Phylogenetic evidence for horizontal transmission of group I introns in the nuclear ribosomal DNA of mushroom-forming fungi

Molecular Biology and Evolution

Volumn 13, Issue 7, 1996, Pages 903-917

  Hibbett, David S ^a  

^a HARVARD UNIVERSITY   (United States)

Author keywords

character weighting; fungi; group I introns; horizontal transmission; phylogeny; ribosomal DNA

Indexed keywords

CELL NUCLEUS DNA; RIBOSOME DNA;

ALGA; ARTICLE; GENE INSERTION; HOMOBASIDIOMYCETES; INHERITANCE; INTRON; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; POLYMERASE CHAIN REACTION;

ALGAE; BASIDIOMYCOTA; CHLOROPHYTA; CLAVICORONA; FUNGI; HOMOBASIDIOMYCETES; LENTINELLUS; PANELLUS;

EID: 0029836453     PISSN: 07374038     EISSN: None     Source Type: Journal    
DOI: 10.1093/oxfordjournals.molbev.a025658     Document Type: Article

References (51)

1. ALTSCHUL, S. F., W. GISH, W. MILLER, E. W. MEYERS, and D. J. LIPMAN. 1990. Basic local alignment search tool. J. Mol. Biol. 215:403-410.
2. CASSIDY, J., D. MOORE, B. LU, and P. PUKKILA. 1984. Unusual organization and lack of recombination in the ribosomal RNA genes of Coprinus cinereus. Curr. Genet. 8:607-613.
3. CECH, T. R. 1990. Self-splicing of Group I introns. Annu. Rev. Biochem. 59:543-568.
4. CECH, T. R., and B. L. BASS. 1986. Biological catalysis by RNA. Annu. Rev. Biochem. 55:599-629.
5. CLARK, J. B., W. P. MADDISON, and M. G. KIDWELL. 1994. Phylogenetic analysis supports horizontal transfer of P transposable elements. Mol. Biol. Evol. 11:40-50.
6. DAVIES, R. W., R. B. WARING, J. A. RAY, T. A. BROWN, and C. SCAZZOCCHIO. 1982. Making ends meet: a model for RNA splicing in fungal mitochondria. Nature 300:719-724.
7. DEPRIEST, P. T., and M. D. BEEN. 1992. Numerous group I introns with a variable distribution in the ribosomal DNA of a lichen fungus. J. Mol. Biol. 228:67-71.
8. DE QUEIROZ, A. 1993. For consensus (sometimes). Syst. Biol. 42:368-372.
9. DODD, J. L. 1972. The genus Clavicorona. Mycologia 64:737-773.
10. DUJON, B. 1989. Group I introns as mobile genetic elements: facts and mechanistic speculations - a review. Gene 82:91-114.
11. FAITH, D. P. 1991. Cladistic permutation tests for monophyly and non-monophyly. Syst. Zool. 40:366-375.
12. FARRIS, J. S., M. KALLERSJO, A. G. KLUGE, and C. BULT. 1994. Testing significance of incongruence. Cladistics 10:315-319.
13. FELSENSTEIN, J. 1993. PHYLIP (phylogeny inference package). Version 3.5p. Department of Genetics SK-50, University of Washington, Seattle.
14. GARGAS, A., P. T. DEPRIEST, M. GRUBE, and A. TEHLER. 1995. Multiple origins of lichen symbioses in fungi suggested by ssu rDNA phylogeny. Science 268:1492-1495.
15. GARGAS, A., P. T. DEPRIEST, and J. W. TAYLOR. 1995. Positions of multiple insertions in SSU rDNA of lichen-forming fungi. Mol. Biol. Evol. 12:208-218.
16. GAST, R. J., P. A. FUERST, and T. J. BYERS. 1994. Discovery of group I introns in the nuclear small subunit ribosomal RNA genes of Acanthamoeba. Nucleic Acids Res. 22:592-596.
17. GILBERT, D. 1992. SeqApp. Computer program distributed by Don Gilbert, Biology Department, Indiana University, Bloomington, Ind.
18. HIBBETT, D. S., and M. J. DONOGHUE. 1995a. Progress toward a phylogenetic classification of the Polyporaceae through parsimony analyses of mitochondrial ribosomal DNA sequences. Can. J. Bot. 73(Suppl. 1):s853-s861.
19. _. 1995b. Evolutionary diversity of polypore fungi: a molecular phylogenetic perspective (Abstract). Am. J. Bot. 82:78-79.
20. HIRSCH, A. M., H. I. MCKHANN, A. REDDY, J. LIAO, Y. FANG, and C. R. MARSHALL. 1995. Assessing horizontal transfer of nifHDK genes in Eubacteria: nucleotide sequence from Frankia strain HFPCcI3. Mol. Biol. Evol. 12:16-27.
21. HOUCK, M. A., J. B. CLARK, K. R. PETERSON, and M. G. KIDWELL. 1991. Possible horizontal transfer of Drosophila senes by the mite Proctolaelaps regalis. Science 253:1125-1129.
22. KIDWELL, M. G. 1993. Lateral transfer in natural populations of eukaryotes. Annu. Rev. Genet. 27:235-256.
23. KISHINO, H., and M. HASEGAWA. 1989. Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data, and the branching order in Hominoidea. J. Mol. Evol. 29:170-179.
24. LAMBOWITZ, A. M. 1989. Infectious introns. Cell 56:323-326.
