Keightley, Peter

Colegrave, Nick

Craig, Rory J.

Biotechnology and Biological Sciences Research Council (BBSRC)

2021-12-10T15:24:47Z

2021-12-10T15:24:47Z

2021-12-07

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.

https://hdl.handle.net/1842/38338

http://dx.doi.org/10.7488/era/1603

en

The University of Edinburgh

Craig RJ, Böndel KB, Arakawa K, Nakada T, Ito T, Bell G, Colegrave N, Keightley PD, Ness RW. 2019. Patterns of population structure and complex haplotype sharing among field isolates of the green alga Chlamydomonas reinhardtii. Mol Ecol 28: 3977-3993.

Craig RJ, Hasan AR, Ness RW, Keightley PD. 2021. Comparative genomics of Chlamydomonas. Plant Cell 33: 1016-1041.

Craig RJ, Yushenova IA, Rodriguez F, Arkhipova IR. 2021. An ancient clade of Penelope- like retroelements with permuted domains is present in the green lineage and protists, and dominates many invertebrate genome. Mol Biol Evol doi:10.1093/molbev/msab225

Craig RJ, Suh A, Wang M, Ellegren H. 2018. Natural selection beyond genes: identification and analyses of evolutionarily conserved elements in the genome of the collared flycatcher (Ficedula albicollis). Mol Ecol 27: 476-492.

Smith DR, Craig RJ. 2021. Does mitochondrial DNA replication in Chlamydomonas require a reverse transcriptase? New Phytol 229: 1192-1195.

Gallaher, D. S., Craig, R. J., Ganesan, I., Purvine, S. O., McCorkle, S. R., Grimwood, J., Strenkert, D., Davidi, L., Roth, M. S., Jeffers, T., Lipton, M. S., Niyogi, K. K., Schmutz, J., Theg, S. M., Blaby-Haas, C. E. & Merchant, S. S. 2021. Widespread polycistronic gene expression in the green algal lineage. Proc Natl Acad Sci U S A 118: e2017714118.

Chaux-Jukic F, O’Donnell S, Craig RJ, Eberhard S, Vallon O, Zhou X. 2021. Architecture and evolution of subtelomeres in the unicellular green alga Chlamydomonas reinhardtii. Nucleic Acids Res 49: 7571-7587

Lopez-Cortegano E, Craig RJ, Chebib J, Samuels T, Morgan AD, Kraemer SA, Bondel KB, Ness RW, Colegrave N, Keightley PD. 2021. De novo mutation rate variation and its determinants in Chlamydomonas. Mol Biol Evol. doi:10.1093/molbev/msab140.

Chlamydomonas reinhardtii

C. reinhardtii

genome sequencing

evolutionary context

Evolutionary genomics of Chlamydomonas

Thesis or Dissertation

Doctoral

PhD Doctor of Philosophy