Sekvenciranje tehnologijom nanopora i sklapanje genoma ogulinske špiljske spužvice Eunapius subterraneus

master's thesis

• Title (english): Sequencing by Nanopore technology and genome assembly of endemic cave sponge Eunapius subterraneus
• Author: Dunja Glavaš
• Mentor: Kristian Vlahoviček (mentor)
• Mentor: Helena Ćetković (mentor)
• Committee member: Kristian Vlahoviček (predsjednik povjerenstva)
• Committee member: Damjan Franjević (član povjerenstva)
• Committee member: Zlatko Liber (član povjerenstva)
• Committee member: Rosa Karlić (član povjerenstva)
• Granter: University of Zagreb; Faculty of Science; (Department of Biology); Zagreb
• Defense date and country: 2018-09-24, Croatia
• Scientific / art field, discipline and subdiscipline: NATURAL SCIENCES; Biology

Abstract

Spužve su zbog ranog odvajanja od ostalih skupina dobar model za proučavanje rane evolucije i razvoja životinja, ali do sada je sekvenciran genom samo jedne vrste. Osim iz evolucijskog i razvojnog gledišta, spužve su zanimljive i kao modelni organizmi za proučavanje prilagodbe okolišu. Poseban interes predstavlja vrsta Eunapius subterraneus, endem krškog područja Hrvatske i jedina poznata slatkovodna stigobiontna spužva na svijetu. Sekvenciranje i sklapanje genoma nije jednostavno zbog prisutnosti brojnih mikroorganizama u i na tijelu spužvi. Sekvenciranjem tehnologijom nanopora dobivaju se dugački očitani sljedovi s većom razinom pogreške nego kod tehnologija sekvenciranja druge generacije. U hibridnom sklapanju genoma dugački sljedovi treće generacije se koriste za spajanje i zatvaranje prekida između neprekinutih sljedova dobivenih sklapanjem kratkih i točnih sljedova druge generacije. Sekvencirala sam genom spužve E. subterraneus pomoću uređaja Oxford Nanopore Technologies MinION. Provela sam hibridno sklapanje genoma pomoću sljedova dobivenih sekvenciranjem tehnologijama Illumina i Oxford Nanopore Technologies koristeći programe temeljene na pohlepnom algoritmu i metodi de Bruijnovog grafa. Procijenila sam kvalitetu sklopljenih genoma. Veći broj dugačkih očitanih sljedova korišten u sklapanju rezultira duljim neprekinutim sljedovima. U sklopljenom genomu su prisutne brojne kontaminacije i potrebno je daljnje sekvenciranje kako bi se genom spužve E. subterraneus sklopio u cijelosti.

Abstract (english)

Sponges are good model organisms for early Metazoan evolution and development because of their early separation from other groups of animals. However, genomic research on sponges is slow because of the scarce availability of genomic information - only one sponge species has had its genome completely sequenced so far. Sponges are also good models for environmental adaptation studies, in which species Eunapius subterraneus is of special interest. E. subterraneus is the only known freshwater stygobiont sponge in the world and it is endemic to karst region of Croatia. Sequencing and assembly of Poriferan genomes is not a trivial task due to the presence of numerous endo- and exosymbiontic microorganisms. Sequencing by Nanopore technology yields long reads with higher error rates in comparison to sequencing technologies of second generation. Hybrid approach to genome assembly uses long third-generation reads for closing gaps and joining contigs assembled from accurate but relatively short second-generation reads. I sequenced the genome of E. subterraneus using Oxford Nanopore Technologies MinION sequencer. I assembled reads sequenced on Illumina and Oxford Nanopore Technologies platforms using hybrid approach and then assesed the quality of assembled genomes. Programs I used for the assembly are based on greedy algorithm and de Bruijn graph method. Using more long third-generation reads resulted in longer contigs. Although I obtained long contigs, my assembly contains many contaminations. Further sequencing is needed in order to complete the genome of E. subterraneus.

• Keywords: tehnologije sekvenciranja treće generacije; hibridno sklapanje genoma; de Bruijnov graf; pohlepni algoritam
• Keywords (english): third generation sequencing; hybrid genome assembly; de Bruijn graph; greedy algorithm
• Language: croatian
• URN:NBN: urn:nbn:hr:217:530982
• 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
• Created on: 2018-10-29 12:47:05