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

分别来自加州大学和霍华德大学基因组研究所（TIGR）的内奥米·沃德博士、乔纳森·艾森博士和凯伦·纳尔逊博士获得了一项研究经费，以确定细菌主要门（群）之间和内部的进化关系。这将通过获取和解释当前基因组测序工作中未代表的7或8种不同细菌群的完整基因组序列来实现。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。所得到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个整体。序列中留下的任何空白将被填补，从而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包括实验室研究，以确认测序基因的功能。其中一些基因将被确定为潜在的系统发育标记-这些基因对测量生物体之间的进化关系特别有用。不同细菌群之间的进化关系将通过从个体系统发育标记推断的进化树和考虑基因组中所有基因存在与否的全基因组分析来确定。虽然细菌的体积很小，但它包含了地球上最古老、最多样化的生命形式。因此，了解它们的进化历史是美国国家科学基金会“组装生命之树”项目的关键组成部分。这个项目的成果预计将对科学界产生深远的影响。对细菌多样性的更完整的描述将为细菌内部的进化关系提供更清晰的画面，以及特定特征（例如光合作用、在高温下生存的能力或无氧生存的能力）是如何进化的。通过公开基因组序列数据，以及为学生和科学界的其他成员提供基因组分析方面的培训，将刺激对未被充分研究的细菌群的研究。

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.