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University of Otago RESEARCH REPORT University of Otago RESEARCH REPORT The role of gene duplication and neofunctionalization in the sexual plasticity of teleost fish Jonika Edgecombe A thesis submitted in partial fulfilment of the Degree of Bachelor of Biomedical Science with Honours. University of Otago, Dunedin, New Zealand October 2020 Abstract Sex determination and differentiation varies widely across vertebrates. In teleost fish these processes are remarkably plastic. In contrast to a gonochoristic system where the sexes are separate, fish that begin life as one sex and change sex as part of their lifecycle are sequentially hermaphroditic. Such a process requires drastic anatomical and physiological changes, requiring a switch between the bistable, antagonistic genetic networks that establish and maintain separate sexes. The trigger of such a change is often a social one and the genetic underpinnings of the process of sex change is still to be fully elucidated. However, recent transcriptomic work exploring sex change in bluehead wrasse has shown sharp up- and downregulation of sex-associated genes. Interestingly, certain genes that were thought to play a role in female sex determination and differentiation were found in multiple copies across the genome, with one copy playing the known role in female sex determination and differentiation and the other copy/copies, on the contrary, being upregulated during transition to the male sex. Multiple copies of a gene typically arise due to gene or whole-genome duplication, with potential subsequent sub/neofunctionalization. Duplicated genes are a well-established substrate for divergent gene evolution. A duplicate gene leads to redundancy, with no evolutionary restriction on the additional copy/copies and therefore facilitated mutation and evolution of a new role. Based on the recently published insights on sex determination in bluehead wrasse, I hypothesise that gene duplication and subsequent neofunctionalization may underpin the sexual plasticity observed in teleost fish – an area that has not yet been extensively researched. This hypothesis can now be investigated thanks to recent advances in genomics research. To gain insight into whether gene duplication and subsequent neofunctionalization is implicated in the evolution of sequential hermaphroditism as an example of a sex-changing reproductive mode, I applied a comparative candidate gene approach, investigating and I comparing the levels of gene duplication in key sex-related genes across and between sex changing and non sex changing species. I here present my analyses based on both, gene annotations and genomic sequence alignments. Overall, I found no statistically significant evidence that gene duplication and subsequent neo- or subfunctionalization is causal to the sexual plasticity observed in teleost fish. Both the genome annotation and sequence alignment approaches did not return any significant results. However, while completing my project, I managed to retrieve valuable preliminary data and identified potential caveats associated with the study of gene duplication. This work is of significance, having implications for our understanding of the evolution of sex determination and differentiation - not only for teleost fish, but for the entirety of the Chordata phylum. II Contributions Dr. Lara Urban provided bioinformatic support. Specifically, aiding troubleshooting and patching of code as well as adapting the code shown in Appendix 7. Additionally she provided me with statistical support, and the generation of the PCA and boxplots shown in Error! Reference source not found., Figure 14 and Figure 15, with code attached in Appendix 12. Professor Neil Gemmell, Dr Lara Urban and Dr Erica Todd all provided me with feedback on my thesis (as appropriate under the guidelines set out in the 2020 BBiomedSci handbook), and supervisory support. III Acknowledgements Firstly a massive thank you to my supervisors. To Professor Neil Gemmell for the opportunity to undertake this honours project, I also thank him for his supervision, guidance and patience in a particularly trying year. I also owe many, many thanks to Dr. Lara Urban who provided me with amazing supervision, which was of huge benefit to me as she guided me into the world of coding and commandline with patience and kindness! I would still be logging onto NeSI without her! Dr Erica Todd also co-supervised me and her insight into the world of sex- changing fish was hugely advantageous - I thank her immensely for zooming in from Australia and always encouraging me and supporting me where possible! I also thank my advisor Dr Megan Wilson for the advice and support, as well as Associate Professor Liz Ledgerwood and Jordan Bunton, all three of whom made the BBiomedsci programme run