PhytoPath: an integrated resource for comparative phytopathogen genomics

PhytoPath：比较植物病原体基因组学的综合资源

基本信息

批准号：
BB/I000488/1
负责人：
Kim Hammond-Kosack
金额：
$ 35.45万
依托单位：
Rothamsted Research
依托单位国家：
英国
项目类别：
Research Grant
财政年份：
2011
资助国家：
英国
起止时间：
2011 至无数据
项目状态：
已结题

来源：
https://gtr.ukri.org/projects?ref=BB%2FI000488%2F1
关键词：
PhytoPath integrated resource comparative phytopathogen

项目摘要

Food security has emerged as one of the most significant challenges for humankind in the 21st century. Food shortages, high energy costs, conflicting demands on crop production for biofuel generation and the soaring demand for food from east and south-east Asia are combining to drive food prices to their highest levels for many years. A significant constraint on crop productivity is disease, which accounts for 10-20% losses in yield every year. Controlling plant diseases furthermore represents a significant cost to farmers both in time and resources. The development of new durable disease control strategies that can be deployed at low cost therefore represents one of the best means of ensuring sustainable food production. Plant pathogens (and other species, including the plants they afflict) are increasingly studied through the use of high throughput, automated experimental approaches that generate large quantities of data. For over ten years, the determination of the sequence of complete genomes (that is, all the information that determines the heritable characteristics of a species) has been possible. More recently, advances in technology have reduced the costs of genome sequencing drastically, and made possible the determination of individual genome sequences (thus allowing the sampling of populations to determine their characteristics). Similar improvements in technology have increased the quantity of data produced describing the expression of genes and proteins in a variety of experimental conditions. However, while public repositories exist for certain types of these new experimental data, there is no integrative resource available that unifies these to facilitate their interpretation. In the absence of such a resource, there is (at worst) a danger that data generated by new technologies is lost; or alternatively that every scientist wishing to exploit such data has to tediously and wastefully integrate and correct information from different data sets. For many scientists, the determination of a coherent, up-to-date body of data from different experiments is a near-impossible challenge, and a distraction from the challenge of using such information to solve real scientific problems. The Ensembl software platform comprises a suite of tools for the analysis, integration and display of data from complete genomes. It includes modules for the handling of population-wide genome variation amongst individuals, and the evolutionary comparison between species. The platform has been used to capture genomes from many species including vertebrates and plants. We now propose creating PhytoPath, a new resource based on Ensembl technology to capture data from phytopathogen genomes, in response to the increased interest in food security and the concomitant increase in high throughput data available for pathogens of interest. PhytoPath will be run by the EBI, Europe's leading bioinformatics service centre, but will take its scientific direction from members of the UK phytopathogen research community, who are directly engaged in producing and exploiting these data. The use of the Ensembl platform is not only cost-effective (taking advantage of solutions already developed for use in other contexts), but also offers the exciting prospect of providing access to host, pathogen (and vector) genomes through a common interface. Particularly, this will facilitate the development of a new type of resource, correlating phenotype (i.e. the symptoms of pathogen-mediated disease) in with genotype (i.e. individual genome sequence) in both host and pathogen. The leading current resource for plant disease phentoypes is the pathogen-host interactions database (PHI-base), maintained by Rothamsted Research. We will develop a new interface for supervised community curation of PHI-base and integrate PHI-base tightly within PhytoPath to ensure that the pathogen phenotype can be studied in its genomic context.

粮食安全已成为21世纪人类面临的最重大挑战之一。粮食短缺、能源成本高昂、生物燃料生产对农作物生产的需求相互矛盾，以及东亚和东南亚对粮食需求的飙升，共同推动粮食价格升至多年来的最高水平。作物生产力的一个重要制约因素是疾病，每年造成 10-20% 的产量损失。此外，控制植物病害对农民来说意味着巨大的时间和资源成本。因此，制定能够以低成本实施的新的持久疾病控制战略是确保可持续粮食生产的最佳手段之一。人们越来越多地通过使用产生大量数据的高通量、自动化实验方法来研究植物病原体（和其他物种，包括它们所影响的植物）。十多年来，确定完整基因组的序列（即决定物种遗传特征的所有信息）已成为可能。最近，技术的进步极大地降低了基因组测序的成本，并使确定个体基因组序列成为可能（从而允许对群体进行抽样以确定其特征）。类似的技术进步增加了描述各种实验条件下基因和蛋白质表达的数据量。然而，虽然某些类型的新实验数据存在公共存储库，但没有可用的综合资源来统一这些数据以促进其解释。如果缺乏这样的资源，（在最坏的情况下）新技术生成的数据将面临丢失的危险；或者，每个希望利用这些数据的科学家都必须乏味且浪费地整合和纠正来自不同数据集的信息。对于许多科学家来说，确定来自不同实验的连贯的、最新的数据体几乎是不可能的挑战，并且会分散人们对使用此类信息解决实际科学问题的挑战的注意力。 Ensembl 软件平台包含一套用于分析、整合和显示完整基因组数据的工具。它包括用于处理个体之间的群体范围基因组变异以及物种之间的进化比较的模块。该平台已用于捕获包括脊椎动物和植物在内的许多物种的基因组。我们现在建议创建 PhytoPath，这是一种基于 Ensembl 技术的新资源，用于从植物病原体基因组中捕获数据，以响应人们对粮食安全日益增长的兴趣以及随之而来的可用于感兴趣病原体的高通量数据的增加。 PhytoPath 将由欧洲领先的生物信息学服务中心 EBI 运营，但其科学方向将接受英国植物病原体研究界成员的指导，这些成员直接参与生产和利用这些数据。 Ensembl 平台的使用不仅具有成本效益（利用已开发用于其他环境的解决方案），而且还提供了通过通用接口访问宿主、病原体（和载体）基因组的令人兴奋的前景。特别是，这将促进新型资源的开发，将宿主和病原体的表型（即病原体介导的疾病的症状）与基因型（即个体基因组序列）相关联。当前植物病害表型的主要资源是由洛桑研究中心维护的病原体-宿主相互作用数据库 (PHI-base)。我们将开发一个新的界面，用于 PHI-base 的监督社区管理，并将 PHI-base 紧密集成到 PhytoPath 中，以确保可以在其基因组背景下研究病原体表型。