Vergleichende Phylogenie zwischen Arten bis hin zum "tree of Life" basierend auf einer ITS- (internal transcribed spacer) Sequenz-Strukturdatenbank und neuen Algorithmen
Final Report Abstract
During the last three years, the major objectives of the funded project have been achieved. We developed alignment algorithms, which are capable to integrate sequence as well as secondary structure information. Furthermore, software was developed that is able to infer phylogenetic trees and to detect compensatory base changes (CBCs) based on sequence-structure alignments. In a simulation study we were able to empirically prove the initial observation that sequence-structure information is beneficial for RNA phylogenetics. We challenged the problem that data of sequence-structure information has been very scarce by developing algorithms for annotation of ITS2 sequences from GenBank data and automated prediction of their secondary structures. The sequences and structures retained from these algorithms are now stored at the ITS2 database and are openly accessible via its web interface. Several biological case studies followed these developments to present the benefits of sequence-structure phylogenetics with the ITS2 marker to the phylogenetic community. To round off this project, we published a review explaining the workflow of state-of-the-art ITS2 secondary structure phylogenetics. In total, we published 27 peer-reviewed grant related articles within the funding period. Taken together, ITS2 based articles published by the applicants have been cited more than 200 times. This underlines, that our developed methodology is accepted and applied by systematic biologists as a new and valuable method for phylogenetic inferences. However, many improvements have still to be done regarding alignment procedures and models of evolution. GenBank annotations concerning ITS2 related sequence information (taxonomy and/or the accurate position of the ITS2 in the ribosomal cistron) turned out to be a more challenging problem than expected. Resolving these annotation problems required an additional amount of work not expected in the proposal. Beside the scientific feedback (more than 300 citations) there was also a great feedback coming from the print media in public news: GfBS news (2010): ITS2-Update - Die ITS2 Datenbank als Werkzeug scinexx (2010): Forscher identifizieren drei neue Überlebenskünstler Ärzte Zeitung (2010): Drei neue Bärtierchen für die biomedizinische Forschung Berliner Zeitung (2010): Wissenschaftler finden neue Bärtierchen idw-online (2010): Biologen der Uni Stuttgart identifizieren drei neue Bärtierchenarten- Vom Norden Alaskas bis zum Pazifik Frankfurter Rundschau (2010): Neue Bärtierchen entdeckt bild der Wissenschaft (2010): Neue Verwandte für die Bärtierchen BLICK (2009): Die Evolution als Rechenaufgabe scinexx (2007): RNA-Molekül hilft beim Erkennen von Arten idw-online (2007): Wie Bioinformatiker Arten unterscheiden GfBS news (2007): Molekularbiologen als Morphologen - Wie karm man Arten unterscheiden?
Publications
- 2007. Distinguishing species. RNA, Vol. 13.2007, Issue 9, pp. 1469-1472.
Tobias Müller, Nicole Philippi, Thomas Dandekar, Jörg Schultz, Matthias Wolf
(See online at https://dx.doi.org/10.1261/rna.617107) - 2007. Placozoa: at least two. Biologia, Band 62.2007, Heft 6, Seiten 641–645.
Matthias Wolf. Christian Selig, Tobias Müller, Nicole Philippi, Thomas Dandekar, Jörg Schultz
(See online at https://dx.doi.org/10.2478/s11756-007-0143-z) - 2008. ProfDistS: (Profile-) Distance based phylogeny on sequence - structure alignments. Bioinformatics, Vol. 24.2008, Issue 20, pp. 2401-2402.
Matthias Wolf. Benjamin Ruderisch, Thomas Dandekar, Jörg Schultz, Tobias Müller
(See online at https://dx.doi.org/10.1093/bioinformatics/btn453) - 2008. Synchronous visual analysis and editing of RNA sequence and secondary structure alignments using 4SALE. BMC Research Notes, Vol. 1.2008: 91.
Philipp N Seibel, Tobias Müller, Thomas Dandekar, Matthias Wolf
(See online at https://dx.doi.org/10.1186/1756-0500-1-91) - 2008. The ITS2 Database II: homology modelling RNA structure for molecular systematics. Nucleic Acids Research 36.2008 (Database issue): D377-D380.
Christian Selig, Matthias Wolf, Tobias Müller, Thomas Dandekar, Jörg Schultz
(See online at https://dx.doi.org/10.1093/nar/gkm827) - 2009. 1TS2 sequence-structure analysis in phylogenetics: a
how-to manual for molecular systematics.Molecular Phylogenetics and Evolution, Vol. 52. 2009, Issue 2, pp. 520–523.
Jörg Schultz, Matthias Wolf
(See online at https://dx.doi.org/10.1016/j.ympev.2009.01.008) - 2009. 5.8S-28S rRNA interaction and HMM-based ITS2 annotation. Gene, Vol. 430. 2009, Issues 1–2, pp. 50–57.
