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UBC Theses and Dissertations

Streamlined high throughput assembly and standardization of reference-grade animal mitochondrial genomes Yang, Lingyu (Cecilia)


Mitochondrial genomes (or mitogenomes) are circular double-stranded DNA (Deoxyribonucleic Acid) present in the mitochondria of a eukaryotic cell, typically containing 16,000 nucleotides. Mitochondrial DNA has several characteristics, including maternal inheritance, low mutation rate, higher copy number and higher resistance to degradation, making it a valuable tool for ecological system monitoring, evolutionary studies as well as forensics identifications. In the past, the importance of the mitochondrial genome was not fully appreciated, and mitochondrial DNA was considered less valuable than nuclear DNA due to its smaller size and limited number of coding regions. As a result, mitogenome records on public data portals are limited compared to nuclear references, particularly for underrepresented species. Nowadays, increased attention is directed toward reconstructing mitogenomes, considering their diverse applications. Scalable and robust mitogenome assembly tools are in high demand due to the large volume of DNA sequencing data produced. In this thesis, I have developed mtGrasp: Mitochondrial Genome Assembly and Standardization Pipeline. mtGrasp is a high throughput in silico tool that generates reference-grade mitogenomes in their final standardized format. Three hundred and twenty eight DNA read libraries from the iTrackDNA project and 23 Sequence Read Archive (SRA) libraries were used. Reads were assembled into contigs by ABySS, followed by mitochondrial sequence filtering, gap-filling, polishing, circularization and standardization, resulting in 274 reference-grade genomes (from iTrackDNA samples) and 15 complete sequences (from SRA samples) while requiring only a moderate timeframe and memory usage.

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