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

加州大学基因组研究所(TIGR)的Naomi Ward博士、Jonathan Eisen博士和Karen Nelson博士分别获得了确定主要细菌门(群)之间和内部进化关系的赠款。这将通过获得和解释来自七八个不同细菌群体成员的完整基因组序列来实现，这些不同的细菌群体在目前的基因组测序工作中没有代表。为了对每个基因组进行测序，DNA将被分解成片段，并随机确定片段的DNA序列。产生的单个序列将使用识别不同序列之间重叠的计算机软件组装成一部分。序列中剩下的任何空白都将被填补，以产生一个完整的基因组。然后将与现有的基因组数据库进行比较，以确定存在的基因。该项目的后期阶段将涉及以实验室为基础的研究，以确认已测序基因的功能。其中一些基因将被确定为潜在的系统发育标记--对衡量生物之间的进化关系特别有用的基因。不同细菌群体之间的进化关系将使用从单个系统发育标记和全基因组分析推断的进化树来确定，全基因组分析考虑基因组中所有基因的存在或不存在。虽然细菌的大小很小，但它包括地球上最古老和最多样化的生命形式。因此，了解它们的进化史是NSF组装生命树计划的关键组成部分。预计该项目的结果将对科学界产生深远影响。对细菌多样性的更完整的表示将提供关于细菌内部进化关系的更清晰的图景，以及特定特征(例如光合作用、在高温下生存的能力或在没有氧气的情况下生存的能力)是如何进化的。通过公开基因组序列数据以及向学生和科学界其他成员提供基因组分析培训，将促进对未被研究的细菌群体的研究。

Drs Naomi Ward, Jonathan Eisen, and Karen Nelson of The Institute for Genomic Research (TIGR), University of California, and Howard University, respectively, 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.