Evolutionary analyses of small-subunit rDNA coding regions and the 1506 group I introns of the Zygnematales (Charophyceae, Streptophyta)

Journal of Phycology

Volumn 35, Issue 3 II, 1999, Pages 560-569

  Besendahl, Anja ^a   Bhattacharya, Debashish ^a  

^a UNIVERSITY OF IOWA   (United States)

Author keywords

Charophyceae; Group I intron; Phylogeny; rDNA; Ribozyme; Secondary structure; Self splicing; Zygnematales

Indexed keywords

INTRON; PHYLOGENETIC ANALYSIS; POPULATION GENETICS; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RIBOSOMAL DNA; RIBOSOMAL RNA; RNA SPLICING; SEQUENCE ANALYSIS; SMALL SUBUNIT RIBOSOMAL DNA;

ALGAE; CHARALES; CLOSTERIUM EHRENBERGII; CLOSTERIUM LITTORALE; CYLINDROCYSTIS BREBISSONII; DESMIDIACEAE; EUKARYOTA; GONATOZYGON ACULEATUM; MESOTAENIACEAE; PENIUM MARGARITACEUM; SIROGONIUM STICTICUM; STAURASTRUM PUNCTULATUM; STREPTOPHYTA; ZYGNEMATACEAE; ZYGNEMATALES;

EID: 0032995529     PISSN: 00223646     EISSN: None     Source Type: Journal    
DOI: 10.1046/j.1529-8817.1999.3530560.x     Document Type: Article

References (52)

