Genome evolution of Symbiodiniaceae Raúl Augusto González Pech MSc in Evolution, Ecology and Systematics BSc in Biology A thesis submitted for the degree of Doctor of Philosophy at The University of Queensland in 2020 Institute for Molecular Bioscience Abstract Symbiotic interactions between dinoflagellates (Symbiodiniaceae) and corals give rise to the ecological complexity and biodiversity of reef ecosystems. Comparative genomic studies can aid in tracing the evolutionary history of these dinoflagellates, and thus elucidate the evolutionary forces that drove their diversification and adaptation as predominantly symbiotic lineages. However, genome data from these ecologically important organisms remain scarce, largely due to their immense sizes and idiosyncratic genome features. The incorporation of genome-scale data from diverse lineages in a comprehensive comparative analysis is essential to better understand the molecular and evolutionary mechanisms that underpin the diversification of Symbiodiniaceae. In this thesis, I first review and discuss the state-of-the-art of Symbiodiniaceae genomics in depth, highlighting the genetic and ecological diversity of these dinoflagellates. In addition, I present a theoretical framework, based on our current knowledge of intracellular bacterial symbionts and parasites, to approach the study of genome evolution in Symbiodiniaceae along the broad spectrum of symbiotic associations they can establish. I also summarise and explain how common methods in comparative genomics can be implemented to improve our understanding of Symbiodiniaceae evolution. Using available genome and transcriptome data in a comparative analysis (Chapter 3), I identified gene functions that distinguish Symbiodiniaceae from other dinoflagellates in Order Suessiales, as well as functions specific to the major lineages within the family. These results show that gene functions shared by all lineages in Symbiodiniaceae are relevant to adaptation to the environment, as well as to the establishment and maintenance of symbiosis. I also determined functions specific to each lineage and highlight their potential use in future research to understand niche specialisation. The basal genus Symbiodinium consists of both free-living and symbiotic forms, and most dinoflagellates external to Symbiodiniaceae are free-living. Genome data from Symbiodinium therefore represent a key analysis platform to assess genome features related to the evolutionary transition from a free-living to a symbiotic lifestyle. Next, I generated and compared high-quality de novo genome assemblies from two Symbiodinium isolates (Chapter 4): the symbiotic Symbiodinium tridacnidorum CCMP2592 and the free-living Symbiodinium natans CCMP2548; these assemblies were generated using both short- and long-read sequence data. My results reveal extensive genome-sequence divergence between these two genomes, and suggest that increased structural rearrangements in the genome of S. tridacnidorum, characterised as distinct types of gene duplication and transposable elements, contribute to the extensive genome divergence between these two species. The distinguishing genome features between these two isolates potentially associate with their evolution towards the distinct ii lifestyles. The results also agree with the notion that the symbiotic lifestyle is a derived trait in Symbiodinium, and that the free-living lifestyle is ancestral. To further assess the divergence within this genus and within family Symbiodiniaceae, I generated de novo genome assemblies from additional five Symbiodinium isolates, encompassing diverse ecological niches. In a comprehensive analysis (Chapter 5) that incorporated all other available genome data of Suessiales (a total of 15 dinoflagellate genomes, nine of which are from Symbiodinium), I assessed, for the first time, genome-sequence divergence within Order Suessiales, within Family Symbiodiniaceae, within Genus Symbiodinium, and among isolates of individual species (i.e. Symbiodinium microadriaticum and Symbiodinium tridacnidorum). Whole-genome comparisons reveal extensive sequence divergence, with no sequence regions common to all 15. Based on similarity of k-mers from whole-genome sequences, the distances among Symbiodinium isolates are similar to those between isolates of distinct genera. Gene functions related to symbiosis and stress response exhibit similar abundance in all analysed genomes. These results suggest that structural rearrangements contribute to genome sequence divergence in Symbiodiniaceae even within a same species, but the gene functions have remained largely conserved in Suessiales. This thesis work is the most comprehensive assessment to date of genome evolution of Symbiodiniaceae, and of the basal genus