Karakterizacija satelitnih DNA kukca brašnara Tribolium freemani Hinton

master's thesis

• Title (english): Characterization of satellite DNAs of the flour beetle Tribolium freemani Hinton
• Author: Damira Veseljak
• Mentor: Brankica Mravinac (mentor)
• Mentor: Višnja Besendorfer (sumentor)
• Committee member: Višnja Besendorfer (predsjednik povjerenstva)
• Committee member: Željka Vidaković-Cifrek (član povjerenstva)
• Committee member: Dijana Škorić (član povjerenstva)
• Committee member: Martina Šeruga Musić (član povjerenstva)
• Granter: University of Zagreb; Faculty of Science; (Department of Biology); Zagreb
• Defense date and country: 2019-12-11, Croatia
• Scientific / art field, discipline and subdiscipline: NATURAL SCIENCES; Biology

Abstract

Satelitne DNA su uzastopno ponavljajuće sekvence DNA dominantno smještene u heterokromatinskim regijama eukariotskih genoma. Iako često zaprimaju značajan udio u genomima, funkcija im još uvijek nije u potpunosti razjašnjena. Kukac brašnar Tribolium freemani, učestali štetnik u skladištima hrane, zanimljiv je za laboratorijska istraživanja zbog bliske srodnosti s modelnim organizmom Tribolium castaneum. Prije četvrt stoljeća u genomu vrste T. freemani opisana je satelitna DNA koja čini gotovo trećinu genomske sekvence. U ovom radu genom vrste T. freemani sekvenciran je tehnologijom sekvenciranja nove generacije (NGS) sa svrhom pronalaženja dosad neotkrivenih satelitnih DNA. Upotrebom bioinformatičkog alata TAREAN koji identificira potencijalne satelitne sekvence na temelju neposloženih NGS očitanja otkriveno je šest novih, niskozastupljenih satelitnih DNA čiji kumulativni udio u genomu iznosi <0,2%. Uzastopno ponovljena organizacija ovih sekvenci uspješno je dokazana metodom hibridizacije Southern blot, dok je pomoću metode fluorescencijske hibridizacije in situ određen njihov kromosomski smještaj. Bioinformatičkom analizom utvrđeno je da u genomu sestrinske vrste T. castaneum postoje sekvence homologne novootkrivenim satelitnim DNA vrste T. freemani, a njihova usporedba pokazala je da satelitni monomeri unutar dviju vrsta evoluiraju slijedeći principe usklađene evolucije.

Abstract (english)

Satellite DNAs are tandemly repeated sequences located mainly in the heterochromatic regions of the eukaryotic genomes. Even though they often take large parts of the genome, their function is still not entirely understood. The flour beetle Tribolium freemani, a common pest in food storage units, is experimentally interesting because its sibling species is Tribolium castaneum, a well-established model organism. Quarter of a century ago, the main satellite DNA that comprises one third of the T. freemani genome has been characterised. In this thesis the T. freemani genome was sequenced by Next Generation Sequencing (NGS) technology in order to detect the satellite sequences that were unidentified until now. Six new low-copy satellite DNAs with a combined percentage of <0.2% were discovered. This was done by using the bioinformatic pipeline TAREAN, which enables detection of putative satellite DNAs from unassembled short reads. The tandemly repeated organisation of these sequences has been successfully proven by using the Southern blot method, while their chromosomal location was determined by fluorescence in situ hybridization. Bioinformatical analysis showed that the newly detected T. freemani satellite DNAs have homologous sequences in their sibling species T. castaneum. The comparison showed that satellite monomers of the two species evolve by the principles of concerted evolution.

• Keywords: Tribolium freemani; satelitna DNA; sekvenciranje nove generacije
• Keywords (english): Tribolium freemani; satellite DNA; Next Generation Sequencing
• Language: croatian
• URN:NBN: urn:nbn:hr:217:864868
• 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: Open access; Embargo expiration date: 2021-12-11
• Created on: 2020-06-09 11:04:13