5.8S motifs for the identification of pseudogenic ITS regions

Botany

Volumn 86, Issue 3, 2008, Pages 300-305

  Harpke, Doerte ^a   Peterson, Angela ^a  

^a MARTIN LUTHER UNIVERSITY HALLE WITTENBERG   (Germany)

Author keywords

5.8s rDNA; Internal transcribed spacer region; Motif; Pseudogene

Indexed keywords

BIOMARKERS; GENES; POLYMORPHISM;

INTERNAL TRANSCRIBED SPACER REGION; PSEUDOGENES;

DNA;

ANGIOSPERM; COLIFORM BACTERIUM; DATA SET; DNA; GENETIC MARKER; IDENTIFICATION METHOD; MOLECULAR ANALYSIS; PHYLOGENETICS; TAXONOMY;

ESCHERICHIA COLI; MAGNOLIOPHYTA; VIRIDIPLANTAE;

EID: 42449146039     PISSN: 19162804     EISSN: None     Source Type: Journal    
DOI: 10.1139/B07-134     Document Type: Article

References (40)

1. Àlvarez, I., and Wendel, J.F. 2003. Ribosomal ITS sequences and plant phylogenetic inference. Mol. Phylogenet. Evol. 29: 417-434. doi:10.1016/S1055-7903(03)00208-2. PMID:14615184.
2. Bailey, C.D., Carr, T.G., Harris, S.A., and Hughes, C.E. 2003. Characterization of angiosperm nrDNA polymorphism, paralogy, and pseudogenes. Mol. Phylogenet. Evol. 29: 435-455. doi:10.1016/j.ympev.2003.08.021. PMID:14615185.
3. Baker, W.J., Hedderson, T.A., and Dransfield, J.U. 2000. Molecular phylogentics of subfamily Calamoideae (Palmae) based on nrDNA ITS and cpDNA rps16 intron sequence data. Mol. Phylogenet. Evol. 14: 195-217. doi:10.1006/mpev.1999.0696. PMID:10679155.
4. Baldwin, B.G., Sanderson, M.J., Porter, J.M., Wojciechowski, M.F., Campbell, C.S., and Donoghue, M.J. 1995. The ITS region of nuclear ribosomal DNA: a valuable source of evidence on angiosperm phylogeny. Ann. Mo. Bot. Gard. 82: 247-277. doi:10.2307/2399880.
5. Bayly, M.J., and Ladiges, P.Y. 2007. Divergent paralogues of ribosomal DNA in eucalypts (Myrtaceae). Mol. Phylogenet. Evol. 44: 346-356. doi:10.1016/j.ympev.2006.10.027. PMID:17188000.
6. Buckler, E.S., IV, Ippolito, A., and Holtsford, T.P. 1997. The evolution of ribosomal DNA: divergent paralogues and phylogenetic implications. Genetics, 145: 821-832. PMID:9055091.
7. Cannone, J.J., Subramanian, S., Schnare, M.N., Collett, J.R., D'Souza, L.M., Du, Y., Feng, B., Lin, N., Madabusi, L.V., Muller, K.M., Pande, N., Shang, Z., Yu, N., and Gutell, R.R. 2002. The comparative RNA web (CRW) site: an online database of comparative sequence and structure information for ribosomal, intron, and other RNAs. BMC Bioinformatics, 3(2). [Correction: BMC Bioinformatics 3(15).] doi:10.1186/1471-2105-3-2. PMID: 11869452.
8. Carr, T.G., O'Neil, K., and Bailey, C.D. 2006. Bootstrap hypothesis testing using BootHyp [online]. Available from biology-web. nmsu.edu/bailey/ Boothyp.html [accessed 30 July 2007].
9. Feliner, G.N., and Rosselló, J.A. 2007. Better the devil you know? Guidelines for insightful utilization of nrDNA ITS in species-level evolutionary studies in plants. Mol. Phylogenet. Evol. 44: 911-919. doi:10.1016/j.ympev.2007.01.013. PMID:17383902.
10. Felsenstein, J. 2005. PHYLIP (Phylogeny Inference Package). Version 3.6. Distributed by the author. Department of Genome Sciences, University of Washington, Seattle, Wash.
