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Researchonline@JCU ResearchOnline@JCU This file is part of the following work: Budd, Alyssa (2020) Epigenetic effects of temperature on sex change in barramundi, Lates calcarifer. PhD Thesis, James Cook University. Access to this file is available from: https://doi.org/10.25903/95mj%2Dpk34 © 2020 Alyssa Budd. The author has certified to JCU that they have made a reasonable effort to gain permission and acknowledge the owners of any third party copyright material included in this document. If you believe that this is not the case, please email [email protected] Epigenetic effects of temperature on sex change in barramundi, Lates calcarifer Thesis submitted by Alyssa Budd 26 May 2020 For the degree of Doctor of Philosophy In Agriculture, Environmental and Related Studies College of Science and Engineering James Cook University ACKNOWLEDGEMENTS Thank you. To the funding bodies and collaborating partners that enabled the work to be carried out. To Professor Dean Jerry, for showing me how you ‘blaze your own trail’ and demonstrating a stubborn sense of optimism that is incredibly powerful. I have learnt a lot from you, I hope you have learnt from me too. To Dr Jose Domingos, for your unwavering enthusiasm and genuine interest in my results. To Dr Roger Huerlimann, for your generosity in offering your time, extensive knowledge and friendship. To Dr Carmel McDougall and Dr Nick Wade, for your unfailing kindness and mentorship. To Dr Carolyn-Smith Keune, for your tremendous dedication to the functionality of the MEEL lab and well-being of its members. To Associate Professor Jan Strugnell, for the opportunity to work for you and your patience whilst I wrote up. To Dr Julie Robins and Dr Olivia Whybird, for your collaborative efforts and contributions to my second chapter. To Dr Dave Jones, for very selflessly offering to proof my chapters, and following through. To my friends and colleagues; Shannon, Melissa, Maria, Jarrod, Johannes and Adrien, for being there for me and each other in the way that you have. You are extraordinary. To my family, for being who you are, accepting me as I am and forgiving me in my absence. You are my favourite people in the world. To all who have accompanied me on this journey, wholly or in part. You have made it what it was. i STATEMENT OF THE CONTRIBUTION OF OTHERS Thesis chapter Publication and/or conference output Nature and extend of contribution of co- on which the chapter is based contributors 1 Budd, A. M., Banh, Q. Q, Domingos, J. Budd A. M. Co-ordinated and executed project, A, Jerry, D. R (2015). Sex control in authored abstract, section on sex determination fish: approaches, challenges and and differentiation and sub-sections pertaining to opportunities for aquaculture. Journal of environmental manipulations. Proofing and Marine Science and Engineering. 3(2), editing of complete manuscript. 329-355 Banh Q. Q. Authored sub-section hormonal manipulation (not included in this thesis). Domingos J. A. Authored sub-section on selection for altered sex ratios (not included in thesis). Jerry D. R. Conception and execution of the project, authored introduction (in part reproduced in and adapted for this thesis), conclusion and sections on chromosome ploidy manipulation (not included in thesis). 2 Budd, A. M., Robins, J. B, Whybird, Budd, A. M. Project co-conception, development O., Jerry, D. R. (2020) Sex-specific and management. Data generation, molecular differences in DNA methylation are methods development and computational analysis. associated with region-specific Results interpretation, figures, writing and editing. variability in total length-at-sex change in a commercially important fish Robins, J. B. Chapter development, data species. Manuscript in preparation. collection and interpretation, proofing and editing. Whybird, O. Sample collection, data collection, chapter development. Jerry, D. R. Initiation of collaboration, Project conception, development and management. Proofing and editing. Funding and supervision. 3 Budd, A. M., Guppy, J. L, Th�pot, V., Budd, A. M. Project development and Domingos, J. A, Jerry, D. R. Is management. Fish husbandry, maintenance and temperature driving protandrous sex experimental management. Data generation, ii change in barramundi? (Poster) 7th molecular methods development and international symposium of vertebrate computational analysis. Results interpretation, sex determination – Kona, Hawaii figures, writing and editing. (2015) Guppy, J. L. Laboratory assistance, histological Budd, A. M., Domingos, J. A., Guppy, procedures, fish husbandry, maintenance and J. L, Th�pot, V., Jerry, D. R. (2020) experimental management. Delayed effect of low rearing temperature on DNA methylation in the Th�pot, V. Fish husbandry, maintenance and gonads of juvenile barramundi, Lates experiment management. calcarifer. Manuscript in preparation. Domingos, J. A. Project management. Assistance with fish husbandry and maintenance. Proofing and editing. Supervision. Jerry, D. R. Project conception, development and management. Proofing and editing. Funding and supervision. 