal DNA partial sequence data

FEMS Microbiology Letters

Volumn 223, Issue 2, 2003, Pages 275-280

  Ueno, Ryohei ^a   Urano, Naoto ^a   Suzuki, Motofumi ^b  

^a JAPAN SCIENCE AND TECHNOLOGY AGENCY   (Japan)

^b RIKEN BIORESOURCE CENTER   (Japan)

Author keywords

Large subunit rDNA; Phylogeny; Prototheca; Small subunit rDNA

Indexed keywords

LARGE SUBUNIT RIBOSOMAL DEOXYRIBONUCLEOSIDE; LARGE SUBUNIT RIBOSOMAL RNA; NUCLEOTIDE; RIBOSOME DNA; SMALL SUBUNIT RIBOSOMAL DEOXYRIBONUCLEOSIDE; SMALL SUBUNIT RIBOSOMAL RNA; UNCLASSIFIED DRUG;

5' UNTRANSLATED REGION; ARTICLE; AUTOTROPHY; AUXENOCHORELLA PROTOTHECOIDES; CHLORELLA; DNA SEQUENCE; GENETIC VARIABILITY; GREEN ALGA; LOWER PLANT; NONHUMAN; NUCLEOTIDE SEQUENCE; PARSIMONY ANALYSIS; PHOTOSYNTHESIS; PHYLOGENETIC TREE; PHYLOGENY; PRIORITY JOURNAL; PROTOTHECA MORIFORMIS; PROTOTHECA ULMEA; PROTOTHECA ZOPFII; SPECIES DIFFERENTIATION; TAXONOMY; TECHNIQUE;

ALGAE; AUXENOCHLORELLA; AUXENOCHLORELLA PROTOTHECOIDES; CHLOROPHYTA; PROTOTHECA; PROTOTHECA MORIFORMIS; PROTOTHECA STAGNORA; PROTOTHECA ULMEA; PROTOTHECA WICKERHAMII; PROTOTHECA ZOPFII; TREBOUXIOPHYCEAE;

EID: 0038771938     PISSN: 03781097     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0378-1097(03)00394-X     Document Type: Article

References (31)

