The distribution of group I introns in lichen algae suggests that lichenization facilitates intron lateral transfer

Molecular Phylogenetics and Evolution

Volumn 14, Issue 3, 2000, Pages 342-352

  Friedl, Thomas ^a   Besendahl, Anja ^b   Pfeiffer, Patrick ^a   Bhattacharya, Debashish ^b  

^a UNIVERSITY OF GÖTTINGEN   (Germany)

^b UNIVERSITY OF IOWA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALGAE; CHLOROPHYCEAE; ESCHERICHIA COLI; TREBOUXIA; TREBOUXIOPHYCEAE; ULVOPHYCEAE;

EID: 0034071813     PISSN: 10557903     EISSN: None     Source Type: Journal    
DOI: 10.1006/mpev.1999.0711     Document Type: Article

References (63)

1. Adams K. L., Clements M. J., Vaughn J. C. The Peperomia mitochondrial coxI group I intron: Timing of horizontal transfer and subsequent evolution of the intron. J. Mol. Evol. 46:1998;689-696.
2. Beck A., Friedl T., Rambold G. Selectivity of photobiont choice in a defined lichen community: Inferences from cultural and molecular studies. New Phytol. 139:1998;709-720.
3. Belfort M., Perlman S. Mechanisms of intron mobility. J. Biol. Chem. 270:1995;30237-30240.
4. Besendahl A., Bhattacharya D. Evolutionary analyses of small subunit rDNA coding regions and the 1506 group I introns of the Zygnematales (Charophyceae, Streptophyta). J. Phycol. 35:1999.
5. Bhattacharya D. Analysis of the distribution of bootstrap tree lengths using the maximum parsimony method. Mol. Phylogenet. Evol. 6:1996;339-350.
6. Bhattacharya D. The origin and evolution of protist group I introns. Protist. 149:1998;113-122.
7. Bhattacharya D., Medlin L. Algal phylogeny and the origin of land plants. Plant Physiol. 116:1998;9-15.
8. Bhattacharya D., Surek B., Ruesing M., Damberger S., Melkonian M. Group I introns are inherited through common ancestry in the nuclear-encoded rDNA of Zygnematales (Charophyceae). Proc. Natl. Acad. Sci. USA. 91:1994;9916-9920.
9. Bhattacharya D., Friedl T., Damberger S. Nuclear-encoded rDNA group I introns: Origin and phylogenetic relationships of insertion site lineages in the green algae. Mol. Biol. Evol. 13:1996;978-989.
10. Bryk M., Quirk S. M., Mueller J. E., Loizos N., Lawrence C., Belfort M. The td intron endonuclease I-TevI makes extensive sequence-tolerant contacts across the minor groove of its DNA target. EMBO J. 12:1993;2141-2149.
11. Burke J. M. Molecular genetics of group I introns: RNA structures and protein factors required for splicing - A review. Gene. 73:1988;273-294.
12. Cech T. R. Conserved sequences and structures of group I introns: Building an active site for RNA catalysis - A review. Gene. 73:1988;259-271.
13. Cech T. R., Damberger S. H., Gutell R. R. Representation of the secondary and tertiary structure of group I introns. Nat. Struct. Biol. 1:1994;273-280.
14. Cho Y., Qiu Y. L., Kuhlman P., Palmer J. D. Explosive invasion of plant mitochondria by a group I intron. Proc. Natl. Acad. Sci. USA. 95:1998;14244-14249.
15. DePriest P. T., Been M. D. Numerous group I introns with variable distributions in the ribosomal DNA of a lichen fungus. J. Mol. Biol. 228:1992;315-321.
16. Dujon B. Group I introns as mobile genetic elements: Facts and mechanistic speculations - A review. Gene. 82:1989;91-114.
17. Ettl H., Gärtner G. Syllabus der Boden-, Luft- und Flechtenalgen. 1995;Fischer, Stuttgart.
18. Friedl T. Thallus development and phycobionts of the parasitic lichen Diploschistes muscorum. Lichenologist. 19:1987;183-191.
19. Friedl T. Comparative ultrastructure of pyrenoids in Trebouxia (Microthamniales, Chlorophyta). Plant Syst. Evol. 164:1989;145-159.
