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W2087820469 abstract "A recent article [ 1 Coleman A.W. Nuclear rRNA transcript processing versus internal transcribed spacer secondary structure. Trends Genet. 2015; 31 (Published online January 30, 2015. http://dx.doi.org/10.1016/j.tig.2015.01.002): 157-163 Abstract Full Text Full Text PDF PubMed Scopus (48) Google Scholar ] in this journal discusses the connections between the fields of internal transcribed spacer (ITS) secondary structure, ribogenesis, and phylogenetics, unfortunately omitting important recent advances in computational biology. rRNA ITS sequences are extensively used to assess phylogenetic relationships. However, many hurdles had to be overcome before this approach yielded accurate results. Because ITS2 has a common core of secondary structure throughout the Eukaryota [ 2 Schultz J. et al. A common core of secondary structure of the internal transcribed spacer 2 (ITS2) throughout the Eukaryota. RNA. 2005; 11: 361-364 Crossref PubMed Scopus (306) Google Scholar ], in several studies ITS2 secondary structures of ribosomal genes have been used to improve the quality of phylogenetic reconstructions. An extensive evaluation of the benefits of integrating secondary structure with phylogenetic analyses, however, was lacking. Today we know that including RNA secondary structures improves accuracy and robustness in the reconstruction of phylogenetic trees [ 3 Keller A. et al. Including RNA secondary structures improves accuracy and robustness in reconstruction of phylogenetic trees. Biol. Direct. 2010; 5: 4 Crossref PubMed Scopus (136) Google Scholar ]. Alignments of ITS2 sequences are no longer just guided by the use of a secondary structure. Today, sequences and their individual secondary structures are simultaneously aligned by automatic alignment programs such as 4SALE [ 4 Seibel P.N. et al. 4SALE – a tool for synchronous RNA sequence and secondary structure alignment and editing. BMC Bioinform. 2006; 7: 11 Crossref PubMed Scopus (17) Google Scholar , 5 Seibel P.N. et al. Synchronous visual analysis and editing of RNA sequence and secondary structure alignments using 4SALE. BMC Res. Notes. 2008; 1: 91 Crossref PubMed Scopus (251) Google Scholar ] (reviewed in [ 6 Wolf M. et al. ITS2, 18S, 16S or any other RNA – simply aligning sequences and their individual secondary structures simultaneously by an automatic approach. Gene. 2014; 546: 145-149 Crossref PubMed Scopus (62) Google Scholar ]). 4SALE uses a specified scoring matrix fitted to a 12-letter alphabet encoding the sequence–structure information and specifically trained on ITS2 sequence–structure data obtained from hundreds of thousands of sequence–structure pairs available on the ITS2 database I–IV [ 7 Schultz J. et al. The internal transcribed spacer 2 database – a web server for (not only) low level phylogenetic analyses. Nucleic Acids Res. 2006; 34: W704-W707 Crossref PubMed Scopus (156) Google Scholar , 8 Selig C. et al. The ITS2 database II: homology modelling RNA structure for molecular systematics. Nucleic Acids Res. 2008; 36: D377-D380 Crossref PubMed Scopus (144) Google Scholar , 9 Koetschan C. et al. The ITS2 database III – sequences and structures for phylogeny. Nucleic Acids Res. 2010; 38: D275-D279 Crossref PubMed Scopus (231) Google Scholar , 10 Koetschan C. et al. ITS2 database IV: interactive taxon sampling for internal transcribed spacer 2 based phylogenies. Mol. Phylogenet. Evol. 2012; 63: 585-588 Crossref PubMed Scopus (127) Google Scholar , 11 Merget B. et al. The ITS2 database. J. Vis. Exp. 2012; 61: 3806 PubMed Google Scholar ]. A 15-min movie explaining the database and linked web services is available at http://www.jove.com/video/3806/the-its2-database. Based on the 12-letter code, phylogenetic relationships are reconstructed using an ITS2 sequence–structure-specific substitution model [ 6 Wolf M. et al. ITS2, 18S, 16S or any other RNA – simply aligning sequences and their individual secondary structures simultaneously by an automatic approach. Gene. 2014; 546: 145-149 Crossref PubMed Scopus (62) Google Scholar , 12 Wolf M. et al. ProfDistS: (profile-) distance based phylogeny on sequence–structure alignments. Bioinformatics. 