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dc.contributor.advisorCox-Singh, Janet
dc.contributor.advisorReynolds, Paul Andrew
dc.contributor.authorOresegun, Damilola Rasheed
dc.coverage.spatial363en_US
dc.date.accessioned2023-03-28T08:35:18Z
dc.date.available2023-03-28T08:35:18Z
dc.date.issued2022-06-17
dc.identifier.urihttps://hdl.handle.net/10023/27274
dc.description.abstractPlasmodium knowlesi is a zoonotic malaria parasite of Southeastern macaque monkeys that causes zoonotic malaria in humans. P. knowlesi is also an experimental model for malaria, and information on P. knowlesi largely stem from experimental lines first isolated >four decades ago, rather than contemporary isolates causing human infections. The experimental lines are laboratory-restricted and have become relatively genetically stagnant and free from the selection pressure that would naturally occur in nature. Within the P. knowlesi genome exist the Schizont Infected Cell Agglutination variant antigen (SICAvar) and Plasmodium knowlesi interspersed repeat (kir) multigene families significant, which are of biological and scientific interest. To provide context using contemporary clinical isolates, this project aimed to generate high-quality genome sequences using long-sequencing from clinical ‘wild-type’ samples from infected patients. This includes generating new information on variant multigene families in P. knowlesi genomes generated from clinical patient whole blood. The work presented here details a method to deplete leucocytes in thawed P. knowlesi-infected patient whole blood samples to generate parasite-enriched DNA for whole-genome sequencing, resulting in >95% human DNA reduction. The extracted DNA was sequenced with long-read sequencing technology to create de novo whole-genome assemblies. From these, two isolate genomes representing the two dimorphic clusters of P. knowlesi in clinical samples were analysed. The generated genomes are highly syntenic to the published reference genome, sharing >4500 orthologous clusters with the PKNH reference genome. However, the number of SICAvar and kir genes present in the dataset deviated from the published reference genomes of P. knowlesi. The successful generation and construction of these patient genomes aid further interrogation of the contemporary P. knowlesi genome, with a focus on the constituent genes present in comparison to the experimental line.en_US
dc.description.sponsorship"This project was funded by the Wellcome Trust ISSF award 204821/Z/16/Z. Bioinformatics and computational biology analyses were supported by the University of St Andrews Bioinformatics Unit (AMD3BIOINF), funded by Wellcome Trust ISSF award 105621/Z/14/Z and 204821/Z/16/Z. The patient sample BioBank was compiled with informed consent (Medical Research Council, www.mrc.ac.uk, grant G0801971). Genome sequencing was supported by Tenovus Scotland (T16/03)."--Fundingen
dc.language.isoenen_US
dc.rightsCreative Commons Attribution-NonCommercial-NoDerivatives 4.0 International*
dc.rights.urihttp://creativecommons.org/licenses/by-nc-nd/4.0/*
dc.subjectPlasmodium knowlesien_US
dc.subjectNanoporeen_US
dc.subjectLong read sequencingen_US
dc.subjectClinical sampleen_US
dc.subjectGenome sequencingen_US
dc.subjectSICAvaren_US
dc.subjectKIRen_US
dc.subjectMultigene familyen_US
dc.subjectBioinformaticsen_US
dc.subjectGenomicsen_US
dc.titleDe novo genome assembly of Plasmodium knowlesi from contemporary clinical isolates - a novel scalable resource to take forward malaria researchen_US
dc.typeThesisen_US
dc.contributor.sponsorWellcome Trust. Institutional Strategic Support Fund (ISSF)en_US
dc.contributor.sponsorMedical Research Council (MRC)en_US
dc.contributor.sponsorTenovus Scotlanden_US
dc.type.qualificationlevelDoctoralen_US
dc.type.qualificationnamePhD Doctor of Philosophyen_US
dc.publisher.institutionThe University of St Andrewsen_US
dc.identifier.doihttps://doi.org/10.17630/sta/370
dc.identifier.grantnumber204821/Z/16/Zen_US
dc.identifier.grantnumber105621/Z/14/Zen_US
dc.identifier.grantnumber204821/Z/16/Zen_US
dc.identifier.grantnumberG0801971).en_US
dc.identifier.grantnumberT16/03en_US


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    Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
    Except where otherwise noted within the work, this item's licence for re-use is described as Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International