20. Friedl T. Inferring taxonomic positions and testing genus level assignments in coccoid green algae: A phylogenetic analysis of 18S ribosomal DNA sequences from Dictyochloropsis reticulata and species of Myrmecia (Chlorophyta, Trebouxiophyceae cl. nov.). J. Phycol. 31:1995;632-639.
21. Friedl T. The evolution of the green algae. Bhattacharya D. Origins of Algae and Their Plastids. 1997;87-102 Springer-Verlag, Wien.
22. Friedl T., Zeltner C. Assessing the relationships of some coccoid green lichen algae and the Microthamniales (Chlorophyta) with 18S rDNA gene sequence comparisons. J. Phycol. 30:1994;500-506.
23. Friedl T., Rokitta C. Species relationships in the lichen alga Trebouxia (Chlorophyta, Trebouxiophyceae): Molecular phylogenetic analyses of nuclear-encoded large subunit rRNA gene sequences. Symbiosis. 23:1997;125-148.
24. Gargas A., DePriest P. T., Taylor J. W. Positions of multiple insertions in SSU rDNA of lichen-forming fungi. Mol. Biol. Evol. 12:1995;208-218.
25. Gilbert, D. G. 1992, SeqApp, V.1.9a169, Biology Department, Indiana Univ. Bloomington.
26. Hasegawa M., Kishino H., Yano K. Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. J. Mol. Evol. 22:1985;160-174.
27. Johansen S., Elde M., Vader A., Haugen P., Haugli K., Haugli F. In vivo mobility of a group I twintron in nuclear ribosomal DNA of the myxomycete Didymium iridis. Mol. Microbiol. 24:1997;737-745.
28. Kimura M. A simple method for estimating evolutionary rates of base substitution through comparative studies of sequence evolution. J. Mol. Evol. 16:1980;111-120.
29. Kishino H., Hasegawa M. Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data, and the branching order in hominoidea. J. Mol. Evol. 29:1989;170-179.
30. Lambowitz A. M., Belfort M. Introns as mobile genetic elements. Annu. Rev. Biochem. 62:1993;587-622.
31. Lonergan K. M., Gray M. W. The ribosomal RNA gene region in Acanthamoeba castellanii mitochondrial DNA: A case of evolutionary transfer of introns between mitochondria and plastids. J. Mol. Biol. 239:1994;476-499.
32. Maddison, W. P, and, Maddison, D. R. 1992, MacClade, V3, Sinauer, Sunderland, MA.
33. Mai J. C., Coleman A. W. The internal transcribed spacer 2 exhibits a common secondary structure in green algae and flowering plants. J. Mol. Evol. 44:1997;258-271.
34. Maidak B. L., Olsen G. J., Larsen N., Overbeek R., McCaughey M. J., Woese C. R. The RDP (Ribosomal Database Project). Nucleic Acids Res. 25:1997;109-111.
35. Melkonian M., Surek B. Phylogeny of the Chlorophyta: Congruence between ultrastructural and molecular evidence. Bull. Soc. Zool. Fr. 120:1995;191-208.
36. Moran J. V., Wernette C. M., Mecklenburg K. L., Butow R. A., Perlman P. S. Intron 5-alpha of the coxI gene of yeast mitochondrial DNA is a mobile group I intron. Nucleic Acids Res. 20:1992;4069-4076.
37. Nishida K., Suzuki S., Kimura Y., Nomura N., Fujie M., Yamada T. Group I introns found in Chlorella viruses: Biological implications. Virology. 242:1998;319-326.
38. Oliveira M. C., Ragan M. A. 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. 11:1994;195-207.
39. Olsen G. J., Matsuda H., Hagstrom R., Overbeek R. fastDNAmL: A tool for construction of phylogenetic trees of DNA sequences using maximum likelihood. Comput. Appl. Biosci. 10:1994;41-48.
40. Ott S. Reproductive strategies in lichens. Peveling E. Progress and Problems in Lichenology in the Eighties. 1987;81-97 Borntraeger, Stuttgart.
41. Page R. D. TreeView: An application to display phylogenetic trees on personal computers. Comput. Appl. Biosci. 12:1996;357-358.
42. Roman J., Woodson S. A. Reverse splicing of the Tetrahymena IVS: Evidence for multiple reaction sites in the 23S rRNA. RNA. 1:1995;478-490.
