Evolutionary genomics of Chlamydomonas
Craig, Rory J.
The unicellular green alga Chlamydomonas reinhardtii is one of the primary model organisms in plant and algal biology. Although the species is fundamental to several research areas, including the study of photosynthesis, cilia and the cell cycle, very little is known about its evolutionary biology. Furthermore, C. reinhardtii research is generally limited to a single line of laboratory strains and no genomic resources exist for any closely related species. Consequently, the species has predominantly been studied in isolation, from both a population and phylogenetic perspective. In this thesis, I explore several aspects of the evolutionary genomics of C. reinhardtii and its closest relatives in the genus Chlamydomonas. I use population genomics approaches to characterise population structure across all known C. reinhardtii field isolates, presenting some of the first insights into the evolutionary ecology of the species. I use long read sequencing technology to produce highly contiguous genome assemblies for the three closest relatives of C. reinhardtii. Using these comparative resources, I describe several novel features of Chlamydomonas genomics, including the putative centromeric repeat. I present near complete reference assemblies for two laboratory strains of C. reinhardtii, characterising structural mutations that have occurred in the laboratory and revealing numerous misassemblies in previous versions. Finally, I present an exhaustively curated library of C. reinhardtii transposable elements and I describe a major new clade of retrotransposons present across the green lineage and animals. This collective work greatly expands our understanding of Chlamydomonas evolutionary genomics and is expected to be integral to the continued development of C. reinhardtii as a model for evolutionary biology research.