Global ETD Search
Search theses and dissertations gathered from participating repositories worldwide. Every result links back to the library that holds it. No account is needed.
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Showing 1 to 19 of 19 for “"pangenome"”.
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Towards a Pangenome Perspective on the Lake Malawi Cichlid Radiation
The cichlid fishes in the East African Rift lakes are one of nature’s most spectacular vertebrate radiations and form an excellent system to study the evolutionary process of speciation. Lake Victoria, Malawi and Tanganyika are each home to hundreds of species with a wide spectrum of sizes, …
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Construction and analysis of the pangenome of Cucurbita moschata to uncover variants associated with virus resistance
… with MWMV resistance in butternut using a pangenome-assisted bulk segregant analysis (BSAseq) approach. To achieve this, a pangenome of C. moschata was first constructed using an iterative mapping and assembly strategy with resequencing data from 18 genetically diverse breeding lines from …
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Genome evolutionary studies of the Salmonella enterica serovars: implications for the dynamics of horizontal gene transfer, the pangenome concept, and bacterial and archaeal taxonomy
… We refer to this phenomenon as the supraspecies pangenome. We also demonstrate that supraspecies pangenomes are widespread across the microbial world; they are found amongst other bacterial lineages and even archaeal lineages. Further, since these genes pools are shared beyond the species level …
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A tale of two clades: genome evolution of oomycetes and fungi.
… other criteria. The fourth study looks at the pangenomes of four model fungal species, and compares the evolution of genomic variation, virulence and environmental adaptation within each species. The final study presents a refined iteration of the methodology used in the previous pangenome …
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Defining genomic drivers of evolution in the entomopathogenic Serratia spp. A thesis submitted in partial fulfilment of the requirements for the Degree of Doctor of Philosophy at Lincoln University
… entomophila may favour a chronic disease state. Pangenome wide analysis of S. entomophila isolates found differences in those from areas devoid of grass grub, suggesting the native pADAP carrying isolates have undergone speciation, coevolving with C. giveni larvae. Comparative genomics showed …
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Investigating virus-host interactions in a changing Arctic Ocean
… AO microbial communities. Next, we present the pangenome of M. polaris, which reveals cryptic diversity within the species and provides genomic evidence in support of a mixotrophic lifestyle. We then compare MpoV genomes and show high diversity among MpoVs, including a cryptic strain and a novel …
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Streptococcus equi subsp. zooepidemicus in New Zealand horses
… invasion. Bioinformatic analysis showed that the pangenome of S. zooepidemicus is open, which demonstrates the ability of species to accessorise its genome enabling the species to diversify and exploit different hosts and environment. An average of 45 new genes are discovered with the addition of …
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Integrative Genomic Approaches for Plant Trait Discovery, Fungal Pathogen Identification and Taxonomy
… genomes. Comparative phylogenomics and pangenome analyses indicated that U.S. isolates form a distinct cluster relative to Ceratobasidium theobromae and revealed gene-content differences, including candidate effectors and secondary metabolite gene clusters, which may contribute to host …
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Molecular mechanisms of salt and osmotic stress tolerance in Frankia strains isolated from Casuarina trees
… species (Frankia casuarinae at p=0.05 level). Pangenome analysis revealed a high abundance of singletons among all Casuarina isolates. The two salt-tolerant strains contained 153 shared unique genes (the majority of which code for hypothetical proteins) that were not found in the salt-sensitive …
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Identifying Pantoea Genetic Factors Involved in Host Association by Integrating Comparative Genomics with a Dictyostelium discoideum Grazing Resistance Model
… lies within both the conserved core and open pangenome.
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Ornithobacterium hominis isolates from a South African birth cohort
… standard bioinformatic tools and a core genome pangenome analysis was performed. Results: Ornithobacterium hominis was present in 32% of samples and abundance increased after six months of age in the cohort. Ornithobacterium hominis was isolated and characterised. The species exhibited four main …
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Pathogen evolution within and between hosts with applications to the pneumococcus and SARS-CoV-2
… methods. Next, the problem of identifying the pangenome (the set of all genes that have been found in a species) is considered and a method is presented that is able to reduce by over 10 fold the number of errors introduced by misannotation. Methods for the inference of transmission chains …
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The ecology and evolutionary history of the Deinococcaceae family
… of the Deinococcus genus arises from its large pangenome. A high abundance of transposase genes and efficient homologous recombination mechanisms enhanced their genetic flexibility and enabled Deinococcus to survive in diverse habitats. Conversely, this ecologically advantageous trait forms a …
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Exploring the Population Structure, Recombination Landscape, and Pan-Genome of the Global Neisseria meningitidis Population
Neisseria meningitidis is a gram-negative species of bacteria which causes meningitis, septicaemia, urethritis, and pneumonia worldwide. Infections are typically asymptomatic carriage, but those which cause disease are extremely difficult to treat, leading to a high case-fatality rate. As such, …
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Creating and analysing an African pan-genome
… feasibility of creating and analysing an African pangenome, and to begin developing tools to achieve this. Several distinct African regional ancestral groups – namely east African Nilo-Saharan, east African Afro-Asiatic, far west Niger-Congo, central west Niger-Congo, Bantu-speaking Niger-Congo, …
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CHROMOSOME-LEVEL DE NOVO GENOME ASSEMBLIES OF AVIAN SPECIES AND THEIR RELEVANCE FOR COMPARATIVE GENOMICS, PANGENOMICS, POPULATION GENOMICS AND SPECIES CONSERVATION.
… barn swallow assemblies, I constructed the first pangenome graph for the species and preliminarily evaluated the extent of core and accessory genes among individuals. We also complemented the nuclear genome-based study with the generation of the complete mitochondrial genome for the species, which …
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Evolution of Toxin Resistance in the Grasshopper Mouse: A Comparative Genomics Perspective
Novel traits enable many rodents to thrive in extreme environmental niches. For example, predatory grasshopper mice have co-evolved resistance to painful and lethal neurotoxins produced by their scorpion prey. Interestingly, toxin resistance in the three species of grasshopper mice (Onychomys …