Evolutionary genomics of the microalga, Chlamydomonas reinhardtii

Chlamydomonas reinhardtii is a member of a diverse group of single-celled plants, the chlorophytes, which are intensively studied as model organisms in plant physiology and genetics. Chlamydomonas is also receiving attention, because chlorophytes are of critical ecological importance: up to one-half of global photosynthesis occurs in the oceans, much of it carried out by microalgae. Moreover, it has potential in generating biofuels. In spite of their key role in ecology and plant genetics, however, very little is known about chlorophytes in nature, especially the extent, nature and causes of genetic diversity. In the proposed project, the student will address a number of fundamental questions concerning the evolutionary genomics of microalgae, taking advantage of genomic resources that have only recently become available via work in the supervisors' labs and via collaborators. The student will become part research group funded by the BBSRC, co-led by Colegrave and Keightley, working on experimental evolution and the impact of new mutations on genetic variation in Chlamydomonas (see e.g. Morgan et al. 2014; Ness et al ,2015). Genomic resources we have produced as parto of this work will be the focus of the project, including whole-genome sequences of multiple natural isolates of C. reinhardtii. Genome sequences of a close relative, C. incerta, and the more distantly related Volvox carteri and Coccomyxa subellipsoidea (http://www.phytozome.net/) are also available.
Key research questions

1. Genomic diversity of C. reinhardtii. There are a number of fundamental questions that the student can straightforwardly address. How much genetic diversity is present within C. reinhardtii populations and how is this diversity distributed across the range of the species? How much population structure exists within the species? To what extent does diversity within C. reinhardtii and divergence between C. reinhardtii and C. incerta vary across the genome? What does this tell us about the nature of the selective forces operating in the genome?

2. The evolutionary significance of noncoding DNA in chloropytes. Annotated proteomes for several chlorophytes have been produced, but little work has been done on the evolutionary significance of noncoding DNA. Using comparative genomics and population genetics, we propose to investigate the nature of selection on noncoding DNA in chlorophytes, and address the following questions. Are signatures of selection detectable in noncoding DNA sequences in chlorophytes? For example, do we see reduced nucleotide divergence or nucleotide diversity compared to neutrally evolving sites? What fraction of the noncoding genome is functional? Are longer noncoding elements (e.g., introns, intergenic regions) more conserved, as has been found in other taxa that have compact genomes, such as invertebrates (Halligan and Keightley 2006)? Are there identifiable ultra-conserved noncoding elements in the chlorophyte genome? Are these elements conserved across the plant kingdom or across the tree of life in general? Is there evidence of positive and negative selection around conserved coding and noncoding elements, and what does this tell us about the nature of the selective forces operating in these regions?