11. Gillespie, J.J., Johnston, J.S., Cannone, J.J., and Gutell, R.R. 2006. Characteristics of the nuclear (18S, 5.8S, 28S and 5S) and mitochondrial (12S and 16S) rRNA genes of Apis mellifera (Insecta: Hymenoptera): structure, organization, and retrotransposable elements. Insect Mol. Biol. 15: 657-686. doi:10.1111/j.1365-2583.2006.00689.x. PMID:17069639.
12. Hall, T.A. 1999. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp. Ser. 41: 95-98.
13. Harpke, D., and Peterson, A. 2006a. Non-concerted ITS evolution in Mammillaria (Cactaceae). Mol. Phylogenet. Evol. 41: 579-593. doi:10.1016/j.ympev.2006.05.036. PMID:16843685.
14. Harpke, D., and Peterson, A. 2006b. Identification of 5.8S nrRNA pseudogenes in Mammillaria (Cactaceae) [online]. Available from www.2006.botanyconference.org/engine/search/index. php?func = detailandaid = 121 [accessed 27 August 2007].
15. Harpke, D., and Peterson, A. 2007. Quantitative PCR revealed a minority of ITS copies to be functional in Mammillaria (Cactaceae). Int. J. Plant Sci. 168: 1157-1160. doi:10.1086/520729.
16. Hartmann, S., Nason, J.D., and Bhattacharya, D. 2001. Extensive ribosomal DNA genic variation in the columnar cactus Lophocereus. J. Mol. Evol. 53: 124-134. PMID:11479683.
17. Hershkovitz, M.A., Zimmer, E.A., and Hahn, W.J. 1999. Ribosomal DNA sequences and angiosperm systematics. In Molecular systematics and plant evolution. Edited by P.M. Hollingsworth, R.M. Bateman, and R.J. Cornall. Taylor and Francis, London, UK. pp. 268-326.
18. Huelsenbeck, J.P., and Ronquist, F. 2001. MrBayes: Bayesian inference of phylogenetic trees. Bioinformatics, 17: 754-755. doi:10.1093/ bioinformatics/17.8.754. PMID:11524383.
19. Hughes, C.E., Bailey, C.D., and Harris, S.A. 2002. Divergent and reticulate species relationships in Leucaena (Fabaceae) inferred from multiple data sources: Insights into polyploid origins and nrDNA polymorphism. Am. J. Bot. 89: 1057-1073.
20. Jobes, D.V., and Thien, L.B. 1997. A conserved motif in the 5.8S ribosomal RNA (rRNA) gene is a useful diagnostic marker for plant internal transcribed spacer (ITS) sequences. Plant Mol. Biol. Rep. 15: 326-334. doi:10.1023/A:1007462330699.
21. Kimura, M. 1980. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J. Mol. Evol. 16: 111-120. doi:10.1007/BF01731581. PMID:7463489.
22. Kumar, S. 1996. PHYLTEST: a program for testing phylogenetic hypothesis. Version 2.0. Institute of Molecular Evolutionary Genetics and Department of Biology, Pennsylvania State University, University Park, Penn.
23. Li, J., Ledger, J., Ward, T., and Del Tredici, P. 2004. Phylogenetics of Calycanthaceae based on molecular and morphological data with special reference to divergent paralogues of the nrDNA ITS region. Harv. Pap. Bot. 9: 69-82.
24. Li, W. 1997. Molecular evolution. Sinauer Associates, Sunderland, Mass.
25. Liston, A., Robinson, W.A., Oliphant, J.M., and Alvarez-Buylla, E.R. 1996. Length variation in the nuclear ribosomal DNA internal transcribed spacer region of non-flowering seed plants. Syst. Bot. 21: 109-120. doi:10.2307/2419742.
26. Liu, J.S., and Schardl, C.L. 1994. A conserved sequence in internal transcribed spacer 1 of plant nuclear rRNA genes. Plant Mol. Biol. 26: 775-778. doi:10.1007/BF00013763. PMID:7948932.
