Microbial Genome Sequencing: High-Resolution Phylogenomics of Halophilic Archaea

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Halophilic archaea share the common ability to live in hypersaline environments (typically in excess of 3M NaCl) but also possess a diverse set of metabolic activities, some of which have already found their way into biotechnological applications. Several members of the archaeal family Halobacteriaceae are being fully sequenced by Dr. Facciotti (UC Davis) and collaborators Dr. Eisen (UC Davis) and postdoc scholar Dr. Darling to advance our understanding of genome organization and evolution of microbial genomes and to provide a foundation for systems biology efforts to experimentally query novel aspects of microbial biochemistry, physiology, metabolism, development and cellular biology. The critical aspect to this study is that these genome sequences will provide sufficient coverage of this phylogenetic family (both in breadth and depth) so that comparative studies on the organization of genomes and the exchange and reshuffling of genetic information will become possible. Because the organisms proposed for sequencing have adapted for life in hypersaline environments, the development of these as model systems will also directly shape our understanding of salt tolerance, an issue that continues to be of great relevance in the development of salt and drought resistant food crops. The PIs also intend to address whether the biological species concept can be applied to archaea. The project will also investigate archaeal DNA replication, which shares aspects with both eukaryotic and prokaryotic genome replication, and genome organization. Since halophiles are excellent model systems for classroom use, the PIs intend to develop a new educational module with high school teachers and students to learn genome sequence analysis. The PIs will make this module freely available via www.halophiles.org.