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Development of a phylogenomic framework for the krill
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
2018 (English)Independent thesis Advanced level (professional degree), 20 credits / 30 HE creditsStudent thesis
Abstract [en]

Over the last few decades, many krill stocks have declined in size and number,likely as a consequence of global climate change (Siegel 2016). A major risk factoris the increased level of carbon dioxide (CO2) in the ocean. A collapse of the krillpopulation has the potential to cause disruption of the ocean ecosystem, as krill arethe main connection between primary producers such as phytoplankton and largeranimals (Murphy et al. 2012). The aim of this project is to produce the firstphylogenomic framework with help of powerful comparative bioinformatics andphylogenomic methods in order to find and analyse the genes that help krill adaptto its environment. Problem with these studies is that we still do not have access toa reference genome sequence of any krill species. To strengthen and increase trustin our studies two different pipelines were performed, each with different OrthologyAssessment Toolkits (OATs), Orthograph and UPhO, in order to establish orthologyrelationships between transcripts/genes. Since UPhO produces well-supportedtrees where the majority of the gene trees match the species tree, it isrecommended as the proper OATs for generating a robust molecular phylogeny ofkrill. The second aim with his project was to estimate the level of positive selectionin E. superba in order to lay a foundation about level of selection acting on proteincodingsequences in krill. As expected, the level of selection was quite high in E.superba, which indicates that krill are adapted to the changing environment bypositive selection rather than natural genetic drift.

Place, publisher, year, edition, pages
2018.
Series
UPTEC X ; 18 016
National Category
Bioinformatics (Computational Biology)
Identifiers
URN: urn:nbn:se:uu:diva-355387OAI: oai:DiVA.org:uu-355387DiVA, id: diva2:1228769
Educational program
Molecular Biotechnology Engineering Programme
Supervisors
Examiners
Available from: 2018-06-29 Created: 2018-06-28 Last updated: 2018-06-29Bibliographically approved

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CiteExportLink to record
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