1. Aimi, T., Yamada, T. & Murooka, Y. 1994. A group-I self-splicing intron in the nuclear small subunit rRNA-encoding gene of the green alga, Chorella ellipsoidea C-87. Gene 139:65-71.
2. Bhattacharya, D. 1996. Analysis of the distribution of bootstrap tree lengths using the maximum parsimony method. Mol. Phylog. Evol. 6:339-50.
3. _ 1998. The origin and evolution of protist group I introns. Protist 149:113-22.
4. Bhattacharya, D., Damberger, S., Surek, B. & Melkonian, M. 1996a. Primary and secondary structure analyses of the rDNA group I introns of the Zygnematales. Curr. Genet. 29:282-6.
5. Bhattacharya, D., Friedl, T. & Damberger, S. 1996b. Nuclear-encoded rDNA group I introns: (Charophyta). Origin and phylogenetic relationships of insertion site lineages in the green algae. Mol. Biol. Evol. 13:978-89.
6. Bhattacharya, D., Surek, B., Rüsing, M., Damberger, S. & Melkonian, M. 1994. Group I introns are inherited through common ancestry in the nuclear-encoded rRNA of Zygnematales (Charophyceae). Proc. Natl. Acad. Sci. USA 91:9916-20.
7. Brook, A. J. 1981. The Biology of Desmids. Botanical Monographs, vol. 16, Blackwell Scientific Publications, Oxford, 276 pp.
8. Burke, J. M. 1988. Molecular genetics of group I introns: RNA structures and protein factors required for splicing - a review. Gene 73:273-94.
9. Cate, J. H., Gooding, A. R., Podell, E., Zhou, K., Golden, B. L., Kundrot, C. E., Cech. T. R. & Doudna, J. A. 1996. Crystal structure of a group I ribozyme domain: principles of RNA packing. Science 273:1678-86.
10. Cech, T. R. 1988. Conserved sequences and structures of group I introns: building an active site for RNA catalysis - a review. Gene 73:259-71.
11. _ 1993. Structure and mechanism of the large catalytic RNAs: group I and group II introns and ribonuclease P. In Gesteland, R. F. & Atkins, J. F. [Eds.] The RNA World. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York, pp. 239-69.
12. Damberger, S. H. & Gutell, R. R. 1994. A comparative database of group I intron structures. Nucleic Acids Res. 22:3508-10.
13. Doyle, J. J. & Doyle, J. L. 1990. Isolation of plant DNA from fresh tissue. Focus 12:13-5.
14. Dujon, B. 1989. Group I introns as mobile genetic elements: facts and mechanistic speculations - a review. Gene 82:91-114.
15. 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.
16. Engels, M. & Mix, M. 1980. 1. Nachtrag zur Liste der Sammlung von Conjugaten-Kulturen im Institut fuer Allgemeine Botanik der Universitaet Hamburg. Mitt. Inst. Allg. Bot. Hamburg 17: 165-71.
17. Felsenstein, J. 1985. Confidence limits on phytogenies: an approach using the bootstrap. Evolution 39:783-91.
18. Gilbert, D. G. 1992. SeqApp, ver. 1.9a169. Biology Department, Indiana University, 23 pp.
19. Gilbert, W. 1986. The RNA world. Nature 319:618.
20. Golden, B. L. & Cech, T. R. 1996. Conformational switches involved in orchestrating the successive steps of group I RNA splicing. Biochemistry 35:3754-63.
21. Hibbett, D. S. 1996. Phylogenetic evidence for horizontal transmission of group I introns in the nuclear ribosomal DNA of mushroom-forming fungi. Mol. Biol. Evol. 13:903-17.
22. Hoshaw, R. W., McCourt, R. M. & Wang, J-C. 1990. Phylum Conjugaphyta. In Margulis, L., Corliss, J. O., Melkonian, M. & Chapman, D. J. [Eds.] Handbook of Prototictista. Jones and Bartlett, Boston, pp. 119-31.
23. Krienitz, L., Huss, V. A. R. & Huemmer, C. 1996. Picoplanktonic Choricystis-species (Chlorococcales, Chlorophyta) and the misconception of 'Nannochloris-like algae'. Phycologia 35:332-41.
24. Kueck, U., Godehardt, I. & Schmidt, U. 1990. A self-splicing group II intron in the mitochondrial large subunit rRNA (LSU rRNA) gene of the eukaryotic alga Scenedestmus obliquus. Nucleic Acids Res. 18:2691-7.
25. Lockhart, P. J., Steel, M. A., Hendy, M. D. & Penny, D. 1994. Recovering evolutionary trees under a more realistic model of sequence evolution. Mol. Biol. Evol. 11:605-12.
26. McCourt, R. M., Karol, K. G., Kaplan, S. & Hoshaw, R. W. 1995. Using rbcL sequences to test hypotheses of chloroplast and thallus evolution in conjugating green algae (Zygnematales, Charophyceae). J. Phycol. 31:989-95.
27. Medlin, L., Elwood, H. J., Stickel, S. & Sogin, M. L. 1988. The characterization of enzymatically amplified eukaryotic 16S-like rRNA-coding regions. Gene 71:491-9.
