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Evolutionary Genomics of Transposable Elements in the Saccharomyces Sensu Lato Complex

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Evolutionary Genomics of Transposable Elements in the Saccharomyces Sensu Lato Complex University of Huddersfield Repository Grace, Cooper A. Evolutionary Genomics of Transposable Elements in the Saccharomyces sensu lato Complex Original Citation Grace, Cooper A. (2018) Evolutionary Genomics of Transposable Elements in the Saccharomyces sensu lato Complex. Doctoral thesis, University of Huddersfield. This version is available at http://eprints.hud.ac.uk/id/eprint/34743/ The University Repository is a digital collection of the research output of the University, available on Open Access. Copyright and Moral Rights for the items on this site are retained by the individual author and/or other copyright owners. 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For more information, including our policy and submission procedure, please contact the Repository Team at: [email protected]. http://eprints.hud.ac.uk/ University of Huddersfield Doctoral Thesis Evolutionary Genomics of Transposable Elements in the Saccharomyces sensu lato Complex Author: Supervisors: Cooper Alastair Grace Dr. Martin Carr Dr. Patrick McHugh A thesis submitted in partial fulfilment of the requirements for the degree of Doctor of Philosophy Department of Biological and Geographical Sciences School of Applied Sciences iii Copyright Statement • The author of this thesis (including any appendices and/ or schedules to this thesis) owns any copyright in it (the “Copyright”) and he has given The University of Huddersfield the right to use such Copyright for any administrative, promotional, educational and/or teaching purposes • Copies of this thesis, either in full or in extracts, may be made only in accordance with the regulations of the University Library. Details of these regulations may be obtained from the Librarian. Details of these regulations may be obtained from the Librarian. This page must form part of any such copies made. • The ownership of any patents, designs, trademarks and any and all other intellectual property rights except for the Copyright (the “Intellectual Property Rights”) and any reproductions of copyright works, for example graphs and tables (“Reproductions”), which may be described in this thesis, may not be owned by the author and may be owned by third parties. Such Intellectual Property Rights and Reproductions cannot and must not be made available for use without permission of the owner(s) of the relevant Intellectual Property Rights and/or Reproductions. v Declaration of Authorship I, Cooper Alastair Grace, declare that this thesis titled, “Evolutionary Genomics of Transposable Elements in the Saccharomyces sensu lato Complex” and the work presented in it are my own. I confirm that: • This work was done wholly or mainly while in candidature for a research degree at this Uni- versity. • Where any part of this thesis has previously been submitted for a degree or any other quali- fication at this University or any other institution, this has been clearly stated. • Where I have consulted the published work of others, this is always clearly attributed. • I have acknowledged all main sources of help. Signed: Date: vii “Believing that I was viewing a basic genetic phenomenon, all attention was given, thereafter, to determining just what it was that one cell had gained that the other cell had lost. These proved to be transposable elements that could regulate gene expression in precise ways. Because of this I called them ’controlling elements’. Their origins and their actions were a focus of my research for many years thereafter.” Barbara McClintock, 1984 ix Abstract Transposable elements (TEs) are almost ubiquitous components of eukaryotic genomes that have long been considered solely deleterious or ’junk DNA’. They are split into two main forms, retro- transposons and DNA transposons, depending on the method of replication employed. Hosts have developed strategies for combating TEs including RNAi, methylation and copy number con- trol. TEs have also evolved ways of persisting in the genome in order to survive, such as target site specificity. Two additional ways which may be utilised by TEs, positive selection and horizontal transfer, were investigated here primarily using the budding yeasts in the Saccharomyces sensu lato complex. These species typically contain up to five families of retrotransposons, designated Ty1-5, and multiple subfamilies, all of varying transpositional activity. Discoveries of insertions evolving under positive selection and providing benefits to their hosts have been sporadic and serendipitous findings in a number of organisms. Full genome screenings for such insertions are rarely published, despite the impact TE insertions have upon their hosts. A population genomics approach was performed to address this issue in the genomes of Saccha- romyces cerevisiae and sister species