Structural partitioning, paired-sites models and evolution of the ITS transcript in Syzygium and Myrtaceae

Molecular Phylogenetics and Evolution

Volumn 43, Issue 1, 2007, Pages 124-139

  Biffin, E ^a   Harrington, M G ^b   Crisp, M D ^a   Craven, L A ^a   Gadek, P A ^b  

^a AUSTRALIAN NATIONAL UNIVERSITY   (Australia)

^b JAMES COOK UNIVERSITY   (Australia)

Author keywords

Bayesian analysis; ITS1; ITS2; Loops; Maximum likelihood; Model selection; Mutational dynamics; RNA specific models; Secondary structure; Stems

Indexed keywords

RIBOSOMAL SPACER DNA; RIBOSOME RNA;

ARTICLE; BASE PAIRING; BAYES THEOREM; BIOLOGICAL MODEL; BIOLOGY; COMPARATIVE STUDY; DNA SEQUENCE; EUGENIA; GENETIC SELECTION; GENETICS; MOLECULAR EVOLUTION; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PHYLOGENY; SEQUENCE ALIGNMENT; SPECIES DIFFERENCE; STATISTICAL MODEL;

BASE PAIRING; BASE SEQUENCE; BAYES THEOREM; COMPUTATIONAL BIOLOGY; DNA, RIBOSOMAL SPACER; EUGENIA; EVOLUTION, MOLECULAR; LIKELIHOOD FUNCTIONS; MODELS, GENETIC; MOLECULAR SEQUENCE DATA; PHYLOGENY; RNA, RIBOSOMAL; SELECTION (GENETICS); SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA; SPECIES SPECIFICITY;

MAGNOLIOPHYTA; MYRTACEAE; SYZYGIUM;

EID: 33947576587     PISSN: 10557903     EISSN: 10959513     Source Type: Journal    
DOI: 10.1016/j.ympev.2006.08.013     Document Type: Article

References (59)

