PhytoPath: an integrated resource for comparative phytopathogen genomics

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、能源成本高企、生物燃料生产对作物生产的相互矛盾的需求，以及东亚和东南亚对粮食的需求飙升，这些因素共同推动粮食价格升至多年来的最高水平。病害是制约作物生产力的一个重要因素，每年造成10-20%的产量损失。此外，控制植物病害给农民带来了巨大的时间和资源成本。因此，制定可以低成本部署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。植物病原体（和其他物种，包括它们所折磨的植物）越来越多地通过使用高通量、自动化实验方法来研究，这些方法可以产生大量数据。十多年来，确定全基因组序列（即决定物种可遗传特征的所有信息）已经成为可能。最近，技术的进步大大降低了基因组测序的成本，并使确定单个基因组序列成为可能（从而允许对种群进行抽样以确定其特征）。技术上的类似改进增加了在各种实验条件下描述基因和蛋白质表达的数据量。然而，虽然这些新实验数据的某些类型存在公共存储库，但没有可用的综合资源来统一这些数据以促进其解释。在缺乏这种资源的情况下，（最坏的情况下）存在新技术产生的数据丢失的危险；或者，每个希望利用这些数据的科学家都必须繁琐而浪费地整合和纠正来自不同数据集的信息。对许多科学家来说，从不同的实验中确定一个连贯的、最新的数据体几乎是不可能的挑战，而且会分散他们对利用这些信息解决真正科学问题的挑战的注意力。Ensembl软件平台包括一套工具，用于分析、整合和显示来自完整基因组的数据。它包括处理个体间全种群基因组变异的模块，以及物种间的进化比较。该平台已被用于捕获包括脊椎动物和植物在内的许多物种的基因组。我们现在提议创建PhytoPath，这是一个基于Ensembl技术的新资源，用于从植物病原体基因组中捕获数据，以响应对食品安全的日益关注以及相关病原体高通量数据的增加。PhytoPath将由欧洲领先的生物信息学服务中心EBI运营，但将从英国植物病原体研究社区的成员那里获得科学指导，他们直接参与生产和利用这些数据。使用Ensembl平台不仅具有成本效益（利用已经开发的可用于其他环境的解决方案），而且还提供了通过公共接口访问宿主，病原体（和载体）基因组的令人兴奋的前景。特别是，这将有助于开发一种新型资源，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）联系起来。目前植物病害表型的主要资源是病原-宿主相互作用数据库（PHI-base），由洛桑研究所维护。我们将开发一个新的接口，用于ph -base的监督社区管理，并将ph -base紧密集成到PhytoPath中，以确保病原体表型可以在其基因组背景下进行研究。

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.