Phylogenetic analysis of the internal transcribed spacer (ITS) region in Menyanthaceae using predicted secondary structure

Molecular Phylogenetics and Evolution
Nicholas P Tippery, Donald H Les

Abstract

Sequences of the nuclear internal transcribed spacer (ITS) regions ITS1 and ITS2 have been used widely in molecular phylogenetic studies because of their relatively high variability and facility of amplification. For phylogenetic applications, most researchers use sequence alignments that are based on nucleotide similarity. However, confidence in the alignment often deteriorates at taxonomic levels above genus, due to increasing variability among sequences. Like ribosomal RNA (rRNA) and other RNA molecules, the ITS transcripts consist in part of conserved secondary structures ('stems' and 'loops') that can be predicted by mathematical algorithm. Researchers have long considered the evolutionary conservation of rRNA secondary structure, but until recently few phylogenetic analyses of the ITS regions specifically incorporated structural data. We outline a novel method by which to derive additional phylogenetic data from ITS secondary structure in order to evaluate support for relationships at higher taxonomic levels. To illustrate the method, we describe an example from the plant family Menyanthaceae. Using predicted ITS secondary structure data, we obtained a well-resolved and moderately supported phylogeny, in which most topolo...Continue Reading

References

Sep 1, 1994·Molecular Phylogenetics and Evolution·M Schöniger, A von Haeseler
Oct 1, 1994·Plant Molecular Biology·J S Liu, C L Schardl
Aug 1, 1996·Nucleic Acids Research·M A Hershkovitz, E A Zimmer
Nov 1, 1996·Molecular Biology and Evolution·M A Hershkovitz, L A Lewis
Jul 22, 1997·Proceedings of the National Academy of Sciences of the United States of America·J R Powell, E N Moriyama
Jan 27, 1999·Bioinformatics·D Posada, K A Crandall
Feb 26, 2000·Annual Review of Genetics·J Venema, D Tollervey
Oct 6, 2000·Molecular Biology and Evolution·B BilloudJ S Deutsch
Mar 27, 2001·Molecular Biology and Evolution·M S Lee
Aug 29, 2001·Bioinformatics·J P Huelsenbeck, F Ronquist
Feb 16, 2002·Journal of Molecular Evolution·Gustavo Caetano-Anollés
Jun 25, 2002·Journal of Molecular Biology·Ivo L HofackerPeter F Stadler
Jul 20, 2002·Current Opinion in Structural Biology·Robin R GutellJamie J Cannone
Jun 26, 2003·Nucleic Acids Research·Michael Zuker
Jul 10, 2003·Trends in Genetics : TIG·Annette W Coleman
Aug 13, 2003·Bioinformatics·Fredrik Ronquist, John P Huelsenbeck
Sep 19, 2003·Molecular Phylogenetics and Evolution·Leslie R GoertzenRobert K Jansen
Jun 28, 2005·Nucleic Acids Research·Nicholas R Markham, Michael Zuker
Oct 20, 2006·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Matthias HöchsmannRobert Giegerich

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Citations

Aug 6, 2010·Cold Spring Harbor Perspectives in Biology·David H MathewsDouglas H Turner
Feb 10, 2012·Molecular Biology and Evolution·Raquel Rodríguez-MartínezRamon Massana
Jun 26, 2010·Molecular Biology Reports·Loredana F CiarmielloPasqualina Woodrow

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