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