Barcoding ciliates: A comprehensive study of 75 isolates of the genus Tetrahymena

International Journal of Systematic and Evolutionary Microbiology

Volumn 57, Issue 10, 2007, Pages 2412-2425

  Chantangsi, Chitchai ^a,e   Lynn, Denis H ^a   Brandl, Maria T ^b   Cole, Jeffrey C ^c   Hetrick, Neil ^c   Ikonomi, Pranvera ^d  

^a UNIVERSITY OF GUELPH   (Canada)

^b WESTERN REGIONAL RESEARCH CENTER   (United States)

^c Protistology Department   (United States)

^d Molecular Authentication Resource Center   (United States)

^e UNIVERSITY OF BRITISH COLUMBIA   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

CYTOCHROME C OXIDASE; CYTOCHROME C OXIDASE 1; PROTOZOAL DNA; UNCLASSIFIED DRUG;

ARTICLE; CILIATE; COLPIDIUM CAMPYLUM; COLPIDIUM COLPODA; CONTROLLED STUDY; FEASIBILITY STUDY; GENE SEQUENCE; GLAUCOMA CHATTONI; INTRASPECIFIC VARIATION; MITOCHONDRIAL GENE; NEIGHBOR JOINING METHOD; NONHUMAN; NUCLEOTIDE SEQUENCE; PARASITE IDENTIFICATION; PARASITE ISOLATION; PHYLOGENETIC TREE; PRIORITY JOURNAL; SPECIES IDENTIFICATION; TAXONOMIC IDENTIFICATION; TETRAHYMENA; TETRAHYMENA BOREALIS; TETRAHYMENA FURGASONI; TETRAHYMENA LWOFFI; TETRAHYMENA PATULA; TETRAHYMENA PYRIFORMIS; TETRAHYMENA SETOSA; TETRAHYMENA THERMOPHILA; TETRAHYMENA TROPICALIS;

ANIMALS; CLUSTER ANALYSIS; CYCLOOXYGENASE 1; DNA, PROTOZOAN; MOLECULAR SEQUENCE DATA; PARASITOLOGY; PHYLOGENY; SEQUENCE ANALYSIS, DNA; SEQUENCE HOMOLOGY; TETRAHYMENINA;

ANIMALIA; CILIOPHORA; COLPIDIUM; COLPIDIUM CAMPYLUM; GLAUCOMA CHATTONI; PROTISTA; TETRAHYMENA; TETRAHYMENA BOREALIS; TETRAHYMENA FURGASONI; TETRAHYMENA PATULA; TETRAHYMENA PYRIFORMIS; TETRAHYMENA SETOSA; TETRAHYMENA THERMOPHILA; TETRAHYMENA TROPICALIS;

EID: 35648972049     PISSN: 14665026     EISSN: None     Source Type: Journal    
DOI: 10.1099/ijs.0.64865-0     Document Type: Article

References (66)

