Phylogenetic analyses suggest reverse splicing spread of group I introns in fungal ribosomal DNA

BMC Evolutionary Biology

Volumn 5, Issue , 2005, Pages

  Bhattacharya, Debashish ^a   Reeb, Valérie ^b   Simon, Dawn M ^a,c   Lutzoni, François ^b  

^a UNIVERSITY OF IOWA   (United States)

^b DUKE UNIVERSITY   (United States)

^c UNIVERSITY OF CALGARY   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

ANIMALIA; HAMILTONAPHIS STYRACI YEAST-LIKE SYMBIONT; SYMBIOTAPHRINA BUCHNERI;

DNA; FUNGAL DNA; RIBOSOME DNA; RIBOSOME RNA; RNA;

ALTERNATIVE RNA SPLICING; ASCOMYCETES; BIOLOGICAL MODEL; EXON; GENETIC RECOMBINATION; GENETICS; INTRON; METABOLISM; MOLECULAR EVOLUTION; PHYLOGENY; POLYMERASE CHAIN REACTION; PROTEIN SECONDARY STRUCTURE; RNA SPLICING;

ALTERNATIVE SPLICING; ASCOMYCOTA; DNA; DNA, FUNGAL; DNA, RIBOSOMAL; EVOLUTION, MOLECULAR; EXONS; INTRONS; MODELS, GENETIC; PHYLOGENY; POLYMERASE CHAIN REACTION; PROTEIN STRUCTURE, SECONDARY; RECOMBINATION, GENETIC; RNA; RNA SPLICING; RNA, RIBOSOMAL;

EID: 28744447849     PISSN: 14712148     EISSN: 14712148     Source Type: Journal    
DOI: 10.1186/1471-2148-5-68     Document Type: Article

References (63)

