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dc.contributor.advisorPoulter, Russell
dc.contributor.authorSumpter, Nicholas Andrew
dc.date.available2018-07-11T20:51:37Z
dc.date.copyright2018
dc.identifier.citationSumpter, N. A. (2018). Hybrid Assembly of the Chytrid Genome - Insights into the Evolution and Outbreak of a Major Amphibian Pathogen (Thesis, Master of Science). University of Otago. Retrieved from http://hdl.handle.net/10523/8196en
dc.identifier.urihttp://hdl.handle.net/10523/8196
dc.description.abstractDevastating amphibian population declines have been observed globally for the last 40 years. These declines have become the interest of several conservationists and researchers, as amphibians form a valuable part of global biodiversity. Researchers identified the causative agent of many of these declines to be the chytrid fungus Batrachochytrium dendrobatidis (Bd). It is clear that Bd is partially responsible for several local extinctions and multiple species extinctions in a variety of anurans (i.e. frogs and toads). Recently, a related chytrid (Batrachochytrium salamandrivorans) has caused similar declines in urodeles (i.e. salamanders and newts). Many studies have been conducted into the evolution and outbreak of Bd, along with its mechanism of disease and methods of halting its progress or curing sick frogs. Two genome sequences were released for the chytrid in the mid 2000s, and nearly all subsequent genetic studies have utilised these assemblies for all their analyses. These assemblies indicated that the organism is probably a diploid that likely is imperfect (i.e. doesn’t undergo sexual reproduction). Many heterozygous positions were identified within these diploid genome assemblies, though a major limitation of these assemblies was that they failed to resolve the "phase" of the heterozygosities. Additionally, these genome assemblies are significantly fragmented, and contain gaps within their genomic scaffolds, particularly around repetitive regions of the genome. This makes many analyses potentially error prone and means that genetic information that may aid in the understanding of the pathogen’s genetic history is not available. In this project, a higher quality genome assembly of Batrachochytrium dendrobatidis strain RTP6 was produced using PacBio long read technology coupled with Illumina short read technology. Using this updated genome assembly it was possible to infer a significant amount of genetic information about the chytrid that was previously unknown, including the structure of its telomeres, the probable centromeric region, and clarification of its mitochondrial genome structure. The long reads also permitted the resolution of the haplotypes for heterozygous regions of the genome. In addition to these discoveries, insights into the phylogenetic structure of the organism were clarified, for both the globally distributed pandemic lineage (BdGPL) and for the other Bd lineages. This improved genome assembly, and the subsequent evolutionary insights, have significant implications for our understanding of Bd and other fungal pathogens.
dc.format.mimetypeapplication/pdf
dc.format.mimetypeapplication/vnd.openxmlformats-officedocument.spreadsheetml.sheet
dc.format.mimetypeapplication/vnd.openxmlformats-officedocument.spreadsheetml.sheet
dc.language.isoen
dc.publisherUniversity of Otago
dc.rightsAll items in OUR Archive are provided for private study and research purposes and are protected by copyright with all rights reserved unless otherwise indicated.
dc.subjectChytrid
dc.subjectGenome
dc.subjectPacBio
dc.subjectHybrid
dc.subjectAssembly
dc.subjectSMRT
dc.subjectBatrachochytrium dendrobatidis
dc.subjectBd
dc.titleHybrid Assembly of the Chytrid Genome - Insights into the Evolution and Outbreak of a Major Amphibian Pathogen
dc.typeThesis
dc.date.updated2018-07-11T05:04:58Z
dc.language.rfc3066en
thesis.degree.disciplineBiochemistry
thesis.degree.nameMaster of Science
thesis.degree.grantorUniversity of Otago
thesis.degree.levelMasters
otago.openaccessOpen
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