Genome assembly of endemic cave sponge (Eunapius subterraneus) using data obtained by nanopore sequencing technology

Šribar, Dora (2016) Genome assembly of endemic cave sponge (Eunapius subterraneus) using data obtained by nanopore sequencing technology. Diploma thesis, Faculty of Science > Department of Biology.

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Abstract

Porifera, a phylum within the Kingdom Animalia (Metazoa), consists of more than 8000 species of sponges. Owing to their simple morphology, sponges have an important role in understanding the early evolution and relationship between different phyla within the kingdom Animalia. Furthermore, sponges represent good models for biological processes in higher animals. Morphological features are becoming insufficient and we need more genomic data from different species within Porifera. However, the entire process of genome sequencing and assembly of Porifera still remains the challenge. Endemic cave sponge Eunapius subterraneus is an interesting model organism due to its unusual characteristics. Using various genomic libraries I conducted genome assembly and subsequent evaluation of the assembled genome of Eunapius subterraneus. I used various approaches based on both de Bruijn graphs and the Overlap-Layout-Consensus and conducted hybrid assembly using long reads obtained from the Oxford Nanopore Technologies MinION device. The hybrid assembly did not yield any improvement. Low assembly quality could be consequence of potential contamination, repetitive sequences and high heterozigosity rate. Further research of Porifera genomic is needed.

Item Type: Thesis (Diploma thesis)
Keywords: hybrid assembly, Next generation sequencing, Overlap-Layout-Consensus, de Bruijn graphs
Supervisor: Vlahoviček, Kristian
Date: 2016
Number of Pages: 31
Subjects: NATURAL SCIENCES > Biology
Divisions: Faculty of Science > Department of Biology
Depositing User: Silvana Šehić
Date Deposited: 24 Mar 2016 12:18
Last Modified: 24 Mar 2016 12:18
URI: http://digre.pmf.unizg.hr/id/eprint/4616

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