2008; 24: 2403-2404 Crossref PubMed Scopus (112) Google Scholar , 13 Schultz J. et al. ITS2 sequence–structure analysis in phylogenetics: a how-to manual for molecular systematics. Mol. Phylogenet. Evol. 2009; 52: 520-523 Crossref PubMed Scopus (161) Google Scholar , 14 Salvi D. et al. Molecular phylogenetics and systematics of the bivalve family Ostreidae based on rRNA sequence–structure models and multilocus species tree. PLoS ONE. 2014; 9: e108696 Crossref PubMed Scopus (66) Google Scholar ]. Beforehand, the 5.8S–28S rDNA interaction, modeled by hidden Markov models (HMMs), is used to automatically annotate ITS2 sequences [ 15 Keller A. et al. 5.8S–28S rRNA interaction and HMM-based ITS2 annotation. Gene. 2009; 430: 50-57 Crossref PubMed Scopus (408) Google Scholar ]. Secondary structures are predicted by homology modeling or energy minimization [ 16 Wolf M. et al. Homology modeling revealed more than 20,000 rRNA internal transcribed spacer 2 (ITS2) secondary structures. RNA. 2005; 11: 1616-1623 Crossref PubMed Scopus (168) Google Scholar ]. Pitfalls and benefits of the homology modeling approach are discussed in Markert et al. [ 17 Markert S.M. et al. ‘Y’ Scenedesmus (Chlorophyta, Chlorophyceae): the internal transcribed spacer 2 rRNA secondary structure re-revisited. Plant Biol. 2012; 14: 987-996 Crossref PubMed Scopus (25) Google Scholar ]. However, working with template structures and homology modeling makes large-scale approaches handling big data possible [ 18 Buchheim M.A. et al. Internal transcribed spacer 2 (nu ITS2 rRNA) sequence–structure phylogenetics: towards an automated reconstruction of the green algal tree of life. PLoS ONE. 2011; 6: e16931 Crossref PubMed Scopus (76) Google Scholar ]. Moreover, all of the approaches discussed here could easily be transferred to other RNAs (e.g., ITS1), even when there is no common core structure available for eukaryotes [ 19 Koetschan C. et al. Internal transcribed spacer 1 secondary structure analysis reveals a common core throughout the anaerobic fungi (Neocallimastigomycota). PLoS ONE. 2014; 9: e91928 Crossref PubMed Scopus (65) Google Scholar ]. With more robust and more accurate results concerning ITS (or any other RNA) sequence–structure alignments and reconstructed phylogenies, our understanding of sequence evolution, sequence motifs (which can be searched for using the ITS2 database), ribogenesis, metagenomes, barcodes, and phylochips will steadily increase. Next-generation sequencing (NGS) is opening the door to analysis of the intragenomic variability of the many ITS copies. These findings are shaping our understanding of concerted evolution, molecular fossils, and the specific types of sequence–structure mutations [ 20 Müller T. et al. Distinguishing species. RNA. 2007; 13: 1469-1472 Crossref PubMed Scopus (287) Google Scholar , 21 Song J. et al. Extensive pyrosequencing reveals frequent intra-genomic variations of internal transcribed spacer regions of nuclear ribosomal DNA. PLoS ONE. 2012; 7: e43971 Crossref PubMed Scopus (129) Google Scholar , 22 Wolf M. et al. Compensatory base changes in ITS2 secondary structures correlate with the biological species concept despite intragenomic variability in ITS2 sequences – a proof of concept. PLoS ONE. 2013; 8: e66726 Crossref PubMed Scopus (112) Google Scholar ]. Last but not least, the first ITS2 tertiary structures have recently been published and the third dimension in sequence–structure phylogenetics is already in sight [ 23 Keller A. et al. Ribosomal RNA phylogenetics: the third dimension. Biologia. 2010; 65: 388-391 Crossref Scopus (7) Google Scholar ]. By combining morphological (structure) and molecular (sequence) data, computational biology has lifted RNA sequence–structure analysis to the next level, and this is just the beginning." @default.
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