YIA-PGR: Tools for Plant Comparative Genomics

模型系统的多样性为应用比较和系统发育方法解决植物功能基因组学中的问题提供了挑战和机遇。为了描述由已知系统发育相关的多种生物的生物序列和图谱的特征，需要新的方法，而不是在忽略系统发育结构的多种生物之间进行简单的成对比较或“扁平”比较。本研究侧重于系统基因组学的两个测试应用：(1)鉴定基因家族中定义特定谱系的保守基序和残基；(2)沿着系统发育重建基因组重排事件，以便能够预测稀疏采样基因组中的基因内容和顺序。由于所提出的一些方法是计算密集型的，并且需要整合来自各种公共来源的数据，因此这项工作是由一个名为Phytome的在线植物系统基因组学数据库的开发所补充的。与生物科学少数民族发展伙伴关系合作，开发了基于探究的K-12教育模块，并通过移动科学教学实验室向北卡罗来纳州的目标公立学校提供。有关我们的植物基因组计划的所有可交付成果的信息将发布在以下网址：http://www.phytome.org

The diversity of model systems presents both challenges and opportunities for applying comparative and phylogenetic approaches to questions in plant functional genomics. New methodologies are needed in order to describe features of biological sequences and maps across multiple organisms that are related by a known phylogeny, as opposed to making either simple pair-wise comparisons or 'flat' comparisons among multiple organisms that ignore the presence of phylogenetic structure. This research focuses on two test applications of phylogenomics: (1) identifying conserved motifs and residues that define particular lineages within a gene family and (2) reconstructing genome rearrangement events along a phylogeny in such a way as to be able to predict gene content and order in sparsely sampled genomes. Because some of the methodology proposed is computationally intensive and requires the integration of data from a variety of public sources, this work is complemented by the development of an online plant phylogenomics database called Phytome. In collaboration with the Partnership for Minority Advancement in the Biosciences, an inquiry-based K-12 educational module is developed and delivered to targeted public schools in North Carolina through a mobile science teaching laboratory. Information regarding all the deliverables for our Plant Genome Project willbe posted at the following URL:http://www.phytome.org