Računalna analiza horizontalnog prijenosa gena u spužvama Suberites domuncula i Eunapius subterraneus

master's thesis

• Title (english): Computational analysis of horizontal gene tranfer in sponge species Suberites domuncula and Eunapius subterraneus
• Author: Luka Buršić
• Mentor: Kristian Vlahoviček (mentor)
• Committee member: Kristian Vlahoviček (predsjednik povjerenstva)
• Committee member: Rosa Karlić (član povjerenstva)
• Committee member: Damjan Franjević (član povjerenstva)
• Committee member: Tomislav Ivanković (član povjerenstva)
• Granter: University of Zagreb; Faculty of Science; (Department of Biology); Zagreb
• Defense date and country: 2025-02-18, Croatia
• Scientific / art field, discipline and subdiscipline: NATURAL SCIENCES; Biology

Abstract

Horizontalni transfer gena (HGT) omogućuje prijenos novih svojstava između evolucijski udaljenih skupina
organizama. Iako je HGT opsežno istražen kod prokariota, kod rano razdvojenih skupina metazoa poput
spužvi i žarnjaka, istraživanja su oskudna. Ovaj rad bavi se otkrivanjem i analizom HGT u dvije vrste spužvi:
Suberites domuncula, kozmopolitskoj morskoj spužvi, i Eunapius subterraneus, hrvatskoj endemskoj
špiljskoj spužvi. Unatoč strogim kriterijima, kombiniranjem različitih računalnih analiza genoma spužvi,
otkriven je značajan broj horizontalno prenesenih gena (HTgs). Istraživane spužve razlikuju se prema razini
prilagodbe HTgs – duljini introna, upotrebi kodona i grupiranju po očuvanosti. Ove razlike ukazuju na
davnije dogadjaje horizontalnog prijenosa u pretku S. domuncula od onog u E. subterranus. Pronađeni HTgs
pokazali su funkcijsku povezanost s regulacijom gena koji sudjeluju u metabolizmu DNA, što potvrđuje
njihova očuvanost u srodnim spužvama. Nisu utvrđene funkcije u sekundarnom metabolizmu kao što je
pokazano u sličnom istraživanju što može biti uzrokovano različitom kvalitetom početnog materijala i
strožom analizom. Također, u radu se ističe potreba za boljim referentnim okvirima u istraživanju spužvi i
doprinos istraživanja spužvi u evoluciji metazoa.

Abstract (english)

Horizontal gene transfer (HGT) enables the transfer of new traits between evolutionarily distant groups of organisms. While HGT has been extensively studied in prokaryotes, research on early-diverging metazoan groups such as sponges and cnidarians remains scarce. This study focuses on the detection and analysis of HGT in two sponge species: Suberites domuncula, a cosmopolitan marine sponge, and Eunapius subterraneus, a Croatian endemic cave sponge. Despite strict criteria, a significant number of horizontally transferred genes (HTgs) were identified through the integration of various computational genome analyzes of the sponges. The studied sponges differ in terms of adaptation levels of HTgs – intron length, codon usage, and grouping by conservation. These differences indicate earlier events of horizontal transfer in the ancestor of S. domuncula compared to E. subterranus. The detected HTgs showed functional associations with the regulation of genes involved in DNA metabolism, supported by their conservation in related sponges. However, no functions related to secondary metabolism were identified, as reported in similar studies. This could be due to differences in the quality of initial material and stricter analyzes applied. The study also emphasizes the need for better reference frameworks in sponge research and highlights the contribution of sponge studies to the understanding of metazoan evolution.

• Keywords: spužve; endosimbionti; arhitektura gena; horizontalni transfer gena; funkcionalna analiza
• Keywords (english): sponges; endosymbionts; gene architecture; horizontal gene transfer; functional analysis
• Language: english
• URN:NBN: urn:nbn:hr:217:681185
• Project: Number: IP-2014-09-6400; Title: Istraživanje razvoja, diferencijacije i evolucije životinja kroz genomiku bazalnih metazoa; Title: Elucidating animal development, differentiation and evolution through basal metazoan genomics; Acronym: BAMGEN; Leader: Kristian Vlahoviček; Jurisdiction: Croatia; Funder: Hrvatska zaklada za znanost; Funding stream: Research Projects
• Study programme: Title: Molecular Biology-University graduate programme; Study programme type: university; Study level: graduate; Academic / professional title: sveučilišni/a magistar/magistra molekularne biologije (sveučilišni/a magistar/magistra molekularne biologije)
• Type of resource: Text
• File origin: Born digital
• Access conditions: Open access
• Created on: 2025-02-27 13:56:17