4 Budd, A. M., Huerlimann, R., Guppy, Budd, A. M. Project development, funding and J. L, Pinto, R. C. C, Domingos, J. A, management. Fish husbandry, maintenance and Jerry, D. R (2020) Whole methylome experimental management. Initiation of and transcriptome effects of collaborations. Data generation, molecular temperature on precocious sex change methods and bioinformatics. Results in the protandrous barramundi, Lates interpretation, figures, writing and editing. calcarifer. Manuscript in preparation. Huerlimann, R. Mentorship, bioinformatics Budd, A. M., Guppy, J. L, Robins, J. B, tutelage and assistance, results interpretation. Whybird, O., Th�pot, V., Domingos, J. A, Jerry, D. R. Is temperature driving Guppy, J. L. Fish maintenance and experimental sex change in barramundi? (15 min talk) management, assistance with interpretation of XIII International Symposium for histological results. Genetics in Aquaculture – Cairns (2018) Pinto, R. J. Fish maintenance and experimental management. Domingos, J. A. Proofing and editing. Supervision. iii Jerry, D. R. Project conception, development and management. Proofing and editing. Initiation of collaborations. Funding and supervision. 5 Prepared as thesis chapter only Budd, A. M. Results interpretation, figures, writing and editing. Jerry, D. R. Proofing and editing. iv ABSTRACT How and why do fish change sex? Whilst sexual development is nearly universal among eukaryotes, phenotypic sex can be established through a variety of complex and rapidly evolving regulatory pathways. In particular, teleost fish display remarkable variety in their systems of sexual development, as well as the molecular mechanisms by which these systems are governed. For example, fish can be gonochoristic, developing as either male or female, or simultaneous hermaphrodites, possessing both functional male and female reproductive organs. Alternatively, fish can be sequential hermaphrodites, undergoing primary development as one sex, but later sex changing to the other, or serial hermaphrodites where sex change occurs not once, but multiple times. The molecular mechanisms governing sex in fish are equally diverse, whereby sex can be determined by endogenous factors (e.g. genetic components), exogenous factors (e.g. environmental or experimental stimuli), or as a result of an interaction between the two. How these differences in phenotypic sex arise from the same genetic template, and what the environmental drivers of this may be, form the basis of the more specific questions that this thesis addresses. Changes in phenotype in the absence of changes in genotype, particularly in response to environmental cues, are hallmarks of epigenetic control. Epigenetic changes are those that occur in the structural or chemical composition of DNA, rather than the sequence itself, and cause changes in gene expression. One particular epigenetic modification, DNA methylation, has been shown to underlie both temperature effects on sexual development in gonochoristic and simultaneous hermaphrodite fish species (i.e. those with stable sexual phenotypes), and sex change in sequential hermaphrodite species. Such evidence is rapidly accumulating to suggest that DNA methylation is a common mechanism underlying the remarkable plasticity of sex in fish. It is unknown, however, if temperature can induce changes in DNA methylation, and thus influence development of the primary sex and/or mediate transition to the secondary sex, in sequential hermaphrodites. Barramundi, Lates calcarifer, are protandrous (male-first) hermaphrodites and, at present, are the only sequentially sex changing fish for which temperature has been reported to affect phenotypic sex. Very recently, it has been shown that male and female barramundi also exhibit differential DNA methylation in key sex-related genes. With a known effect of temperature on v sexual development and differential DNA methylation between the sexes, barramundi presents an experimental model with which to test the hypothesis that temperature-induced DNA methylation is an experimental and/or environmental driver of sex change in a sequential hermaphrodite. In this species, sex change is strongly associated with body length, but substantial differences in length-at-sex change are observed between regions and culture environments, the causes of which are unknown. The resulting inability to predict and control sex change in barramundi presents the single biggest impediment to the instigation of commercial
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