Symbiodinium. The thesis includes, for the first time, comparisons at the intra-generic and intra-specific levels using extensive whole-genome sequence data. Through this thesis research, seven de novo genome assemblies from diverse Symbiodinium isolates, as well as their corresponding transcriptomes and predicted protein-coding genes, were generated. Customised and novel bioinformatic methods were implemented to accommodate the complexity and idiosyncrasy of dinoflagellate genomes. Knowledge generated from this body of research provide novel insights into genome evolution of Symbiodiniaceae linked to their transition to symbiosis, and the molecular mechanisms that underpin the diversification of the family. The data and analytic workflows from this research can be readily applied in comparative genomic studies of other dinoflagellates and microbial eukaryotes. iii Declaration by author This thesis is composed of my original work, and contains no material previously published or written by another person except where due reference has been made in the text. I have clearly stated the contribution by others to jointly authored works that I have included in my thesis. I have clearly stated the contribution of others to my thesis as a whole, including statistical assistance, survey design, data analysis, significant technical procedures, professional editorial advice, financial support and any other original research work used or reported in my thesis. The content of my thesis is the result of work I have carried out since the commencement of my higher degree by research candidature and does not include a substantial part of work that has been submitted to qualify for the award of any other degree or diploma in any university or other tertiary institution. I have clearly stated which parts of my thesis, if any, have been submitted to qualify for another award. I acknowledge that an electronic copy of my thesis must be lodged with the University Library and, subject to the policy and procedures of The University of Queensland, the thesis be made available for research and study in accordance with the Copyright Act 1968 unless a period of embargo has been approved by the Dean of the Graduate School. I acknowledge that copyright of all material contained in my thesis resides with the copyright holder(s) of that material. Where appropriate I have obtained copyright permission from the copyright holder to reproduce material in this thesis and have sought permission from co-authors for any jointly authored works included in the thesis. iv Publications included in this thesis González-Pech RA, Ragan MA & Chan CX. (2017). Signatures of adaptation and symbiosis in genomes and transcriptomes of Symbiodinium. Scientific Reports 7(1), 15021. DOI: 10.1038/s41598- 017-15029-w González-Pech RA, Bhattacharya D, Ragan MA & Chan CX. (2019). Genome evolution of coral reef symbionts as intracellular residents. Trends in Ecology and Evolution 34(9), 799-806. DOI: 10.1016/j.tree.2019.04.010 González-Pech RA, Stephens TG, Chen Y, Mohamed AR, Cheng Y, Burt DW, Bhattacharya D, Ragan MA & Chan CX. (2019). Structural rearrangements drive extensive genome divergence between symbiotic and free-living Symbiodinium. bioRxiv, 783902. DOI: 10.1101/783902 González-Pech RA, Chen Y, Stephens TG, Shah S, Mohamed AR, Lagorce R, Bhattacharya D, Ragan MA & Chan CX. (2019). Genomes of Symbiodiniaceae reveal extensive sequence divergence but conserved functions at family and genus levels. bioRxiv, 800482. DOI: 10.1101/800482 v Submitted manuscripts included in this thesis No manuscripts submitted for publication. Other publications during candidature Peer-reviewed papers and pre-prints: González-Pech RA, Vargas S, Francis WR & Wörheide G. (2017). Transcriptomic resilience of the Montipora digitata holobiont to low pH. Frontiers in Marine Science 4, 403. DOI: 10.3389/fmars.2017.00403 Voigt O, Erpenbeck D, González-Pech RA, Al-Aidaroos AM, Berumen ML & Wörheide G. (2017). Calcinea of the Red Sea: providing a DNA barcode inventory with description of four new species. Marine Biodiversity, 1-26. DOI: 10.1007/s12526-017-0671-x Liu H, Stephens TG, González-Pech RA, Beltran VH, Lapeyre B, Bongaerts P, Cooke I, Aranda M, Bourne DG, Forêt S, Miller DJ, van Oppen MJH, Voolstra CR, Ragan MA & Chan CX. (2018). Symbiodinium genomes reveal adaptive evolution of functions related to coral-dinoflagellate symbiosis. Communications Biology 1, 95. DOI: 10.1038/s42003-018-0098-3 González-Pech RA, Stephens TG & Chan CX. (2018). Commonly misunderstood parameters of NCBI BLAST and important considerations for users. Bioinformatics 35(15), 2697-2698. DOI: 10.1093/bioinformatics/bty1018 Stephens TG, González-Pech RA, Cheng Y, Mohamed AR, Bhattacharya D, Ragan MA & Chan CX. (2019).