1. Avise, J. C. (2000). Phylogeography. the History and Formation of Species. Cambridge, MA: Harvard University Press.
2. Ball, S. L., Hebert, P. D. N., Burian, S. K. & Webb, J. M. (2005). Biological identifications of mayflies (Ephemeroptera) using DNA barcodes. J N Am Benthol Soc 24, 508-524.
3. Barrett, R. D. H. & Hebert, P. D. N. (2005). Identifying spiders through DNA barcodes. Can J Zool 83, 481-491.
4. Barth, D., Krenek, S., Fokin, S. I. & Berendonk, T. U. (2006). Intraspecific genetic variation in Paramecium revealed by mitochondrial cytochrome c oxidase I sequences. J Eukaryot Microbiol 53, 20-25.
5. Borden, D., Whitt, G. S. & Nanney, D. L. (1973a). Electrophoretic characterization of classical Tetrahymena pyriformis strains. J Protozool 20, 693-700.
6. Borden, D., Whitt, G. S. & Nanney, D. L. (1973b). Isozymic heterogeneity in Tetrahymena strains. Science 181, 279-280.
7. Borden, D., Miller, E. T., Whitt, G. S. & Nanney, D. L. (1977). Electrophoretic analysis of evolutionary relationships in Tetrahymena. Evolution 31, 91-102.
8. Brandl, M. T., Rosenthal, B. M., Haxo, A. F. & Berk, S. G. (2005). Enhanced survival of Salmonella enterica in vesicles released by a soilborne Tetrahymena species. Appl Environ Microbiol 71, 1562-1569.
9. Brown, J. W., Miller, S. E. & Horak, M. (2003). Studies on New Guinea moths. 2. Description of a new species of Xenothictis Meyrick (Lepidoptera: Tortricidae: Archipini). Proc Entomol Soc Wash 105, 1043-1050.
10. Brunk C. F., Lee, C. L., Tran, A. B. & Li, J. (2003). Complete sequence of the mitochondrial genome of Tetrahymena thermophila and comparative methods for identifying highly divergent genes. Nucleic Acids Res 31, 1673-1682.
11. 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, 365-380.
12. Corliss, J. O. (1952). Le cycle autogamique de Tetrahymena rostrata. C R Acad Sci 235, 399-402 (in French).
13. Corliss, J. O. (1953). Silver impregnation of ciliated protozoa by the Chatton-Lwoff technic. Stain Technol 28, 97-100.
14. Corliss, J. O. (1972). Tetrahymena and some thoughts on the evolutionary origin of endoparasitism. Trans Am Microsc Soc 91, 566-573.
15. Corliss, J. O. (1973). History, taxonomy, ecology, and evolution of species of Tetrahymena. In Biology of Tetrahymena, pp. 1-55. Edited by A. M. Elliott. Stroudsburg, PA: Dowden, Hutchinson & Ross.
16. Corliss, J. O. & Daggett, P.-M. (1983). "Paramecium aurelia" and "Tetrahymena pyriformis": Current status of the taxonomy and nomenclature of these popularly known and widely used ciliates. Protistologica 19, 307-322.
17. Cummings, D. J. (1992). Mitochondrial genomes of the ciliates. Int Rev Cytol 141, 1-64.
18. Czapik, A. (1968). La famille Tetrahymenidae et son importance dans la systématique et 1'évolution des ciliés. Acta Protozool 5, 315-357 (in French).
19. Dawkins, R. (1998). Unweaving the Rainbow.- Science, Delusion and the Appetite for Wonder. Boston: Houghton Mifflin.
20. Elliott, A. M. (1970). The distribution of Tetrahymena pyriformis. J Protozool 17, 162-168.
21. Elwood, H. J., Olsen, G. J. & Sogin, M. L. (1985). The small-subunit ribosomal RNA gene sequences from the hypotrichous ciliates Oxytricha nova and Stylonychia pustulata. Mol Biol Evol 2, 399-410.
22. Felsenstein, J. (2004). PHYLIP (phylogeny inference package), version 3.6. Distributed by the author. Department of Genome Sciences, University of Washington, Seattle, USA.
23. Fenchel, T. & Finlay, B. J. (2004). The ubiquity of small species: Patterns of local and global diversity. Bioscience 54, 777-784.
24. Folmar, O., Black, M., Hoeh, W., Lutz, R. & Vrijenhoek, R. (1994). DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates. Mol Mar Biol Biotechnol 3, 294-297.
25. Gruchy, D. F. (1955). The breeding system and distribution of Tetrahymena pyriformis. J Protozool 2, 178-185.
