Identification and characterization of transposable elements in sponges (Porifera)

doctoral thesis

• Title (english): Identifikacija i karakterizacija pokretnih genetičkih elemenata u spužvama (Porifera)
• Author: Maja Kuzman
• Mentor: Kristian Vlahoviček (mentor)
• Committee member: Helena Ćetković (predsjednik povjerenstva)
• Committee member: Rosa Karlić (član povjerenstva)
• Granter: University of Zagreb; Faculty of Science; (Department of Biology); Zagreb
• Defense date and country: 2020-09-29, Croatia
• Scientific / art field, discipline and subdiscipline: NATURAL SCIENCES; Biology
• Universal decimal classification (UDC): 57 - Biological sciences. Physical anthropology. Biodiversity

Abstract

Transposable elements constitute a large portion of most eukaryotic genomes and play an important role in transcriptional regulation, shaping gene regulatory networks and genome evolution. Due to a lack of quality genome assemblies of non-model organisms, not much is known about the diversity, distribution and the role of transposable elements across Metazoa. In this thesis I present high quality genome assemblies for the sponge species Eunapius subterraneus and Suberites domuncula. I use computational genomics techniques to identify, characterize and compare transposable elements in the publicly available sponge genomes and in-house assembled genomes by analysing the abundance and conservation of the transposable elements in different sponge species. I assess the impact of transposable elements on the evolution of the host genomes by analysing their contribution to genome organization and correlation with gene expression. Finally, I present a catalog of the homologs of piRNA pathway in sponges and analyse their transcriptional activity.

Abstract (english)

Prijenosni genetički elementi (transpozoni) sačinjavaju velik dio većine eukariotskih genoma i igraju važnu ulogu u regulaciji transkripcije, oblikovanju regulatornih mreža gena i evoluciji genoma. Zbog nedostatka kvalitetno sklopljenih genoma ne-modelnih organizama, ne zna se mnogo o raznolikosti, rasprostranjenosti i ulozi transpozona u skupini Metazoa. U ovom radu predstavljam visokokvalitetne sklopove genoma za vrste spužva Eunapius subterraneus i Suberites domuncula. Korištenjem tehnika računalne genomike identificiram, karakteriziram i uspoređujem pokretne elemente u javno dostupnim genomima spužvi i interno skupljenim genomima analizom brojnosti i očuvanja transpozona u različitim vrstama spužvi. Procjenjujem utjecaj transpozona na evoluciju genoma domaćina analizom njihovog doprinosa u organizaciji genoma i povezanosti s ekspresijom gena. Na kraju predstavljam katalog homologa piRNA puta u spužvama i analiziram njihovu transkripcijsku aktivnost.

• Keywords: Transposons; genome assembly; porifera; computational genomics
• Keywords (english): transpozoni; sklapanje genoma; spužve; računalna genomika
• Language: croatian
• URN:NBN: urn:nbn:hr:217:082440
• Promotion: 2020
• Study programme: Title: Biology; Study programme type: university; Study level: postgraduate; Academic / professional title: doktor/doktorica znanosti, područje prirodnih znanosti, polje biologija (doktor/doktorica znanosti, područje prirodnih znanosti, polje biologija)
• Type of resource: Text
• File origin: Born digital
• Access conditions: Open access
• Created on: 2020-10-27 10:06:33