Horizontal gene transfer and among phyla relationships

水平基因转移和门之间的关系

• 批准号: 0830024
• 负责人: Johann Peter Gogarten
• 金额: $ 250万
• 依托单位: University of Connecticut
• 依托单位国家: 美国
• 项目类别: Continuing Grant
• 财政年份: 2009
• 资助国家: 美国
• 起止时间: 2009-01-01 至 2014-12-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=0830024&HistoricalAwards=false
• 关键词: Horizontal; gene; transfer; among; phyla

A tree has been the organizing image to explain the relationships among living creatures since before Darwin's explanations for natural descent. The modern practice of comparing DNA and protein sequences to discern these relationships, however, has revealed complexities in the process of descent never before imagined. Organisms, particularly microbes, evolve by horizontal as well as vertical inheritance of traits with different groups of organisms exchanging genes, in addition to passing them down to the next generation. This research project addresses the question: Can the large scale structure of the tree/web of life be discerned? While the current data may be interpreted to mean that the depiction of life's history as a single bifurcating tree is incomplete, this should not be seen as justification to give up on reconstructing life's history. The working hypothesis underlying this research is that a reconstruction of life's early history is indeed possible, provided care is taken to guard against artifacts and that new, informative molecular characters are added to the analyses. Four complementary approaches will be used to address the question through analyses of microbial genome sequences. (1) Genome sequence data will be examined to find ancient horizontal gene transfer events that created useful taxonomic characters. An automated genome analysis pipeline will be developed to find these events, and these characters will be incorporated into new examinations of evolutionary relationships. (2) Complete genome sequences allow comparisons of all the genes of an organism with those of others to measure their evolutionary relatedness. However, the impact of horizontal acquisition of genes on these analyses is unknown. Computer simulations and genome sequences from two unrelated groups of microbes that have undergone extensive horizontal gene transfer, the Haloarchaea and the Thermotogales, will be used to gauge the extent to which different phylogenomic approaches are impacted by highways of gene sharing between different groups of organisms. (3) A public database will be constructed to store information on all putatively identified gene transfer events. This database will be a valuable resource for the wider scientific community to trace the role of gene transfer in the assembly of metabolic pathways and to examine the adaptation of organisms to new ecological niches. (4) The nature of the last common ancestor of all living creatures, the trunk of the tree of life, has been difficult to discern given all the changes in nucleotide composition that have occurred during evolutionary time. A compositional analysis will be used to detect the remaining signal of the genetic code's expansion that occurred early in life's history in order to "root" the tree of life. These in-depth analyses of several prokaryotic and eukaryotic genomes will offer insights into the impacts of horizontal gene transfer on genome evolution and phylogenetic reconstructions, as well as identify natural groups in the tree of life and help to resolve its deep structure. Unraveling the structure of the tree of life will have percussions in all fields of biology.This research program and its associated education activities will provide an ideal training ground in which high school, undergraduate, and graduate students along with postdoctoral fellows can learn about genome and organismal evolution. Plans are for three postdoctoral fellows, nine graduate students, and about twenty undergraduate and high school students to be trained through computational and laboratory research experiences. The goal is to train computer scientists and biologists to become experts in their respective disciplines and to become effective in trans-disciplinary communication; thereby enabling successful interdisciplinary collaborations. Results from the proposed research will be introduced into related courses on three campuses and will be accessible through an integrated database, which also includes a forum for public discussions on topics related to gene transfer and organismal evolution.

在达尔文对自然血统的解释之前，树一直是解释生物之间关系的组织图像。然而，通过比较DNA和蛋白质序列来辨别这些关系的现代实践揭示了人类进化过程中前所未有的复杂性。生物体，特别是微生物，通过水平和垂直遗传特征进化，不同的生物体群体交换基因，除了将它们传递给下一代。这个研究项目解决了一个问题：生命树/网络的大规模结构可以被识别吗？虽然目前的数据可能会被解释为意味着生命的历史作为一个单一的分叉树的描述是不完整的，这不应该被视为放弃重建生命的历史的理由。这项研究的工作假设是，重建生命的早期历史确实是可能的，只要注意防范人工制品，并在分析中添加新的，信息丰富的分子特征。将通过分析微生物基因组序列，采用四种互补方法来解决这一问题。(1)基因组序列数据将被检查，以找到古老的水平基因转移事件，创造有用的分类特征。将开发一个自动化的基因组分析管道来发现这些事件，这些特征将被纳入对进化关系的新检查中。(2)完整的基因组序列允许将一个生物体的所有基因与其他生物体的基因进行比较，以衡量它们的进化相关性。然而，水平获取基因对这些分析的影响是未知的。计算机模拟和基因组序列从两个不相关的群体的微生物，已经经历了广泛的水平基因转移，盐古菌和Thermotogales，将被用来衡量不同的基因组方法的影响程度的公路之间的基因共享不同的生物体。(3)将建立一个公共数据库，以储存所有经鉴定的基因转移事件的信息。该数据库将成为更广泛的科学界的宝贵资源，以追踪基因转移在代谢途径组装中的作用，并研究生物体对新生态环境的适应。(4)所有生物的最后一个共同祖先，生命之树的树干，由于进化过程中发生的核苷酸组成的所有变化，很难辨别。成分分析将用于检测生命历史早期发生的遗传密码扩展的剩余信号，以便“扎根”生命之树。这些对几个原核和真核基因组的深入分析将深入了解水平基因转移对基因组进化和系统发育重建的影响，以及确定生命树中的自然群体，并帮助解决其深层结构。解开生命之树的结构将在生物学的所有领域产生影响。本研究计划及其相关的教育活动将提供一个理想的培训场所，高中生，本科生和研究生沿着博士后研究员可以学习基因组和生物进化。计划是三个博士后研究员，九名研究生，约20名本科生和高中生通过计算和实验室研究经验进行培训。目标是培养计算机科学家和生物学家成为各自学科的专家，并在跨学科交流中发挥作用;从而实现成功的跨学科合作。拟议研究的结果将被引入三个校区的相关课程，并将通过一个综合数据库访问，该数据库还包括一个论坛，供公众讨论与基因转移和生物进化有关的主题。