1. Krüger W. Beiträge zur Kenntniss der Organismen des Saftflusses (sog. Schleimflusses) der Laubbäume. Parts I and II. Zopf's Beitr. Physiol. Morphol. Nied. Organ. (Leipzig). 4:1894;69-116.
2. Pore R.S. Nutritional basis for relating Prototheca and Chlorella. Can. J. Microbiol. 18:1972;1175-1177.
3. Conte M.V., Pore R.S. Taxonomic implications of Prototheca and Chlorella cell wall polysaccharide characterization. Arch. Mikrobiol. 92:1973;227-233.
4. Kessler E. Physiological and biochemical contributions to the taxonomy of the genus Prototheca. I. Hydrogenase, acid tolerance, salt tolerance, thermophily, and liquefaction of gelatin. Arch. Microbiol. 113:1977;139-141.
5. Kessler, E. (1982) Chemotaxonomy in the Chlorococcales. In: Progress in Phycological Research, Vol. 1 (Round, F.E. and Chapman, D.J., Eds.), pp. 111-135. Elsevier Biomedical, Amsterdam.
6. Huss V.A.R., Sogin M.L. Phylogenetic position of some Chlorella species within the Chlorococcales based upon complete small-subunit ribosomal RNA sequences. J. Mol. Evol. 31:1990;432-442.
7. Huss V.A.R., Frank C., Hartmann E.C., Hirmer M., Kloboucek A., Seidel B.M., Wenzeler P., Kessler E. Biochemical taxonomy and molecular phylogeny of the genus Chlorella sensu lato (Chlorophyta). J. Phycol. 35:1999;587-598.
8. Ueno R., Urano N., Wada S., Kimura S. Optimization of heterotrophic culture conditions for n-alkane utilization and phylogenetic position based on the 18S rDNA sequence of a thermotolerant Prototheca zopfii strain. J. Biosci. Bioeng. 94:2002;160-165.
9. 2 from glucose at 40°C. Arch. Microbiol. 177:2002;244-250.
10. Pore, R.S. (1998) Prototheca, a yeastlike alga. In: The Yeasts, A Taxonomic Study, 4th edn. (Kurtzman, C.P. and Fell, J.W., Eds.), pp. 881-887. Elsevier Science, Amsterdam.
11. Kerfin W., Kessler E. Physiological and biochemical contributions to the taxonomy of the genus ProtothecaII. Starch hydrolysis and base composition of DNA. Arch. Microbiol. 116:1978;105-107.
12. Kurtzman C.P., Robnett C.J. Identification and phylogeny of ascomycetous yeasts from analysis of nuclear large subunit (26S) ribosomal DNA partial sequences. Antonie van Leeuwenhoek. 73:1998;331-371.
13. Xing S., Aharon G. A method for RNA isolation from marine macro-algae. Anal. Biochem. 174:1988;650-657.
14. Kim C.S., Lee C.H., Shin J.S., Chung Y.S., Hyung N.I. A simple and rapid method for isolation of high quality genomic DNA from fruit trees and conifers using PVP. Nucleic Acids Res. 25:1997;1085-1086.
15. Medlin L., Elwood H.J., Stickel S., Sogin M.L. The characterization of enzymatically amplified eukaryotic 16S-like rRNA-coding regions. Gene. 71:1988;491-499.
16. O'Donnell, K. (1993) Fusarium and its near relatives. In: The Fungal Holomorph: Mitotic, Meiotic and Pleomorphic Speciation in Fungal Systematics (Reynolds, D.R. and Taylor, J.W., Eds.), pp. 225-233. CAB International, Wallingford.
17. Elwood H.J., Olsen G.J., Sogin M.L. The small-subunit ribosomal RNA gene sequences from the hypotrichous ciliates Oxytricha nova and Stylonychia pustulata. Mol. Biol. Evol. 2:1985;399-410.
18. Sanger F., Nicklen S., Coulson A.R. DNA sequencing with chain-terminating inhibitors. Proc. Natl. Acad. Sci. USA. 74:1977;5463-5467.
19. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution. 39:1985;783-791.
20. Kimura M. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J. Mol. Evol. 16:1980;111-120.
21. Saitou N., Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4:1987;406-425.
22. Thompson J.D., Higgins D.G., Gibson T.J. Clustal W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22:1994;4673-4680.
23. Maddison, D.R. and Maddison, W.P. (2000) MacClade, version 4.0. Analysis of Phylogeny and Character Evolution. Sinauer Associates, Sunderland, MA.
24. Swofford, D.L. (2001) PAUP*. Phylogenetic Analysis using Parsimony (*and Other Methods), version 4. Sinauer Associates, Sunderland, MA.
25. Altschul S.F., Madden T.L., Schäffer A.A., Zhang J., Zhang Z., Miller W., Lipman D.J. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25:1997;3389-3402.
26. Tartar A., Boucias D.G., Adams B.J., Becnel J.J. Phylogenetic analysis identifies the invertebrate pathogen Helicosporidium sp. as a green alga (Chlorophyta). Int. J. Syst. Evol. Microbiol. 52:2002;273-279.
27. Nedelcu A.M. Complex patterns of plastid 16S rRNA gene evolution in nonphotosynthetic green algae. J. Mol. Evol. 53:2001;670-679.
28. Pore R.S. Prototheca taxonomy. Mycopathologia. 90:1985;129-139.
29. Pore R.S. The association of Prototheca spp. with slime flux in Ulmus americana and other trees. Mycopathologia. 94:1986;67-73.
30. Kurtzman C.P., Robnett C.J. Identification of clinically important ascomycetous yeasts based on nucleotide divergence in the 5′ end of the large-subunit (26S) ribosomal DNA gene. J. Clin. Microbiol. 39:1997;539-543.
31. Huss V.A.R., Wein K.H., Kessler E. Deoxyribonucleic acid reassociation in the taxonomy of the genus ChlorellaIV. Chlorella protothecoides and its relationship to the genus Prototheca. Arch. Microbiol. 150:1988;509-511.