28. Meiers, S. T., Rootes, W. L., Proctor, V. M. & Chapman, R. L. 1997. Phylogeny of the Characeae (Charophyta) inferred from organismal and molecular characters. Arch. Protistenkd. 148:309-18.
29. Michel, F., Hanna, M., Green, R., Bartel, D. P. & Szostak, J. W. 1989. The guanosine binding site of the Tetrahymena ribozyme. Nature 342:391-5.
30. Michel, F. & Westhof, E. 1990. Modelling the three-dimensional architecture of group I catalytic introns based on comparative sequence analysis. J. Mol. Biol. 216:585-610.
31. Nikolcheva T. & Woodson, S. A. 1997. Association of a group I intron with its splice junction in 50S ribosomes: implications for intron toxicity. RNA 3:1016-27.
32. Oliveira, M. G. & Ragan, M. A. 1994. Variant forms of a self-splicing group I intron in nuclear small-subunit rRNA genes of the marine red alga Porphyra spiralis var amplifolia. Mol. Biol. Evol. 11:195-207.
33. Pace, N. R. & Marsh, T. K. 1985. RNA catalysis and the origin of life. Origins Life 16:97-116.
34. Park, N. E., Karol, K. G., Hoshaw, R. W. & McCourt, R. M. 1996. Phylogeny of Gonatozygon and Genicularia (Gonatozygaceae, Desmidiales) based on rbcL sequences. Eur. J. Phytol. 31:309-13.
35. Price, J. V. & Cech, T. R. 1988. Determinants of the 3′ splice site for self-splicing of the Tetrahymena pre-rRNA. Genes Dev. 2: 1439-47.
36. Saitou, N. & Nei, M. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4:406-25.
37. Schlösser, U. G. 1994. SAG-Sammlung von Algenkulturen at the University of Göttingen. Bot. Acta 107:111-86.
38. Shinohara, M. L., LoBuglio, K. F. & Rogers, S. O. 1996. Group-I intron family in the nuclear ribosomal RNA small subunit genes of Cenococcum geophilum isolates. Curr. Genet. 29:377-87.
39. Sluiman, H J. 1985. A cladistic evaluation of the higher and lower green plants (Viridiplantae). Plant Syst. Evol. 149:217-32.
40. Sogin, M. L. & Edman, J. C. 1989. A self-splicing intron in the small subunit rRNA gene of Pneumocystis carinii. Nucleic Acids Res. 17:5349-59.
41. Starr, R. C. & Zeikus, J. 1993. UTEX - the culture collection of algae at the university of Texas at Austin. J. Phycol. 29(Suppl.): 1-106.
42. Steinkötter, J., Bhattacharya, D., Semmelroth, I., Bibeau, C. & Melkonian, M. 1994. Prasinophytes form independent lineages within the Chlorophyta: evidence from ribosomal RNA sequence comparisons. J. Phycol. 30:340-5.
43. Surek, B., Beemelmanns, U., Melkonian, M. & Bhattacharya, D. 1994. Ribosomal RNA sequence comparisons demonstrate an evolutionary relationship between Zygnematales and charophytes. Plant Syst. Evol. 191:171-81.
44. Swofford, D. L. 1998. PAUP: phylogenetic analysis using parsimony, ver. 4.0b1. Smithsonian Institution, Washington, D.C.
45. Szostak, J. W. 1986. Enzymatic activity of the conserved core of a group I self-splicing intron. Nature 322:83-6.
46. Turmel, M., Gutell, R. R., Mercier, J. P., Otis, C. & Lemieux, C. 1993. Analysis of the chloroplast large subunit ribosomal RNA gene from 17 Chlamydomonas taxa. Three internal transcribed spacers and 12 group I intron insertion sites. Mol. Biol. 232:446-67.
47. Uhlenbeck, O. C. 1995. Keeping RNA happy. RNA 1:4-6.
48. Wallasch, C., Moerl, M., Niemer, I. & Schmelzer, C. 1991. Structural requirements for selection of 5′- and 3′-splice sites of group II introns. Nucleic Acids Res. 19:3307-14.
49. Wallweber, G. J., Mohr, S., Rennard, R., Caprara, M. G. & Lambowitz, A. M. 1997. Characterization of Neurospora mitochondrial group I introns reveals different CYT-18 dependent and independent splicing strategies and an alternative ′' splice site for an intron ORF. RNA 3:114-31.
50. Woodson, S. A. & Cech, T. R. 1989. Reverse self-splicing of the Tetrahymena group I intron: implication for the directionality of splicing and for intron transposition. Cell 57:335-45.
51. Xu, M-Q., Kathe, S. D., Goodrich-Blair, H., Nierzwicki-Bauer, S. A. & Shub, D. A. 1990. Bacterial origin of a chloroplast intron: conserved self-splicing group I introns in cyanobacteria. Science 250:1566-70.
52. Zaug, A. J., Grabowski, P. J. & Cech, T. R. 1983. Autocatalytic cyclization of an excised intervening sequence RNA is a cleavage-ligation reaction. Nature 301:578-83.