1. Cech TR: Self-splicing RNA: implications for evolution. Int Rev Cytol 1985, 93:3-22.
2. Lambowitz AM, Belfort M: Introns as mobile genetic elements. Annu Rev Biochem 1993, 62:587-622.
3. Bhattacharya D: The origin and evolution of protist group I introns. Protist 1998, 149:113-122.
4. Haugen P, Simon D, Bhattacharya D: The natural history of group I introns. Trends Genet 2005, 21:111-119.
5. Bhattacharya D, Cannone JJ, Gutell RR: Group I intron lateral transfer between red and brown algal ribosomal RNA. Curr Genet 2001, 40:82-90.
6. Chevalier BS, Stoddard BL: Homing endonucleases: structural and functional insight into the catalysts of intron/intein mobility. Nucleic Acids Res 2001, 29:3757-3774.
7. Dujon B: Group I introns as mobile genetic elements: facts and mechanistic speculations-a review. Gene 1989, 82:91-114.
8. Belfort M, Perlman PS: Mechanisms of intron mobility. J Biol Chem 1995, 270:30237-30240.
9. Goddard MR, Burt A: Recurrent invasion and extinction of a selfish gene. Proc Natl Acad Sci USA 1999, 96:13880-13885.
10. Haugen P, Reeb V, Lutzoni F, Bhattacharya D: The evolution of homing endonuclease genes and group I introns in nuclear rDNA. Mol Biol Evol 2004, 21:129-140.
11. Haugen P, Runge HJ, Bhattacharya D: Long-term evolution of the S788 fungal nuclear small subunit rRNA group I introns. RNA 2004, 10:1084-1096.
12. Bhattacharya D, Friedl T, Helms G: Vertical evolution and intragenic spread of lichen-fungal group I introns. J Mol Evol 2002, 55:74-84.
13. Woodson SA, Cech TR: Reverse self-splicing of the Tetrahymena group I intron: implication for the directionality of splicing and for intron transposition. Cell 1989, 57:335-345.
14. Roman J, Woodson SA: Reverse splicing of the Tetrahymena IVS: evidence for multiple reaction sites in the 23S rRNA. RNA 1995, 1:478-490.
15. Roman J, Woodson SA: Integration of the Tetrahymena group I intron into bacterial rRNA by reverse splicing in vivo. Proc Natl Acad Sci USA 1998, 95:2134-2139.
16. Roman J, Rubin MN, Woodson SA: Sequence specificity of in vivo reverse splicing of the Tetrahymena group I intron. RNA 1999, 5:1-13.
17. Lynch M, Conery JS: The origins of genome complexity. Science 2001, 302:1401-1404.
18. Noda H, Kodama K: Phylogenetic position of the yeastlike endosymbionts of anobiid beetles. Appl Environ Microbiol 1996, 62:162-167.
19. Lonergan KM, Gray MW: The ribosomal RNA gene region in Acanthamoeba castellanii mitochondrial DNA A case of evolutionary transfer of introns between mitochondria and plastids? J Mol Biol 1994, 239:476-499.
20. Hibbett DS: Phylogenetic evidence for horizontal transmission of group I introns in the nuclear ribosomal DNA of mushroom-forming fungi. Mol Biol Evol 1996, 13:903-917.
21. Cho Y, Qiu YL, Kuhlman P, Palmer JD: Explosive invasion of plant mitochondria by a group I intron. Proc Natl Acad Sci USA 1998, 95:14244-14249.
22. Friedl T, Besendahl A, Pfeiffer P, Bhattacharya D: The distribution of group I introns in lichen algae suggests that lichenization facilitates intron lateral transfer. Mol Phylogenet Evol 2000, 14:342-352.
23. Simon DM, Moline J, Helms G, Friedl T, Bhattacharya D: Divergent histories of rDNA group I introns in the lichen family Physciaceae. J Mol Evol 2005, 60:434-446.
24. Jones KG, Blackwell M: Ribosomal DNA sequence analysis places the yeast-like genus Symbiotaphrina within filamentous ascomycetes. Mycologia 1996, 88:212-218.
25. Nikoh N, Fukatsu T: Evolutionary dynamics of multiple group I introns in nuclear ribosomal RNA genes of endoparasitic fungi of the genus Cordyceps. Mol Biol Evol 2001, 18:1631-1642.
26. Johansen S, Haugen P: A complex group I intron in Nectria galligena rDNA. Microbiology 1999, 145:516-517.
27. Perotto S, Nepote-Fus P, Saletta L, Band C, Young JP: A diverse population of introns in the nuclear ribosomal genes of ericoid mycorrhizal fungi includes elements with sequence similarity to endonuclease-coding genes. Mol Biol Evol 2000, 17:44-59.
28. Haugen P, Huss VA, Nielsen H, Johansen S: Complex group-I introns in nuclear SSU rDNA of red and green algae: evidence of homing-endonuclease pseudogenes in the Bangiophyceae. Curr Genet 36:345-353.
29. Birgisdottir AB, Johansen S: Site-specific reverse splicing of a HEG-containing group I intron in ribosomal DNA. Nucleic Acids Res 2005, 33:2042-2051.
30. Palmer JD, Adams KL, Cho Y, Parkinson CL, Qiu YL, Song K: Dynamic evolution of plant mitochondrial genomes: mobile genes and introns and highly variable mutation rates. Proc Natl Acad Sci U S A 2000, 97:6960-6966.
31. Bhattacharya D, Surek B, Ruesing M, Melkonian M: Group I introns are inherited through common ancestry in the nuclearencoded rRNA of Zygnematales (Charophyceae). Proc Natl Acad Sci USA 1994, 91:9916-9920.
32. Nielsen H, Engberg J: Sequence comparison of the rDNA introns from six different species of Tetrahymena. Nucleic Acids Res 1985, 13:7445-7455.
33. Johanningmeier U, Heiss S: Construction of a Chlamydomonas reinhardtii mutant with an intronless psbA gene. Plant Mol Biol 1993, 22:91-99.
34. Belfort M: Phage T4 introns: self-splicing and mobility. Annu Rev Genet 1990, 24:363-385.
35. Cech TR: Self-splicing of group I introns. Annu Rev Biochem 1990, 59:543-568.