27. Márquez, L.M., Miller, D.J., MacKenzie, J.B., and Oppen, M.J.H. 2003. Pseudogenes contribute to the extreme diversity of nuclear ribosomal DNA in the hard coral Acropora. Mol. Biol. Evol. 20: 1077-1086. doi:10.1093/molbev/msg122. PMID:12777522.
28. Mathews, D.H., Sabina, J., Zuker, M., and Turner, D.H. 1999. Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. J. Mol. Biol. 288: 911-940. doi:10.1006/jmbi.1999. 2700. PMID:10329189.
29. Muir, G., Fleming, C.C., and Schloetterer, C. 2001. Three divergent rDNA clusters predate the species divergence in Quercus petraea (Matt.) Liebl., and Quercus robur L. Mol. Biol. Evol. 18: 112-119. PMID:11158370.
30. Peterson, A., John, H., Koch, E., and Peterson, J. 2004. A molecular phylogeny of the genus Gagea (Liliaceae) in Germany inferred from non-coding chloroplast and nuclear DNA sequences. Plant Syst. Evol. 245: 145-162. doi:10.1007/s00606-003-0114-y.
31. Razafimandimbison, S.G., Kellogg, E.A., and Bremer, B. 2004. Recent origin and phylogenetic utility of divergent ITS putative pseudogenes: A case study from Naucleeae (Rubiaceae). Syst. Biol. 53: 177-192. doi:10.1080/10635150490423278. PMID: 15205048.
32. Ruggiero, M.V., and Procaccini, G. 2004. The rDNA ITS region in the Lessepsian marine angiosperm Halophila stipulacea (Forssk.) Aschers. (Hydrocharitaceae): Intragenomic variability and putative pseudogenic sequences. J. Mol. Evol. 58: 115-121. doi:10.1007/s00239-003-2536-0. PMID:14743319.
33. Schnare, M.N., Damsberger, S.H., Gray, M.W., and Gutell, R.R. 1996. Comprehensive comparison of structural characteristics in eukaryotic cytoplasmic large subunit (23 S-like) ribosomal RNA. J. Mol. Biol. 256: 701-719. doi:10.1006/jmbi.1996.0119.PMID:8642592.
34. Suh, Y., Thien, L.B., and Zimmer, E.A. 1992. Nucleotide sequences of the internal transcribed spacers and 5.8S rRNA gene in Canella winterana (Magnoliales; Canellaceae). Nucleic Acids Res. 20: 6101-6102. doi:10.1093/nar/20.22.6101. PMID:1461743.
35. Takezaki, N., Razhetsky, A., and Nei, M. 1995. Phylogenetic test of the molecular clock and linearized trees. Mol. Biol. Evol. 12: 823-833. PMID:7476128.
36. Wissemann, V. 2003. Hybridization and the evolution of the nrITS spacer region. In Plant genome, biodiversity and evolution. Part A. Phanerogams. Edited by A.K. Sharma and A. Sharma. Sci. Publ. Inc. Vol. 1. Enfield, N.H. pp. 57-71.
37. Won, H., and Renner, S.S. 2005. The internal transcribed spacer of nuclear ribosomal DNA in the gymnosperm Gnetum. Mol. Phylogenet. Evol. 36: 581-597. doi:10.1016/j.ympev.2005.03.011. PMID:16099382.
38. Wuyts, J., De Rijk, P., Van de Peer, Y., Winkelmans, T., and De Wachter, R. 2001. The European large subunit ribosomal RNA database. Nucleic Acids Res. 29: 175-177. doi:10.1093/nar/29.1.175. PMID:11125083.
39. Zhang, D., and Sang, T. 1999. Physical mapping of ribosomal RNA genes in Peonies (Paeonia, Paeoniaceae) by fluorescent in situ hybridization: implications for phylogeny and concerted evolution. Am. J. Bot. 86: 735-740. doi:10.2307/2656583. PMID:10330077.
40. Zuker, M. 2003. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res. 31: 3406-3415. doi:10.1093/nar/gkg595. PMID:12824337.