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. 1996 Aug 1;24(15):2857–2867. doi: 10.1093/nar/24.15.2857

Conservation patterns in angiosperm rDNA ITS2 sequences.

M A Hershkovitz 1, E A Zimmer 1
PMCID: PMC146035  PMID: 8760866

Abstract

The two internal transcribed spacers (ITS1 and ITS2) of nuclear ribosomal DNA have become commonly exploited sources of informative variation for interspecific-/intergeneric-level phylogenetic analyses among angiosperms and other eukaryotes. We present an alignment in which one-third to one-half of the ITS2 sequence is alignable above the family level in angiosperms and a phenetic analysis showing that ITS2 contains information sufficient to diagnose lineages at several hierarchical levels. Base compositional analysis shows that angiosperm ITS2 is inherently GC-rich, and that the proportion of T is much more variable than that for other bases. We propose a general model of angiosperm ITS2 secondary structure that shows common pairing relationships for most of the conserved sequence tracts. Variations in our secondary structure predictions for sequences from different taxa indicate that compensatory mutation is not limited to paired positions.

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Selected References

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  1. Bakker F. T., Olsen J. L., Stam W. T. Evolution of nuclear rDNA ITS sequences in the Cladophora albida/sericea clade (Chlorophyta). J Mol Evol. 1995 Jun;40(6):640–651. doi: 10.1007/BF00160512. [DOI] [PubMed] [Google Scholar]
  2. Baldwin B. G. Phylogenetic utility of the internal transcribed spacers of nuclear ribosomal DNA in plants: an example from the compositae. Mol Phylogenet Evol. 1992 Mar;1(1):3–16. doi: 10.1016/1055-7903(92)90030-k. [DOI] [PubMed] [Google Scholar]
  3. Campbell B. C., Steffen-Campbell J. D., Werren J. H. Phylogeny of the Nasonia species complex (Hymenoptera: Pteromalidae) inferred from an internal transcribed spacer (ITS2) and 28S rDNA sequences. Insect Mol Biol. 1993;2(4):225–237. doi: 10.1111/j.1365-2583.1994.tb00142.x. [DOI] [PubMed] [Google Scholar]
  4. Fritz G. N., Conn J., Cockburn A., Seawright J. Sequence analysis of the ribosomal DNA internal transcribed spacer 2 from populations of Anopheles nuneztovari (Diptera: Culicidae). Mol Biol Evol. 1994 May;11(3):406–416. doi: 10.1093/oxfordjournals.molbev.a040122. [DOI] [PubMed] [Google Scholar]
  5. Gultyaev A. P., van Batenburg F. H., Pleij C. W. The computer simulation of RNA folding pathways using a genetic algorithm. J Mol Biol. 1995 Jun 30;250(1):37–51. doi: 10.1006/jmbi.1995.0356. [DOI] [PubMed] [Google Scholar]
  6. Gutell R. R., Larsen N., Woese C. R. Lessons from an evolving rRNA: 16S and 23S rRNA structures from a comparative perspective. Microbiol Rev. 1994 Mar;58(1):10–26. doi: 10.1128/mr.58.1.10-26.1994. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Liu J. S., Schardl C. L. A conserved sequence in internal transcribed spacer 1 of plant nuclear rRNA genes. Plant Mol Biol. 1994 Oct;26(2):775–778. doi: 10.1007/BF00013763. [DOI] [PubMed] [Google Scholar]
  8. Muse S. V. Evolutionary analyses of DNA sequences subject to constraints of secondary structure. Genetics. 1995 Mar;139(3):1429–1439. doi: 10.1093/genetics/139.3.1429. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Olsthoorn R. C., Licis N., van Duin J. Leeway and constraints in the forced evolution of a regulatory RNA helix. EMBO J. 1994 Jun 1;13(11):2660–2668. doi: 10.1002/j.1460-2075.1994.tb06556.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Ritland C. E., Ritland K., Straus N. A. Variation in the ribosomal internal transcribed spacers (ITS1 and ITS2) among eight taxa of the Mimulus guttatus species complex. Mol Biol Evol. 1993 Nov;10(6):1273–1288. doi: 10.1093/oxfordjournals.molbev.a040067. [DOI] [PubMed] [Google Scholar]
  11. Schlötterer C., Hauser M. T., von Haeseler A., Tautz D. Comparative evolutionary analysis of rDNA ITS regions in Drosophila. Mol Biol Evol. 1994 May;11(3):513–522. doi: 10.1093/oxfordjournals.molbev.a040131. [DOI] [PubMed] [Google Scholar]
  12. 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. 1994 Feb 18;236(2):455–468. doi: 10.1006/jmbi.1994.1157. [DOI] [PubMed] [Google Scholar]
  13. Thompson J. D., Higgins D. G., Gibson T. J. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 1994 Nov 11;22(22):4673–4680. doi: 10.1093/nar/22.22.4673. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Vilgalys R., Sun B. L. Ancient and recent patterns of geographic speciation in the oyster mushroom Pleurotus revealed by phylogenetic analysis of ribosomal DNA sequences. Proc Natl Acad Sci U S A. 1994 May 10;91(10):4599–4603. doi: 10.1073/pnas.91.10.4599. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Vogler A. P., DeSalle R. Evolution and phylogenetic information content of the ITS-1 region in the tiger beetle Cicindela dorsalis. Mol Biol Evol. 1994 May;11(3):393–405. doi: 10.1093/oxfordjournals.molbev.a040121. [DOI] [PubMed] [Google Scholar]
  16. Wesson D. M., Porter C. H., Collins F. H. Sequence and secondary structure comparisons of ITS rDNA in mosquitoes (Diptera: Culicidae). Mol Phylogenet Evol. 1992 Dec;1(4):253–269. doi: 10.1016/1055-7903(92)90001-w. [DOI] [PubMed] [Google Scholar]
  17. Wheeler W. C., Honeycutt R. L. Paired sequence difference in ribosomal RNAs: evolutionary and phylogenetic implications. Mol Biol Evol. 1988 Jan;5(1):90–96. doi: 10.1093/oxfordjournals.molbev.a040480. [DOI] [PubMed] [Google Scholar]
  18. Yeh L. C., Lee J. C. Structural analysis of the internal transcribed spacer 2 of the precursor ribosomal RNA from Saccharomyces cerevisiae. J Mol Biol. 1990 Feb 20;211(4):699–712. doi: 10.1016/0022-2836(90)90071-S. [DOI] [PubMed] [Google Scholar]
  19. Zuker M. On finding all suboptimal foldings of an RNA molecule. Science. 1989 Apr 7;244(4900):48–52. doi: 10.1126/science.2468181. [DOI] [PubMed] [Google Scholar]
  20. van Nues R. W., Rientjes J. M., Morré S. A., Mollee E., Planta R. J., Venema J., Raué H. A. Evolutionarily conserved structural elements are critical for processing of Internal Transcribed Spacer 2 from Saccharomyces cerevisiae precursor ribosomal RNA. J Mol Biol. 1995 Jun 30;250(1):24–36. doi: 10.1006/jmbi.1995.0355. [DOI] [PubMed] [Google Scholar]

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