S. paradoxus. Signatures of positive selection acting upon Ty insertions were identified using Tajima’s statistical D test. Neighbouring genes were also anal- ysed to ascertain the true target of selection where hitchhiking linked the two. A subset of LTR-gene pairings were explored using qPCR in order to identify any effects on host gene expression the occupied loci may cause. Two genes displayed significantly increased levels of expression, which may be due to the presence of positive selection candidate LTRs, which in turn may contribute to improving host fitness. This thesis further documents the systematic screening for Ty-like elements of all available genomes of budding yeast and related species. Extensive phylogenetic analyses estimated evo- lutionary relationships and possible horizontal transfer events of elements between the species. Evidence for in excess of 75 horizontal transfer events was uncovered here, around half of which x were successful in propagating in new genomes. The occurrence of horizontal transfer of TEs in the genomes of budding yeast is therefore far more common than previously documented. During screening of genomes, a further potential method of avoiding host defences was un- covered. The divergence of the highly active Ty4 family, which coincided with population isolation of multiple Saccharomyces species into subfamilies, was surprising given previous reports of this family being of particularly low activity. Such events are rarely recorded in eukaryotic genomes, and may also illustrate the compulsive spread of a new subfamily via horizontal transfer. The investigations reported here represent the first genomic screening of Ty insertions in Sac- charomyces for signatures of positive selection, and an updated, comprehensive search for evi- dence of HT between species of budding yeast. Both may act as methods for TE families to persist in the genomes of their hosts, and represent far more than simply ’junk DNA’. xi Acknowledgements I would like to acknowledge the following: The entertaining folks in the office and hotdesking area – Marina, Katharina, Alessandro, George, Bobby, Gonzalo, Georgia, Fabiola, Daisy, Adam, Alex, Sophie, Zoe, Asma, Makhosi and Kim. Keep on procrastinatin’ Claire. Each of you helped me in various ways, even if it was just random conversations here and there that prevented me from completely losing my mind. I only hope my badgering you about writing worked! Marisa for giving me a push towards writing my thesis in LaTex rather than watching me fight through another day with Microsoft Word. The amazing Dr. Catherine Finch, who understood the difficulties in completing a PhD and experienced them alongside me. Your friendship and support in the past year or so have been incredibly important to me. Dr Patrick McHugh as my secondary supervisor and Cathy McHugh for your help with qPCR, and their students Bethan and Laura with qbase+. Drs Jarek Bryk, Chris Cooper and Dougie Clarke for helpful discussions and always being such nice guys. My study mentor Mary for her help and support over the last few years. The amazing biology lab technicians Sophie, Felix, Elena and Maggie, without whom I’d proba- bly still be looking for a sterile loop and a tub of sorbitol. They helped me become a better scientist while appreciating my sense of humour, for which I will always be grateful. The other members of the research team Bernardo (I’ll always bring you water), Holly for ran- dom lab conversations, Ginés, and of course Jade, who picked me up when my motivation waned and watched me draw crazy mind maps on whiteboards. Andromeda is also rather grateful for the endless supply of almost empty peanut butter jars… Last but not least, my primary supervisor Dr Martin Carr. If you were hoping to inspire me to pursue a life of researching transposable elements, well done, you succeeded. So long, and thanks for all the tea. xiii Contents Copyright Statement iii Declaration of Authorship v Abstract ix Acknowledgements xi List of Figures xxiii List of Tables xxvii List of Abbreviations xxix 1 Introduction 1 1.1 Transposable Elements . 1 1.1.1 DNA transposons . 2 1.1.2 Retrotransposons . 2 1.1.2.1 LTR retrotransposons . 4 1.1.2.2 LTRs and retrotransposition . 5 1.2 Saccharomycetaceae . 6 1.2.1 The Saccharomyces sensu stricto complex . 8 1.2.2 Sensu stricto species . 11 1.2.2.1 S. cerevisiae ................................ 11 1.2.2.2 S. paradoxus and S. cariocanus ..................... 11 1.2.2.3 S. mikatae ................................. 12 1.2.2.4 S. kudriavzevii ............................... 12 1.2.2.5 S. arboricola ................................ 13 1.2.2.6 S. eubayanus ............................... 13 xiv 1.2.2.7 S. uvarum ................................. 13 1.2.2.8 A new species: Saccharomyces jurei . 13 1.2.3 The complexity of the Saccharomyces sensu stricto species: hybridisation . 14 1.3 Transposable elements in Saccharomyces cerevisiae: a model organism . 15 1.3.1 Recombination and solo LTRs .
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