1. Albach D.C., and Chase M.W. Incongruence in Veroniceae (Plantaginaceae): evidence from two plastid and a nuclear ribosomal DNA region. Mol. Phys. Evol. 32 (2003) 183-197
2. Alvarez I., and Wendel J.F. Ribosomal ITS sequences and plant phylogenetic inference. Mol. Phylogenet. Evol. 29 (2003) 417-434
3. Bailey C.D., Carr T.G., Harris S.A., and Hughes C.E. Characterization of angiosperm nrDNA polymorphism, paralogy, and pseudogenes. Mol. Phylogenet. Evol. 29 (2003) 435-455
4. Baldwin B.G. Phylogenetic utility of the internal transcribed spacers of nuclear ribosomal DNA in plants: an example from the Compositae. Mol. Phylogenet. Evol. 1 (1992) 3-16
5. Biffin E., Craven L.A., Crisp M.D., and Gadek P.A. Molecular systematics of Syzygium and allied genera (Myrtaceae): evidence from the chloroplast genome. Taxon 55 (2006)
6. Buckler E.S., and Holtsford T.P. Zea ribosomal repeat evolution and substitution patterns. Mol. Biol. Evol. 13 (1996) 623-632
7. Buckley T.R. Model misspecification and probabilistic tests of topology: evidence from empirical data sets. Syst. Biol. 51 (2002) 509-523
8. Buckley T.R., and Cunningham C.W. The effects of nucleotide substitution model assumptions on estimates of nonparametric bootstrap support. Mol. Biol. Evol. 19 (2002) 394-405
9. Coleman A.W. ITS2 is a double-edge tool for Eukaryote evolutionary comparisons. Trends Genet. 19 (2003) 370-375
10. Côté C.A., and Peculis B.A. Role of the ITS2-proximal stem and evidence for indirect recognition of processing sites in pre-rRNA processing in yeast. Nucleic Acid Res. 29 (2001) 2106-2116
11. Dixon M.T., and Hillis D.M. Ribosomal RNA secondary structure: compensatory mutations and implications for phylogenetic analysis. Mol. Biol. Evol. 1 (1993) 256-267
12. Doyle J.J., and Doyle J.L. The isolation of plant DNA from fresh tissue. Search 12 (1990) 13-15
13. Felsenstein, J. 1993. PHYLIP (Phylogeny Inference Package) version 3.5c. Distributed by the author. Department of Genetics, University of Washington, Seattle.
14. Gardner P.P., and Giegerich R. A comprehensive comparison of comparative RNA structure prediction approaches. BMC Bioinform. 5 (2004) 140
15. Gautheret D., Konings D., and Gutell R.R. G·U base pairing motifs in ribosomal RNA. RNA 1 (1995) 807-814
16. Goertzen L.R., Cannone J.J., Gutell R.R., and Jansen R.K. ITS secondary structure derived from comparative analysis: implications for sequence alignment and phylogeny of the Asteraceae. Mol. Phylogenet. Evol. 29 (2003) 216-234
17. Gottschling M., Hilger H.H., Wolf M., and Diane N. Secondary structure of the ITS1 transcript and its application in a reconstruction of the Phylogeny of Boraginales. Plant Biol. 3 (2001) 629-636
18. Guindon S., and Gascuel O. A simple, fast, and accurate algorithm to estimate phylogenies by maximum likelihood. Syst. Biol. 52 (2003) 696-704
19. Gutell R.R., Cannone J.J., Shang Z., Du Y., and Serra M.J. A story: unpaired adenosine bases in ribosomal RNAs. J. Mol. Biol. 304 (2000) 335-354
20. Gutell R.R., Lee J.C., and Cannone J.J. The accuracy of RNA comparative structure models. Curr. Opin. Struct. Biol. 12 (2002) 301-310
21. Harrington M.A., and Gadek P.A. Molecular systematics of the Acmena Alliance (Myrtaceae): phylogenetic analyses and evolutionary implications with respect to Australian taxa. Aust. Syst. Bot. 17 (2004) 63-72
22. Hershkovitz M.A., and Lewis L.A. Deep-level diagnostic value of the rDNA-ITS region. Mol. Biol. Evol. 13 (1996) 1276-1295
23. Hershkovitz M.A., and Zimmer E.A. Conservation patterns in angiosperm ITS2 sequences. Nucleic Acid Res. 24 (1996) 2857-2867
24. Hershkovitz, M.A., Zimmer, E.A., Hahn, W.J., 1998. Ribosomal DNA sequences and angiosperm systematics. In: Hollingsworth, P.M., Bateman, R.M., Gornall, R.J. (Eds.), Molecular Systematics and Plant Evolution, The Systematics Association Special Volume Series 57, Taylor and Francis. pp. 269-326.
25. Higgs P.G. RNA secondary structure: physical and computational aspects. Q. Rev. Biophys. 33 (2000) 199-253
26. Huang Y.L., and Shi S.H. Phylogenetics of the Lytheraceae Sensu. Lato: a preliminary analysis based upon chloroplast rbcL gene, psA-ycf3 spacer, and nuclear rDNA internal transcribed spacer (ITS) sequences. Int. J. Plant Sci. 163 (2002) 215-225
27. Hudelot C., Gowri-Shankar V., Jow H., Rattray M., and Higgs P. RNA-based phylogenetic methods: application to mammalian mitochondrial RNA sequences. Mol. Phylogenet. Evol. 28 (2003) 241-252
28. Joseph N., Krauskopf E., Vera M.I., and Michot B. Ribosomal internal transcribed spacer 2 (ITS2) exhibits a common core of secondary structure in vertebrates and yeast. Nucleic Acid Res. 27 (1999) 4533-4540
29. Jow H., Hudelot C., Rattray M., and Higgs P.G. Bayesian phylogenetics using an RNA substitution model applied to early Mammalian evolution. Mol. Biol. Evol. 19 (2002) 1591-1601
30. Juan V., and Wilson C. RNA secondary structure prediction based on free energy and phylogenetic analysis. J. Mol. Biol. 289 (1999) 935-947
