ATOL: Phylogenomics:A Genome Level Approach to Assembling the Bacterial Branches of the Tree of Life

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ABSTRACTDEB-0228651Drs Naomi Ward, Jonathan Eisen, and Karen Nelson of The Institute for Genomic Research (TIGR) have been awarded a grant to determine the evolutionary relationships between and within the major phyla (groups) of Bacteria. This will be achieved by obtaining and interpreting complete genome sequences from members of seven or eight diverse bacterial groups that are not represented in current genome sequencing efforts. To sequence each genome, DNA will be broken into fragments and the DNA sequence of the fragments determined randomly. The resulting individual sequences will be assembled into one piece using computer software that recognizes overlaps between the different sequences. Any gaps left in the sequence will be filled in to produce a completed genome. Comparisons will then be made with existing genome databases, to identify the genes present. A later stage of the project will involve lab-based studies to confirm the function of the sequenced genes. Some of these genes will be identified as potential phylogenetic markers - genes that are especially useful for measuring the evolutionary relationships between organisms. The evolutionary relationships between the different bacterial groups will be determined using evolutionary trees inferred from both individual phylogenetic markers, and whole-genome analyses which consider the presence or absence of all the genes in the genome. While microscopic in size, Bacteria include the oldest and most diverse forms of life on Earth. Accordingly, understanding their evolutionary history is a critical component in the NSF's Assembling the Tree of Life program. The results of this project are expected to have far-reaching impacts on the scientific community. A more complete representation of bacterial diversity will provide a clearer picture of evolutionary relationships within the Bacteria, and how specific characteristics (e.g., photosynthesis, the ability to live at high temperatures, or to live without oxygen) evolved. Research on understudied bacterial groups will be stimulated by making the genome sequence data publicly available, as well as by providing training in genome analysis to students and other members of the scientific community.