43. Roman J., Woodson S. A. Integration of the Tetrahymena group I intron into bacterial rRNA by reverse splicing in vivo. Proc. Natl. Acad. Sci. USA. 95:1998;2134-2139.
44. Rzhetsky A., Nei M. Statistical properties of the ordinary least-squares, generalized least-squares, and minimum-evolution methods of phylogenetic inference. J. Mol. Evol. 35:1992;367-375.
45. Saiki R. K., Gelfand D. H., Stoffel S., Scharf S. J., Higuchi R., Horn G. T., Mullis K. B., Erlich H. A. Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase. Science. 239:1988;487-491.
46. Saitou N., Nei M. The neighbor-joining method: A new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4:1987;406-425.
47. Sanger F., Nicklen S., Coulson A. R. DNA sequencing with chain-terminating inhibitors. Proc. Natl. Acad. Sci. USA. 74:1977;5463-5467.
48. Schlösser U. G. SAG-Sammlung von Algenkulturen at the University of Göttingen. Bot. Acta. 107:1994;111-186.
49. Schroeder-Diedrich J. M., Fuerst P., Byers T. J. Group-I introns with unusual sequences occur at three sites in nuclear 18S rRNA genes of Acanthamoeba lenticulata. Curr. Genet. 34:1998;71-78.
50. Starr R. C., Zeikus J. UTEX - The culture collection of algae at the university of Texas at Austin. J. Phycol. 29(Suppl.):1993;1-106.
51. Suh E. R., Waring R. B. Base pairing between the 3′ exon and an internal guide sequence increases 3′ splice site specificity in the Tetrahymena self-splicing rRNA intron. Mol. Cell. Biol. 10:1990;2960-2965.
52. Swofford, D. L. 1999, PAUP: Phylogenetic Analysis Using Parsimony, V4.0b2, Smithsonian Institution, Washington, DC.
53. Szostak J. W., Orr-Weaver T. L., Rothstein R. J., Stahl F. W. The double-strand-break repair model for recombination. Cell. 33:1983;25-35.
54. Thompson A. J., Herrin D. L. A chloroplast group I intron undergoes the first step of reverse splicing into host cytoplasmic 5.8 S rRNA: Implications for intron-mediated RNA recombination, intron transposition and 5.8 S rRNA structure. J. Mol. Biol. 236:1994;455-468.
55. Turmel M., Côté V., Otis C., Mercier J.-P., Gray M. W., Lonergan K. M., Lemieux C. Evolutionary transfer of ORF-containing group I introns between different subcellular compartments (chloroplast and mitochondrion). Mol. Biol. Evol. 12:1995;533-545.
56. Van Oppen M. J. H., Olsen J. L., Stam W. T. Evidence for independent acquisition of group I introns in green algae. Mol. Biol. Evol. 10:1993;1317-1326.
57. Watanabe K. I., Ehara M., Inagaki Y., Ohama T. Distinctive origins of group I introns in the COXI genes of three green algae. Gene. 213:1998;1-7.
58. Wilcox L. W., Lewis L. A., Fuerst P. A., Floyd G. L. Group I introns within the nuclear-encoded small-subunit rRNA gene of three green algae. Mol. Biol. Evol. 9:1992;1103-1118.
59. Woodson S. Splicing and evolution of introns in ribosomal RNA. Green R., Schroeder R. Ribosomal RNA and Group I Introns. 1996;199-219 Landes, Austin.
60. Woodson S. A., Cech T. R. Reverse self-splicing of the Tetrahymena group I intron: Implication for the directionality of splicing and for intron transposition. Cell. 57:1989;335-345.
61. Yamada T., Songsri P., Tamura K. Horizontal transmission of group-I ribozymes: Viruses as a carrier of the introns. Nucleic Acids Symp. Ser. 34:1995;119-120.
62. Yang Z. Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: Approximate methods. J. Mol. Evol. 39:1994;306-314.
63. Zaug A. J., Grabowski P. J., Cech T. R. Autocatalytic cyclization of an excised intervening sequence RNA is a cleavage-ligation reaction. Nature. 301:1983;578-583.