Alexander Keller, Tina Schleicher, Jörg Schultz. Tobias Müller. Thomas Dandekar, Matthias Wolf
(See online at https://dx.doi.org/10.1016/j.gene.2008.10.012) - 2009. ITS2 secondary Structure improves phylogeny estimation in a radiation of blue butterflies ofthe subgenus Agrodiaetus (Lepidoptera: Lycaenidae: Polyommatus). BMC Evolutionary Biology, Vol. 9.2009: Art. Nr. 300.
Martin Wiemers, Alexander Keller, Matthias Wolf
(See online at https://dx.doi.org/10.1186/1471-2148-9-300) - 2010. Compensatory base changes illuminate morphologically difficult taxonomy. Molecular Phylogenetics and Evolution, Vol. 54. 2010, Issue 2, pp. 664–669.
Michael W. Ruhl, Matthias Wolf. Trade M Jenkins
(See online at https://dx.doi.org/10.1016/j.ympev.2009.07.036) - 2010. Evolutionary distances in the twilight zone-a rational kemel approach. PLoS One, Vol. 5. 2010, Issue 12: el5788.
Roland F Schwarz, William Fletcher, Frank Förster, Benjamin Merget, Matthias Wolf, Jörg Schultz. Florian Markowetz
(See online at https://dx.doi.org/10.1371/journal.pone.0015788) - 2010. ITS2 sequence-structure phylogeny in the Scenedesmaceae with special reference to Coelastrum (Chlorophyta, Chlorophyceae), including the new genera Comasiella and Pectinodesmus.
Phycologia, Vol. 49. 2010, No. 4, pp. 325-335.
Eberhard Hegewald, Matthias Wolf, Alexander Keller, Thomas Friedl, Lothar Krienitz
(See online at https://dx.doi.org/10.2216/09-61.1) - 2010. Microevolution and Speciation in Thalassiosira weissflogii (Bacillariophyta). Protist, Vol. 161. 2010, Issue 2, pp. 237–249.
Ulf Sorhannus, Joseph D Ortiz, Matthias Wolf. Martin G. Fox
(See online at https://dx.doi.org/10.1016/j.protis.2009.10.003) - 2010. The ITS2 Database 111 - sequences and stmctures for phylogeny. Nucleic Acids Research, Vol. 38.2010, Issue suppl 1, pp. D275-D279.
Christian Koetschan, Frank Förster, Alexander Keller, Tina Schleicher, Benjamin Ruderisch, Roland Schwarz, Tobias Müller, Matthias Wolf, Jörg Schultz
(See online at https://dx.doi.org/10.1093/nar/gkp966) - 2011. Internal Transcribed Spacer 2 (nu ITS2 rRNA) Sequence Structure Phylogenetics: Towards an Automated Reconstmction of the Green Algal Tree of Life. PLoS One, Vol. 6.2011, Issue 2: el6931.
Mark A Buchheim, Alexander Keller, Christian Koetschan, Frank Förster, Benjamin Merget, Matthias Wolf
(See online at https://dx.doi.org/10.1371/journal.pone.0016931) - 2012. "Y" Scenedesmus (Chlorophyta, Chlorophyceae): the intemal transcribed spacer 2 (ITS2) rRNA secondary structure re-revisited. Plant Biology, Vol. 14. 2012, Issue 6, pp. 987–996.
Sebastian M. Markert, Tobias Müller, Christian Koetschan, Thomas Friedl, Matthias Wolf
(See online at https://doi.org/10.1111/j.1438-8677.2012.00576.x) - 2012. ITS2 Database IV: Interactive Taxon Sampling for Intemal Transcribed Spacer 2 based Phylogenies. Molecular Phylogenetics and Evolution, Vol. 63. 2012, Issue 3, pp. 585–588.
Christian Koetschan, Thomas Hackl, Tobias Müller. Matthias Wolf. Frank Förster, Jörg Schultz
(See online at https://doi.org/10.1016/j.ympev.2012.01.026) - 2012. Phylogeny of Oedogoniales, Chaetophorales and Chaetopeltidales (Chlorophyceae): inferences from sequence-structure analysis of ITS2. Annals of Botany, Vol. 109.2012, Issue 1, pp. 109-116.
Mark A. Buchheim, Danica M Sutherland, Tina Schleicher, Frank Förster, Matthias Wolf
(See online at https://doi.org/10.1093/aob/mcr275) - 2012. The ITS2 Database. Journal of Visualized Experiments, Vol. 61. 2912: e3806.
Benjamin Merget, Christian Koetschan, Thomas Hackl, Frank Förster, Thomas Dandekar, Tobias Müller. Jörg Schultz. Matthias Wolf
(See online at https://doi.org/10.3791/3806)