smoothly. Secondly I would like to acknowledge the University of Otago for the scholarships that enabled me to undertake an honours year. I am extremely grateful for the financial support and for the opportunity to pursue my passion. Lastly my support network; Thank you to my parents Don & Karen for dealing with my constant Facetimes - I would not have made it through this year without you. A special mention to Monica Vallender, for your unwavering support and friendship through a year that has been particularly hard for me. Thank you to the fantastic group that is the Gemmell Lab, you guys rock and I am so glad to have spent the year in such an awesome environment. Last but definitely not least a massive shoutout to my office gals! Rosie, Rebecca and Lin you guys made this year amazing and I am so grateful for the support we have shared, the giggles, tears and sushi trips! IV Contents ABSTRACT _______________________________________________________________ I CONTRIBUTIONS_______________________________________________________ III ACKNOWLEDGEMENTS ________________________________________________ IV CONTENTS______________________________________________________________ V LIST OF ABBREVIATIONS ______________________________________________ IX LIST OF FIGURES ______________________________________________________ XII LIST OF TABLES ______________________________________________________ XIV INTRODUCTION__________________________________________________________ 1 1.1 Broadness of sex determination systems across vertebrates ________________ 1 1.1.1 Teleost fish and hermaphroditism ___________________________________ 2 1.1.2 Why change sex? _______________________________________________ 3 1.1.3 Who changes sex and how? _______________________________________ 5 1.1.4 Master Regulators and effectors of sex determination ___________________ 7 1.1.5 Paradigms of sex determination ___________________________________ 10 1.2 Models for gene evolution and functional diversity ______________________ 12 1.2.1 Potential of teleost genomic architecture to contribute to sexual plasticity __ 13 1.2.2 Neofunctionalization ____________________________________________ 14 1.2.3 Subfunctionalization. ___________________________________________ 15 1.2.4 Isoforms _____________________________________________________ 15 1.3 Genes that have been duplicated and implicated in sex change ____________ 16 1.3.1 Sex-determining genes __________________________________________ 16 1.3.2 Sex-steroid related genes ________________________________________ 17 V 1.3.3 Female pathway genes. __________________________________________ 19 1.3.4 Epigenetic genes _______________________________________________ 19 1.4 Rationale of this investigation _______________________________________ 20 1.4.1 Advances in genomics enable further investigation. ___________________ 21 1.4.2 Brief Summary of thesis aims and approach _________________________ 22 2. METHODS __________________________________________________________ 23 2.1 Pipeline Overview _________________________________________________ 23 2.2 Species selection __________________________________________________ 23 2.3 Candidate Gene Selection___________________________________________ 28 2.3.1 Nomenclature adjustments _______________________________________ 28 2.3.2 Download protein sequences. _____________________________________ 29 2.4 Genome Assembly & Annotation and Protein Download _________________ 30 2.5 Genome Annotation Search and counts. _______________________________ 33 2.6 Custom Genome Database creation __________________________________ 34 2.6.1 Genome sequence alignment (tBLASTn) ____________________________ 35 2.6.2 File reformatting _______________________________________________ 35 2.6.3 Create Protein Databases ________________________________________ 36 2.6.4 BLASTx _____________________________________________________ 36 2.6.5 Alternative Plan _______________________________________________ 37 2.6.6 Statistical analysis of gene counts__________________________________ 39 2.6.7 Phylogenetic tree construction. ____________________________________ 40 3. RESULTS ___________________________________________________________ 42 3.1 Genome Annotation Search _________________________________________ 44 3.2 Genomic Sequence Alignment (tBLASTn) _____________________________ 46 VI 3.3 Preliminary phylogeny results _______________________________________ 56 4. DISCUSSION ________________________________________________________ 58 4.1 Key findings ______________________________________________________ 58 4.1.1 Genome annotation search _______________________________________ 58 4.1.2 Genome Sequence Alignment (tBLASTn) ___________________________ 60 4.1.3 Pseudogene detection ___________________________________________
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