31. Kelchner S.A. Group II introns as phylogenetic tools: structure, function and evolutionary constraints. Am. J. Bot. 89 (2002) 1651-1669
32. Kjer K.M. Aligned 18S and insect phylogeny. Syst. Biol. 53 (2004) 506-514
33. Knudsen B., and Hein J. Pfold: RNA secondary structure prediction using stochastic context-free grammars. Nucleic Acid Res. 31 (2003) 3423-3428
34. Lalev A.I., and Nazar R.N. Structural equivalence in the transcribed spacers of pre-rRNA transcripts in Schizosaccharomyces pombe. Nucleic Acid Res. 27 (1999) 3071-3078
35. Lalev A.I., and Nazar R.N. A chaperone for ribosome maturation. JBC 276 (2001) 16655-16659
36. Lalev A.I., Abeyrathne P.D., and Nazar R.N. Ribosomal RNA maturation in Schizosaccharomyces pombe is dependent on a large Ribonucleoprotein complex of the Internal Transcribed Spacer 1. Nucleic Acid Res. 27 (2000) 3071-3078
37. Liston A., Robinson W.A., Oliphant J.M., and Alvarez-Buylla E.R. Length variation in the nuclear ribosomal DNA internal transcribed spacer region of non-flowering seed plants. Syst. Bot. 21 (1996) 109-120
38. Liu J.S., and Schardl C.L. A conserved sequence in internal transcribed spacer 1 of plant nuclear rRNA genes. Plant Mol. Biol. 26 (1994) 775-778
39. Mai J.C., and 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
40. Mathews D.H., Disney M.D., Childs J.L., Schroeder S.J., Zuker M., and Turner D.H. Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure. Proc. Natl. Acad. Sci. USA 101 (2004) 7287-7292
41. Mayol M., and Rosselló J.A. Why nuclear ribosomal DNA spacers (ITS) tell different stories inQuercus. Mol. Phylogenet. Evol. 19 (2001) 167-176
42. Noller H.F. Structure of ribosomal RNA. Annu. Rev. Biochem. 53 (1984) 119-162
43. Nickrent D.L., Schuette K.P., and Starr E.M. A molecular phylogeny of Arceuthobium (Viscaceae) based on nuclear ribosomal DNA internal transcribed spacer sequences. Am. J. Bot. 81 (1994) 1149-1160
44. van Nues R.W., Rientjes J.M.J., van der Sande C.A.F.M., Zerp S.F., Sluiter C., Venema J., Planta R.J., and Raue H.A. Separate structural elements within internal transcribed spacer 1 of Saccharomyces cerevisiae precursor ribosomal RNA direct the formation of 17S and 26S rRNA. Nucleic Acid Res. 22 (1994) 912-919
45. Nylander J.A.A. MrAIC.pl. Program distributed by the author (2004), Evolutionary Biology Centre, Uppsala University
46. Savill N.J., Hoyle D.C., and Higgs P.G. RNA sequence evolution with secondary structure constraints: comparison of substitution rate models using maximum likelihood methods. Genetics 157 (2001) 399-411
47. Schöniger M., and von Haeseler A. Toward assigning helical regions in alignments of ribosomal RNA and testing the appropriateness of evolutionary models. J. Mol. Evol. 49 (1999) 691-698
48. Schultz J., Maisel S., Gerlach D., Müller T., and Wolf M. A common core of secondary structure of the internal transcribed spacer 2 (ITS2) throughout the Eukaryota. RNA 11 (2005) 361-364
49. Simmons M.P., and Freudenstein J.V. The effects of increasing genetic distance on alignment of, and tree construction from, rDNA internal transcribed spacer sequences. Mol. Phylogenet. Evol. 26 (2003) 444-451
50. Sugiura N. Further analysis of the data by Akaike's information criterion and the finite corrections. Commun. Stat. Theory Methods A7 (1978) 13-26
51. Swofford, D.L., 1998. PAUP*: Phylogenetic Analysis Using Parsimony (*and other methods). Version 4.08b. Sinauer, Massachusetts.
52. Sytsma K.J., Litt A., Zjhra M.L., Pires J.C., Nepokroeffk M., Conti E., Walker J., and Wilson P.G. Clades, clocks, and continents: historical and biogeographical analysis of Myrtaceae, Vochysiaceae, and relatives in the southern hemisphere. Int. J. Plant Sci. 165 4 Suppl. (2004) S85-S105
53. Telford M.J., Wise M.J., and Gowri-Shankar V. Consideration of RNA secondary structure significantly improves likelihood-based estimates of phylogeny: examples from the bilateria. Mol. Biol. Evol. 22 (2005) 1129-1136
54. Tillier E.R.M., and Collins R.A. High apparent rate of simultaneous compensatory base-pair substitutions in ribosomal RNA. Genetics 148 (1998) 1993-2002
55. Wheeler W.C., and Honeycutt R.L. Paired sequence difference in ribosomal RNAs: evolution and phylogenetic implications. Mol. Biol. Evol. 5 (1988) 90-96
56. White T.J., Bruns T., Lee S., and Taylor J. Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In: Innis M.D., Gelfand D., Sninsky J., and White T. (Eds). PCR Protocols: A Guide to Methods and Applications (1990), Academic Press, San Diego 315-322
57. Wilgenbusch J., and De Querioz K. Phylogenetic relationships among the Phrynosomatid Sand Lizards inferred from mitochondrial DNA sequences generated by heterogeneous evolutionary processes. Syst. Biol. 49 (2000) 592-612
58. Wilson P.G., O'Brien M.M., Heslewood M.M., and Quinn C.J. Relationships within Myrtaceae sensu lato based on a matK phylogeny. Plant Syst. Evol. 251 (2005) 3-19
59. Zuker M., and Jacobson A.B. ' Well-determined' regions in RNA secondary structure prediction: analysis of small sub-unit ribosomal RNA. Nucleic Acid Res. 23 (1995) 2791-2798