A Plant Genome Duplication Database

格鲁吉亚大学获得了一笔拨款，用于开发一套计算工具，帮助研究人员了解开花植物（被子植物）单个基因和整个基因组的复制。被子植物基因组序列的迅速发展为研究基因和基因组复制的功能和进化后果提供了基础，也为推断特定基因之间的其他神秘关系提供了手段。由于被子植物全基因组重复频率高和重复基因的持续存在，现有的基因组比较算法在很大程度上是不够的。该项目将扩展一种新方法（MCScan）的功能，用于在这种基因组复制（旁系同源丰富的基因组）内和之间进行比对，将基因同源性和基因共线性的元素结合起来，以区分直系同源和旁系同源。基于统一标准的被子植物基因组内和基因组间比对的免费在线可用性对比较基因组学至关重要。该研究将采用新的计算方法，并尽可能多地采样分类多样性，以减少谱系特定进化限制的影响。产品（结果）将通过植物基因组复制数据库（PGDD）提供给生物科学研究界，扩大了试点实施的功能，以更好地与其他几个相关资源对接，并加快对特定基因的精细研究（直系同源物与近缘同源物检测）。更好地了解被子植物之间的关系（开花植物）基因和基因组承诺（1）通过提供来自理想分类群的丰富的精心整理的数据集并基于统一的分析标准，授权新的计算机模拟和经验研究，以推进对基因组复制在高等真核生物进化中所起的核心作用的认识;阐明被子植物的进化历史，并为翻译基因组学提供坚实的基础，利用来自树冠植物模型的来之不易的结构和功能基因组信息来剖析许多其他生物体的特定进化新奇性。该项目有助于教育本科生和研究生，并包括教师实习计划。这个项目的教师在夏天花时间在实验室参加研究活动。有关该项目的更多信息可在http://www.plantgenome.uga.edu上找到。

The University of Georgia has been awarded a grant to develop a set of computational tools to help researchers understand the duplication of individual genes and entire genomes of flowering plants (angiosperms). The burgeoning set of angiosperm genome sequences provide the foundation for a host of investigations into the functional and evolutionary consequences of gene and genome duplication, as well as the means to deduce otherwise-cryptic relationships among particular genes. Existing algorithms for genome comparisons are largely inadequate for angiosperms due to the high frequency of whole-genome duplication and persistence of many duplicated genes. The project will extend the functionality of a new approach (MCScan) for alignment within and between such genome duplication (paralog-rich genomes), incorporating elements of both gene phylogeny and gene colinearity to distinguish between orthology and paralogy. The free online availability of intra- and inter-genome alignments for angiosperms from a single resource based on uniform standards that have been empirically validated is of utmost importance to comparative genomics. The research will employ new computational approaches and sampling as much taxonomic diversity as possible to reduce the impact of lineage-specific evolutionary constraints. Products (results) will be made available to the biological sciences research community via the Plant Genome Duplication Database (PGDD), with the functionality of a pilot implementation broadened to better interface with several other relevant resources and to expedite fine-scale studies of specific genes (ortholog versus paralog detection).Better understanding of the relationships among angiosperm (flowering plant) genes and genomes promises (1) to empower new in silico and empirical studies to advance knowledge of the central role played by genome duplication in evolution of higher eukaryotes, by providing a wealth of well-groomed data sets from an ideal taxon and based on uniform analytical standards; and (2) to clarify angiosperm evolutionary history and provide a firm foundation upon which to base translational genomics, the leveraging of hard-won structural and functional genomic information from crown botanical models to dissect specific evolutionary novelties in many additional organisms.The project helps to educate undergraduate and graduate students and includes a teacher internship program. Teachers in this program spend time in the summer in the lab participating in research activities. Additional information about the project may be found at http://www.plantgenome.uga.edu.