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、能源成本居高不下、生物燃料生产对作物生产的需求相互矛盾，以及东亚和东南亚对粮食的需求不断飙升，这些因素共同将粮食价格推高至多年来的最高水平。作物生产力的一个重要制约因素是病害，每年造成10%-20%的产量损失。此外，控制植物病害对农民来说在时间和资源上都是一项巨大的成本。因此，制定可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(以及其他物种，包括它们所危害的植物)的研究越来越多地通过使用产生大量数据的高通量、自动化的实验方法来进行。十多年来，确定完整基因组序列(即决定一个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采样以确定其特征)。技术上的类似改进也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，虽然存在某些类型的新实验数据的公共存储库，但没有可用的综合资源来统一这些数据以便于解释。在没有这种资源的情况下，(在最坏的情况下)新技术产生的数据有丢失的危险；或者，每一位希望利用这种数据的科学家都必须冗长而浪费地整合和更正来自不同数据集的信息。对于许多科学家来说，从不同的实验中确定一个连贯的、最新的数据体几乎是一个不可能的挑战，而且会分散人们对使用这些信息解决真正的科学问题这一挑战的注意力。EnSembl软件平台包括一套用于分析、集成和显示来自完整基因组的数据的工具。它包括处理种群范围内个体间基因组变异的模块，以及物种之间的进化比较。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，以应对人们对食品安全的日益关注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，但它的科学方向将来自英国植物病原体研究社区的成员，他们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(利用已经开发用于其他环境的解决方案)，而且还提供了通过一个公共接口提供对宿主、病原体(和媒介)基因组的访问的令人兴奋的前景。特别是，这将有助于开发一种新类型的资源，将寄主和病原体中的表型(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来源是由Rothamsted Research维护的病原体-寄主相互作用数据库(PHI-BASE)。我们将开发一个新的接口来监督PHI-BASE的社区管理，并将PHI-BASE紧密地整合到PhytoPath中，以确保可以在其基因组环境中研究病原体的表型。

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.