Coccolithophores are unicellular algae that play crucial roles in marine carbon cycling. The genome of the E. huxleyi strain RCC1217 is currently being sequenced at The BBSRC Genome Analysis Centre (TGAC) in Norwich. This represents the second E. huxleyi strain to be fully sequenced and provides a rich resource for understanding genome evolution and adaptation in coccolithophores through comparison to the fully sequenced genome of another strain, CCMP1516. The aim of this studentship is to identify genomic differences between strains and to link them with ecology and evolution. Both strains have very different phenotypes: CCMP1516 is a weakly calcifying and non-flagellated diploid cell originating from the tropical ocean whereas RCC1217 is the non-calcifying flagellate haploid cell originating from a heavily calcified diploid strain RCC1216 from temperate waters. These phenotypic differences appear to reflect differences in both gene regulation and gene content. A recent comparison of strains using expressed sequence tags (ESTs) already indicated important regulator genes that vary in expression and even presence between strains, including Myb transcription factors and histones (von Dassow et al. 2009). We assume that these regulator genes may represent strain-specific gene networks that might be important to understand how evolution has shaped their phenotypes. Workpackage 1 of this studentship aims to identify significant differences (e.g. insertions/deletions, genomic rearrangements, SNPs) between the genomes of both strains in collaboration with bioinformaticians at TGAC. Workpackage 2 will select key regulator genes, which are strain specific and/or show a significant response (differential gene expression) to different environmental conditions (e.g. N-, Fe-limitation, high-light stress, temperature stress, ocean acidification). A protocol for chromatin immunoprecipitation with massively parallel DNA sequencing (Chip-Seq) will be established for some of these regulatory genes to identify binding sites for the reconstruction of genetic networks involved in evolution and adaptation to important environmental conditions including ocean acidification.

This studentship project will be conducted with two major partners: 1) TGAC in Norwich and 2) Prof. Peter von Dassow (School of Biological Sciences, Pontificia Universidad Católica de Chile). The ideal candidate for this studentship project is expected to have strong interests in comparative genomics, bioinformatics, evolution and physiology.

Von Dassow et al. (2009) Transcriptome analysis of functional differentiation between haploid and diploid cells of Emiliania huxleyi, a globally significant photosynthetic calcifying cell. Genome Biology, 10:R114