36. Turmel M, Cote V, Otis C, Mercier JP, Gray MW, Lonergan KM, Lemieux C: Evolutionary transfer of ORF-containing group I introns between different subcellular compartments (chloroplast and mitochondrion). Mol Biol Evol 1995, 12:533-545.
37. Bhattacharya D, Simon D, Huang J, Cannone JJ, Gutell RR: The exon context and distribution of rRNA introns. BMC Evol Biol 2003, 3:7.
38. Suh S-O, McHugh JV, Pollock DD, Blackwell M: The beetle gut: a hyperdiverse source of novel yeasts. Mycol Res 2005, 109:261-265.
39. Gardes M, Bruns TD: TS primers with enhanced specificity for basidiomycetes-application to the identification of mycorrhizae and rusts. Mol Ecol 1993, 2:113-118.
40. Gargas A, Taylor JW: Polymerase chain reaction (PCR) primers for amplifying and sequencing 18S rDNA from lichenized fungi. Mycologia 1992, 84:589-592.
41. Guadet J, Julien J, Lafay JF, Brygoo Y: Phylogeny of some Fusarium species, as determined by large-subunit rRNA sequence comparison. Mol Biol Evol 1989, 6:227-242.
42. Kauff F, Lutzoni F: Phylogeny of the Gyalectales and Ostropales (Ascomycota, Fungi): among and within order relationships based on nuclear ribosomal RNA small and large subunits. Mol Phylogenet Evo 2002, 25:138-156.
43. Miadlikowska J, McCune B, Lutzoni F: Pseudocyphellaria perpetua, a new lichen from western North America. Bryologist 2002, 105:1-10.
44. Reeb V, Lutzoni F, Roux C: Contribution of RPB2 to multilocus phylogenetic studies of the euascomycetes (Pezizomycotina, Fungi) with special emphasis on the lichen-forming Acarosporaceae and evolution of polyspory. Mol Phylogenet Evol 2004, 32:1036-1060.
45. Spatafora JW, Mitchell TG, Vilgalys R: Analysis of genes coding for small-subunit rRNA sequences in studying phylogenetics of dematiaceous fungal pathogens. J Clin Microbiol 1995, 33:1322-1326.
46. Vilgalys R, Hester M: Rapid genetic identification and mapping of enzymatically amplified ribosomal DNA from several Cryptococcus species. J Bacteriol 1990, 172:4238-4246.
47. White TJ, Bruns T, Lee S, Taylor J: Amplification and direct sequencing of fungal ribosomal RNA gene for phylogenetics. In PCR Protocols: a Guide to Methods and Applications Edited by: Innes MA, Gelfand DH, Sninsky JJ, White TJ. San Diego: Academic Press; 1990:315-322.
48. Ronquist F, Huelsenbeck JP: MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 2003, 19:1572-1574.
49. Lutzoni F, Kauff F, Cox CJ, McLaughlin D, Celio G, Dentinger B, Padamsee M, Hibbett D, James TY, Baloch E, Grube M, Reeb V, Hofstetter V, Schoch C, Arnold AE, Miadlikowska J, Spatafora J, Johnson D, Hambleton S, Crockett M, Shoemaker R, Sung G-H, Lücking R, Lumbsch T, O'Donnell K, Binder M, Diederich P, Ertz D, Gueidan C, Hall B, Hansen K, Harris RC, Hosaka K, Lim Y-W, Liu Y, Matheny B, Nishida H, Pfister D, Rogers J, Rossman A, Schmitt I, Sipman H, Stone J, Sugiyama J, Yahr R, Vilgalys R: Assembling the fungal tree of life: progress, classification, and evolution of subcellular traits. Amer J Bot 2004, 91:1446-1480.
50. Cannone JJ, Subramanian S, Schnare MN, Collett JR, D'Souza LM, Du Y, Feng B, Lin N, Madabusi LV, Müller KM, Pande N, Shang Z, Yu N, Gutell RR: The Comparative RNA Web (CRW) Site: an online database of comparative sequence and structure information for ribosomal, intron, and other RNAs. BMC Bioinformatics 2002, 3:1-31.
51. Michel F, Westhof E: Modelling of the three-dimensional architecture of group I catalytic introns based on comparative sequence analysis. J Mol Biol 1990, 216:585-610.
52. Golden BL, Gooding AR, Podell ER, Cech TR: A preorganized active site in the crystal structure of the Tetrahymena ribozyme. Science 1998, 282:259-264.
53. DePriest PT, Been MD: Numerous group I introns with variable distributions in the ribosomal DNA of a lichen fungus. J Mol Biol 1992, 228:315-321.
54. Suh SO, Jones KG, Blackwell M: A group I intron in the nuclear small subunit rRNA gene of Cryptendoxyla hypophloia, an ascomycetous fungus: evidence for a new major class of group I introns. J Mol Evol 1999, 48:493-500.
55. Coates BS, Hellmich RL, Lewis LC: Nuclear small subunit rRNA group I intron variation among Beauveria spp provide tools for strain identification and evidence of horizontal transfer. Curr Genet 2002, 41:414-424.
56. Jukes TH, Cantor CR: Evolution of protein molecules. In Mammalian Protein Metabolism Edited by: Munro HN. New York: Academic Press; 1969:21-132.
57. Bruno WJ, Halpern AL: Topological bias and inconsistency of maximum likelihood using wrong models. Mol Biol Evol 1999, 16:564-566.
58. Piontkivska H: Efficiencies of maximum likelihood methods of phylogenetic inferences when different substitution models are used. Mol Phylogenet Evol 2004, 31:865-873.
59. Nei M, Kumar S, Takahashi K: The optimization principle in phylogenetic analysis tends to give incorrect topologies when the number of nucleotides or amino acids used is small. Proc Natl Acad Sci USA 1998, 95:12390-12397.
60. Swofford DL: PAUP*: Phylogenetic Analysis Using Parsimony (* and Other Methods) 40b10 Sunderland: Sinauer; 2003.
61. Rodriguez F, Oliver JF, Marin A, Medina JR: The general stochastic model of nucleotide substitutions. J Theor Biol 1990, 142:485-501.
62. Felsenstein J: PHYLIP, V3.63 Seattle: Department of Genome Sciences, University of Washington; 2004.
63. Shimodaira H, Hasegawa M: Multiple comparisons of log-likelihoods with applications to phylogenetic inference. Mol Biol Evol 1999, 16:1114-1116.