Transposable elements in the salmonid genome

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dc.contributor.authorMinkley, David Richard
dc.contributor.supervisorKoop, Benjamin F
dc.date.accessioned2018-04-30T16:42:17Z
dc.date.copyright2018en_US
dc.date.issued2018-04-30
dc.degree.departmentDepartment of Biology
dc.degree.levelMaster of Science M.Sc.en_US
dc.description.abstractSalmonids are a diverse group of fishes whose common ancestor experienced an evolutionarily important whole genome duplication (WGD) event approximately 90 MYA. This event has shaped the evolutionary trajectory of salmonids, and may have contributed to a proliferation of the repeated DNA sequences known as transposable elements (TEs). In this work I characterized repeated DNA in five salmonid genomes. I found that over half of the DNA within each of these genomes was derived from repeats, a value which is amongst the highest of all vertebrates. I investigated repeats of the most abundant TE superfamily, Tc1-Mariner, and found that large proliferative bursts of this element occurred shortly after the WGD and continued during salmonid speciation, where they have produced dramatic differences in TE content among extant salmonid lineages. This work provides important resources for future studies of salmonids, and advances the understanding of two important evolutionary forces: TEs and WGDs.en_US
dc.description.embargo2019-04-19
dc.description.scholarlevelGraduateen_US
dc.identifier.bibliographicCitationLien, S., Koop, B.F., Sandve, S.R., Miller, J.R., Kent, M.P., Nome, T., Hvidsten, T.R., Leong, J.S., Minkley, D.R., Zimin, A., Grammes, F., Grove, H., Gjuvsland, A., Walenz, B., Hermansen, R.A., von Schalburg, K., Rondeau, E.B., Di Genova, A., Samy, J.K.A., Olav Vik, J., Vigeland, M.D., Caler, L., Grimholt, U., Jentoft, S., Inge Våge, D., de Jong, P., Moen, T., Baranski, M., Palti, Y., Smith, D.R., Yorke, J.A., Nederbragt, A.J., Tooming-Klunderud, A., Jakobsen, K.S., Jiang, X., Fan, D., Hu, Y., Liberles, D.A., Vidal, R., Iturra, P., Jones, S.J.M., Jonassen, I., Maass, A., Omholt, S.W., and Davidson, W.S. 2016. The Atlantic salmon genome provides insights into rediploidization. Nature 533: 200-205. Nature Publishing Group. doi:10.1038/nature17164.en_US
dc.identifier.bibliographicCitationChristensen, K.A., Leong, J.S., Sakhrani, D., Biagi, C.A., Minkley, D.R., Withler, R.E., Rondeau, E.B., Koop, B.F., Devlin, R.H. 2018. Chinook salmon (Oncorhynchus tshawytscha) genome and transcriptome. PLoS One 13(4):e0195461en_US
dc.identifier.urihttp://hdl.handle.net/1828/9287
dc.languageEnglisheng
dc.language.isoenen_US
dc.rightsAvailable to the World Wide Weben_US
dc.subjectTransposable elementsen_US
dc.subjectSalmonen_US
dc.subjectGenome annotationen_US
dc.subjectRepeatsen_US
dc.subjectGenome evolutionen_US
dc.subjectBioinformaticsen_US
dc.subjectSpeciationen_US
dc.subjectEvolutionen_US
dc.subjectTc1-Marineren_US
dc.subjectWhole genome duplicationen_US
dc.subjectPolyploidyen_US
dc.subjectFishen_US
dc.subjectRainbow trouten_US
dc.subjectArctic charen_US
dc.subjectAtlantic salmonen_US
dc.subjectCoho salmonen_US
dc.subjectChinook salmonen_US
dc.subjectSalmo salaren_US
dc.subjectSalvelinus alpinusen_US
dc.subjectOncorhynchus mykissen_US
dc.subjectOncorhynchus kisutchen_US
dc.subjectOncorhynchus tshawytschaen_US
dc.titleTransposable elements in the salmonid genomeen_US
dc.typeThesisen_US

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