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Vergleichende Phylogenie zwischen Arten bis hin zum "tree of Life" basierend auf einer ITS- (internal transcribed spacer) Sequenz-Strukturdatenbank und neuen Algorithmen

Applicant Dr. Tobias Müller
Subject Area Bioinformatics and Theoretical Biology
Term from 2007 to 2011
Project identifier Deutsche Forschungsgemeinschaft (DFG) - Project number 37802341
 
Final Report Year 2012

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?

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