26. Hajibabaei, M., Janzen, D. H., Burns, J. M., Hallwachs, W. & Hebert, P. D. N. (2006). DNA barcodes; distinguish species of tropical Lepidoptera. Proc Natl Acad Sci U S A 103, 968-971.
27. Hebert, P. D. N., Ratnasingham, S. & deWaard, J. R. (2003a). Barcoding animal life: Cytochrome c oxidase subunit I divergences among closely related species. Proc Biol Sci 270 (Suppl. 1), S96-S99.
28. Hebert, P. D. N., Cywinska, A., Ball, S. L. & deWaard, J. R. (2003b). Biological identifications through DNA barcodes. Proc Biol Sci 270, 313-321.
29. Hebert, P. D. N, Penton, E- H., Burns, J. M., Janzen, D. H. & Hallwachs, W. (2004a). Ten species in one: DNA barcoding reveals cryptic species in the neotropical skipper butterfly Astraptes fulgerator. Proc Natl Acad Sci U S A 101, 14812-14817.
30. Hebert P. D. N, Stoeckle, M. Y., Zemlak, T. S. & Francis, C. M. (2004b). Identification of birds through DNA barcodes. PLoS Biol 2, e312.
31. Hogg, I. D. & Hebert P. D. N. (2004). Biological identification of springtails (Hexapoda: Collembola) from the Canadian Arctic, using mitochondrial DNA barcodes. Can J Zool 82, 749-754.
32. Holz, G. G. & Corliss, J. O. (1956). Tetrahymena seqera n. sp., a member of the genus Tetrahymena with a caudal cilium. J Protozool 3, 112-118.
33. Janczewski, D. N., Modi, W. S., Stephens, J. C. & O'Brien, S. J. (1995). Molecular evolution of mitochondrial 12S RNA and cy-tochrome b sequences in the pantherine lineage of Felidae. Mol Biol Evol 12, 690-707.
34. Jerome, C. A. & Lynn, D. H. (1996). Identifying and distinguishing sibling species in the Tetrahymena pyriformis complex (Ciliophora, Oligohymenophorea) using PCR/RFLP analysis of nuclear ribosomal DNA. J Eukaryot Microbiol 43, 492-497.
35. Kahl, A. (1926). Neue und wenig bekannte Formen der holotrichen und heterotrichen Ciliaten. Arch Protistenkd 55, 197-438 (in German).
36. Kimura, M. (1980). A simple method of estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16, 111-120.
37. Kumar, S., Tamura, K & Nei, M. (2004). MEGA3: Integrated software for molecular evolutionary genetics analysis and sequence alignment. Brief Bioinform 5, 150-163.
38. Kumazawa, Y. & Nishida, M. (1993). Sequence evolution of mitochondrial tRNA genes and deep-branch animal phylogenetics. J Mol Evol 37, 380-398.
39. Lynn, D. H. & Strüder-Kypke, M. C. (2006). Species of Tetrahymena identical by small subunit rRNA gene sequences are discriminated by mitochondrial cytochrome c oxidase I gene sequences. J Eukaryot Microbiol 53, 385-387.
40. Mardulyn, P. & Whitfield, J. B. (1999). Phylogenetic signal in the COI, 16S, and 28S genes for inferring relationships among genera of Microgastrinae (Hymenoptera; Braconidae): Evidence of a high diversification rate in this group of parasitoids. Mol Phylogenet Evol 12, 282-294.
41. Medlin, L., Elwood, H. J., Stickel, S. & Sogin, M. L (1988). The characterization of enzymatically amplified eukaryotic 16S-like rRNA-coding regions. Gene 71, 491-499.
42. Meyer, E. B. & Nanney, D. L. (1987). Isozymes in the ciliated protozoa. In Isozymes (Current Topics in Biological and Medical Research, vol. 13), pp. 61-101. Edited by M. C. Rattazzi. New York: Alan R. Liss.
43. Monaghan, M. T., Balke, M., Gregory, T. R. & Vogler, A. P. (2005). DNA-based species delineation in tropical beetles using mitochondrial and nuclear markers. Philos Trans R Soc Lond B Biol Sci 360, 1925-1933.
44. Nanney, D. L. & McCoy, J. W. (1976). Characterization of the species of the Tetrahymena pyriformis complex. Trans Am Microsc Soc 95, 664-682.
45. Nanney, D. L, Meyer, E. B., Simon, E. M. & Preparata, R.-M. (1989). Comparison of ribosomal and isozymic phylogenies of tetrahymenine ciliates. J Protozool 36, 1-8.