25. LAWRENCE, J. G., and D. L. HARTL. 1992. Inference of horizontal genetic transfer from molecular data: an approach using the bootstrap. Genetics 131:735-760.
26. LIN, H. L., M. T. NIU, T. YOGANATHAN, and G. A. BUCK. 1992. Characterization of the rRNA-encoding genes and transcripts, and a group-I self-splicing intron in Pneumocystis carinii. Gene 119:163-173.
27. LIU, Y., and M. J. LEIBOWTTZ. 1993. Variation and in vitro splicing of group I introns in rRNA genes of Pneumocystis carinii. Nucleic Acids Res. 21:2415-2421.
28. LOHE, A. R., E. N. MORIYAMA, D.-A. LIDHOLM, and D. L. HARTL. 1995. Horizontal transmission, vertical inactivation, and stochastic loss of Mariner-like transposable elements. Mol. Biol. Evol. 12:62-72.
29. MADDISON, W. P., and D. R. MADDISON. 1992. MacClade. Version 3. Sinauer, Sunderland, Mass.
30. MICHEL, F., and D. J. CUMMINGS. 1985. Analysis of class I introns in a mitochondrial plasmid associated with senescence of Podospora anserina reveals extraordinary resemblance to the Tetrahymena ribosomal intron. Curr. Genet. 10:69-79.
31. MICHEL, F., and E. WESTHOF. 1990. Modelling of the three-dimensional architecture of group I catalytic introns based on comparative sequence analysis. J. Mol. Biol. 216:585-610.
32. MILLER, O. K., JR. 1971. The genus Panellus in North America. Mich. Bot. 9:17-30.
33. MILLER, O. K., JR., and L. STEWART. 1970. The genus Lentinellus. Mycologia 63:333-369.
34. NISHIDA, H., P. A. BLANZ, and J. SUGIYAMA. 1993. The higher fungus Protomyces inouyei has two group I introns in the 18S rRNA gene. J. Mol. Evol. 37:25-28.
35. NISHIDA, H., and J. SUGIYAMA. 1995. A common group I intron between a plant parasitic fungus and its host. Mol. Biol. Evol. 12:883-886.
36. OLIVEIRA, M. C., and M. A. RAGAN. 1994. Variant forms of a group I intron in nuclear small-subunit rRNA genes of the marine red alga Porphyra spiralis var. amplifolia. Mol. Biol. Evol. 11:195-207.
37. RODRIGO, A. G., M. KELLY-BORGES, P. R. BERGQUIST, and P. L. BERGQUIST. 1993. A randomisation test of the null hypothesis that two cladograms are sample estimates of a parametric phylogenetic tree. N. Z. J. Bot. 31:257-268.
38. RUBSTOV, P., M. MUSAKHANOV, V. ZAKHARYEV, A. KRAYEV, K. SKRYABIN, and A. BAYEV. 1980. The structure of the yeast ribosomal genes. I. The complete sequence of the 18S ribosomal RNA gene from Saccharomyces cerevisiae. Nucleic Acids Res. 8:5779-5794.
39. RUSSELL, P., S. WAGNER, K. RODLAND, R. FEINBAUM, J. RUSSELL, M. BRET-HARET, S. FREE, and R. METZENBERG. 1984. Organization of the ribosomal ribonucleic acid genes in various wild-type strains and wild-collected strains of Neurospora. Mol. Gen. Genet. 196:275-282.
40. SHARP, P. A. 1985. On the origin of RNA splicing and introns. Cell 42:397-400.
41. SOGIN, M. L., A. INGOLD, M. KARLOK, H. NIELSEN, and J. ENGBERG. 1986. Phylogenetic evidence for the acquisition of ribosomal RNA introns subsequent to the divergence of some of the major Tetrahymena groups. EMBO J. 5:3625-3630.
42. SWANN, E. C., and J. W. TAYLOR. 1993. Higher taxa of basidiomycetes: an 18S rRNA gene perspective. Mycolosia 85: 923-936.
43. _. 1995a. Phylogenetic perspectives on basidiomycete systematics: evidence from the 18S rRNA gene. Can. J. Bot. 73(Suppl. 1):s862-s868.
44. _. 1995b. Phylogenetic diversity of yeast-producing basidiomycetes. Mycol. Res. 99:1205-1210.
45. SWOFFORD, D. L. 1993. PAUP: phylogenetic analysis using parsimony. Version 3.1. Illinois Natural History Survey, Champaign.
46. SYVANEN, M. 1994. Horizontal gene tranfer: evidence and possible consequences. Annu. Rev. Genet. 28:237-261.
47. TEMPLETON, A. 1983. Phylogenetic inference from restriction endonuclease cleavage site maps with particular reference to the evolution of humans and the apes. Evolution 37:221-224.
48. VAN ZAAYEN, A. 1979. Mushroom viruses. Pp. 239-324 in P. A. LEMKE, ed. Viruses and plasmids in fungi. Marcel Dekker, New York.
49. WELLS, K. 1994. Jelly fungi, then and now! Mycologia 86:18-48.
50. WHITE, T. J., T. D. BRUNS, S. B. LEE, and J. W. TAYLOR. 1990. Amplification and direct sequencing of fungal ribosomal genes for phylogenetics. Pp. 315-322 in M. A. Innis, D. H. Gelfand, J. J. Sninsky, and T. J. White, eds. PCR protocols. Academic Press, San Diego, Calif.
51. YARUS, M. 1988. A specific amino acid binding site composed of RNA. Science 240:1751-1758.