Filostratigrafska analiza bakterije Bacillus subtilis

master's thesis

• Title (english): Phylostratigraphic analyses of bacterium Bacillus subtilis
• Author: Maša Lenuzzi
• Mentor: Tomislav Domazet-Lošo (mentor)
• Mentor: Dunja Leljak-Levanić (mentor)
• Committee member: Dunja Leljak-Levanić (predsjednik povjerenstva)
• Committee member: Tomislav Domazet-Lošo (član povjerenstva)
• Committee member: Damjan Franjević (član povjerenstva)
• Committee member: Mladen Kučinić (član povjerenstva)
• Granter: University of Zagreb; Faculty of Science; (Department of Biology); Zagreb
• Defense date and country: 2014-02-28, Croatia
• Scientific / art field, discipline and subdiscipline: NATURAL SCIENCES; Biology

Abstract

Filogenija bakterija predmet je neslaganja unutar znanstvene zajednice sve od njihovog otkrića u 17. stoljeću i još do danas se ne nazire općeprihvaćeno riješenje. Brojni problemi, od kojih su najznačajniji horizontalni transfer i brza stopa mutacija bakterijskog genoma, otežavaju izradu robusnog filogenetskog stabla bakterija. Genomska filostratigrafija jedna je od metoda proučavanja evolucije vrste. Filostratigrafske analize dosad su rađene samo na eukariotima. U ovom radu izrađena je prva filostratigrafska mapa bakterije na soju Bacilus subtilis subsp. subtilis str. 168. Rezultati su pokazali jasnu preraspodjelu gena po filostratumima što ukazuje na značajni vertikalni prijenos gena tijekom evolucije bakterija. Postojanost filostratigrafske mape provjerena je analizom reduciranih proteinskih baza dobivenih klasteriranjem proteinskih sljedova izvorne baze eukariota, arheja i bakterija. Primjena filostrastigrafske analize na reduciranim bazama rezultirala je gotovo identičnom filostratigrafskom mapom što potvrđuje robusnost metode za analizu bakterijskih genoma.

Abstract (english)

Bacterial phylogeny has been highly controversial subject from the first description of bacteria in 17th. century, and it seems that generally accepted solution is not yet within reach. There are many issues related to bacterial phylogeny, of which most important are horizontal gene transfer and fast mutation rate in bacterial genomes. For these reasons it is hard to construct a robust phylogenetic tree of bacteria. Genomic phylostratigraphy is a method for tracking evolutionary context of species. Until now, phylostratigraphic maps have been made solely in eukaryotes. In this thesis first phylostratigraphic map of a bacterium, namely Bacilus subtilis subsp. subtilis str. 168 strain, was obtained. Results showed clear distribution of genes through phylostrata, pointing to significance of vertical gene transfer in bacterial evolution. The robustness of the map was additionally tested on reduced protein databases obtained by clustering of original protein database of Eukarya, Archaea and Bacteria. Results obtained by using phylostratigraphic analyses on reduced protein databases resulted in nearly identical phylostratigraphic maps.

• Keywords: filostratigrafija; filogenija; CD-HIT; biološke baze podataka
• Keywords (english): phylostratigraphy; phylogeny; CD-HIT; bioinformatic databases
• Language: croatian
• URN:NBN: urn:nbn:hr:217:209926
• Study programme: Title: Molecular Biology; Study programme type: university; Study level: graduate; Academic / professional title: magistar/magistra molekularne biologije (magistar/magistra molekularne biologije)
• Type of resource: Text
• File origin: Born digital
• Access conditions: Access restricted to students and staff of home institution
• Created on: 2017-04-26 10:23:00