Računalna optimizacija sljedova genomske DNA spužve Eunapius subterraneus sekvenciranih tehnologijom nanopora

master's thesis

• Title (english): Computer optimization of genomic DNA nanopore sequences from the sponge Eunapius subterraneus
• Author: Zoe Jelić Matošević
• Mentor: Kristian Vlahoviček (mentor)
• Mentor: Helena Ćetković (mentor)
• Committee member: Kristian Vlahoviček (predsjednik povjerenstva)
• Committee member: Damjan Franjević (član povjerenstva)
• Committee member: Tomislav Ivanković (član povjerenstva)
• Committee member: Rosa Karlić (član povjerenstva)
• Granter: University of Zagreb; Faculty of Science; (Department of Biology); Zagreb
• Defense date and country: 2018-09-26, Croatia
• Scientific / art field, discipline and subdiscipline: NATURAL SCIENCES; Biology

Abstract

Ogulinska špiljska spužvica, Eunapius subterraneus Sket & Velikonja, 1984 (Porifera, Demospongia), jedina je stigobiontna slatkovodna spužva na svijetu. Spužve (Porifera) su najstarije živuće koljeno životinja. Karakterizira ih jednostavna tjelesna građa te nedostatak pravih tkiva i organa. Zbog filogenetski bazalnog položaja u odnosu na ostale životinje, spužve su idealni modelni organizmi za proučavanje evolucije gena i genoma te razvoja višestaničnosti unutar životinja (Metazoa). Kako bi to bilo moguće potrebno je sekvencirati i sklopiti genome spužvi koje želimo proučavati. Metodom sekvenciranja tehnologijom nanopora u kombinaciji s metodom reverzibilnog zaustavljanja sinteze (Illumina) mogu se sklopiti čak i repetitivni genomi viših eukariota, ali često je potrebno ispraviti sljedove iz nanopora prije samog sklapanja genoma. Dodatan problem u radu sa spužvama predstavlja kontaminacija sekvenciranih knjižnica. U ovom radu izolirala sam visokomolekularnu genomsku DNA Eunapius subterraneus iz primorfa te sam pokazala kako ovaj pristup doprinosi smanjenju kontaminacije u uzorcima. Sljedove iz nanopora ispravila sam koristeći program NaS te sam dokazala njihovu točnost pretragom baze neredundantnih proteinskih sljedova programom DIAMOND. Za iskorištavanje punog potencijala tehnologije sekvenciranja nanoporama u budućnosti potrebno je razvijati algoritme prilagođene specifičnom profilu greške ove tehnologije.

Abstract (english)

The Ogulin cave sponge, Eunapius subterraneus Sket & Velikonja, 1984 (Porifera, Demospongia), is the only freshwater stygobiont sponge in the world. Sponges (Porifera) are the oldest living animal phylum. Their bodies have a simple structure and lack true tissues and organs. Because of their basal position among the Metazoa they are useful for researching gene and genome evolution as well as the evolution of multicellularity in the phylum Metazoa. To do that we need to sequence and assemble their genomes. The nanopore sequencing technology in combination with Illumina’s reversible-terminator-based sequencing by synthesis can help to produce good assemblies even of repetitive higher-eukaryote genomes. However, a correction step for the nanopore reads is often necessary before assembly. When working with sponges sample and library contamination present an additional problem. I have isolated highmolecular- weight genomic DNA from sponge primmorphs of Eunapius subterraneus and shown that DNA isolation from primmorphs can drastically reduce sample contamination. I have corrected nanopore reads using the programme NaS and proven the accuracy of the corrected reads by comparing them to the non-redundant protein database using DIAMOND. In the future for nanopore sequencing to live up to its potential, algorithms that can deal with the specific error profile of nanopore reads will have to be developed.

• Keywords: Eunapius subterraneus; tehnologija sekvenciranja nanoporama; sklapanje genoma
• Keywords (english): Eunapius subterraneus; nanopore sequencing; genome assembly
• Language: croatian
• URN:NBN: urn:nbn:hr:217:518418
• 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: 2018-11-09 11:11:29