46. Nanney, D. L., Park C., Preparata, R. & Simon,. M. (1998). Comparison of sequence differences in a variable 23S rRNA domain among sets of cryptic species of ciliated protozoa. J Eukaryot Microbiol 45, 91-100.
47. Nelsen, E. M. & Debault, L. E. (1978). Transformation in Tetrahymena pyriformis: Description of an inducible phenotype. J Protozool 25, 113-119.
48. Nyberg, D. (1981). Three new "biological" species of Tetrahymena (T. hegewischi n. sp., T. sonneborni n. sp., T. nipissingi n. sp.) and temperature tolerance of members of the " pyriformis" complex. J Protozool 28, 65-69.
49. Preparata, R. M., Meyer, E. B., Preparata, F. P., Simon, E. M., Vossbrinck, C. R. & Nanney, D. L. (1989). Ciliate evolution: The ribosomal phylogenies of the tetrahymenine ciliates. J Mol Evol 28, 427-441.
50. Remigio, E. A. & HeberL P. D. N. (2003). Testing the utility of partial COI sequences for phylogenetic estimates of gastropod relationships. Mol Phylogenet Evol 29, 641-647.
51. Sadler, L. A. & Brunk, C. F. (1992). Phylogenetic relationships and unusual diversity in histone H4 proteins within the Tetrahymena pyriformis complex. Mol Biol Evol 9, 70-84.
52. Saitou, N. & Nei, M. (1987). The neighbor-joining method: A new method for reconstructing phylogenetic trees. Mol Biol Evol 4, 406-425.
53. Saunders, G. W. (2005). Applying DNA barcoding to red macroalgae: a preliminary appraisal holds promise for future applications. Philos Trans R Soc Lond B Biol Sci 360, 1879-1888.
54. Scheffer, S. J., Lewis, M. L. & Joshi, R. C. (2006). DNA barcoding applied to invasive leafminers (Diptera: Agromyzidae) in the Philippines. Ann Entomol Soc Am 99, 204-210.
55. Schlegel, M., Elwood, H. J. & Sogin, M. L. (1991). Molecular evolution in hypotrichous cihates: Sequence of the small subunit RNA genes from Onychodromus quadricornutus and Oxytricha granulifera (Oxytrichidae, Hypotrichida, Ciliophora). J Mol Evol 32, 64-69.
56. Simon, E. M., Meyer, E. B. & Preparats, R. M. (1985). New wild Tetrahymena from Southeast Asia, China, and North America, including Tetrahymena malaccensis, Tetrahymena asiatica, Tetrahymena nanneyi, Tetrahymena caudata, and Tetrahymena silvana n. spp. J Protozool 32, 183-189.
57. Smith, M. A., Fisher, B. L. & Hebert, P. D. N. (2005). DNA barcoding for effective biodiversity assessment of a hyperdiverse arthropod group: The ants of Madagascar. Philos Trans R Soc Lond B Biol Sci 360, 1825-1834.
58. Sogin, M. L. & Elwood, H. J. (1986). Primary structure of the Paramecium tetraurelia small-subunit rRNA coding region: phylogenetic relationships within the Ciliophora. J Mol Evol 23, 53-60.
59. Strüder-Kypke, M. C., Wright, A.-D. G., Jerome, C. A. & Lynn, D. H. (2001). Parallel evolution of histophagy in ciliates of the genus Tetrahymena. BMC Evol Biol 1, 5.
60. Tautz, D., Arctander, P., Minelli, A., Thomas, R. H. & Vogler, A. P. (2002). DNA points the way ahead in taxonomy. Nature 418, 479.
61. Tautz, D., Arctander, P., Minelli, A., Thomas, R. H. & Vogler, A. P. (2003). A plea for DNA taxonomy. Trends Ecol Evol 18, 70-74.
62. Thompson, J. D., Higgins, D. G. & Gibson, T. J. (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.
63. Walsh, P. S., Metzger, D. A. & Higuchi, R. (1991). Chelex 100 as a medium for simple extraction of DNA for PCR-based typing from forensic material. Biotechniques 10, 506-513.
64. Ward, R. D., Zemlak, T. S., Innes, B. H., Last, P. R. & Hebert, P. D. N. (2006). DNA barcoding Australia's fish species. Philos Trans R Soc Lond B Biol Sci 360, 1847-1857.
65. Williams, N. E., Buhse, H. E, Jr & Smith, M. G. (1984). Protein similarities in the genus Tetrahymena and a description of Tetrahymena leucophrys n. sp. J Protozool 31, 313-321.
66. 2-terminal extension and a 108 amino acid insert. Curr Genet 12, 357-368.