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

• 批准号: BB/I001077/1
• 负责人: Paul Kersey
• 金额: $ 55.25万
• 依托单位: European Bioinformatics Institute
• 依托单位国家: 英国
• 项目类别: Research Grant
• 财政年份: 2010
• 资助国家: 英国
• 起止时间: 2010 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=BB%2FI001077%2F1
• 关键词: PhytoPath; integrated; resource; comparative; phytopathogen

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.

粮食安全已成为人类在21世纪世纪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冲突的需求，以及东亚和东南亚对粮食需求的飙升，这些因素加在一起，将粮食价格推高至多年来的最高水平。农作物生产力的一个重要制约因素是病害，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个巨大的成本。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，包括它们所危害的植物）越来越多地通过使用高通量，自动化的实验方法，产生大量的数据进行研究。十多年来，确定完整基因组的序列（即决定一个物种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（从而允许对人口进行抽样以确定其特征）。技术上的类似改进增加了描述基因和蛋白质在各种实验条件下表达的数据量。然而，虽然公共知识库存在某些类型的这些新的实验数据，有没有综合资源，统一这些，以促进他们的解释。如果没有这样的资源，（最坏的情况下）就有可能丢失新技术产生的数据;或者，每一位希望利用这些数据的科学家都必须冗长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、最新的数据集几乎是一个不可能的挑战，而且会分散他们对利用这些信息解决真实的科学问题的注意力。Ensembl软件平台包括一套用于分析、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的基因组变异以及物种之间的进化比较的模块。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兴趣增加以及随之而来的病原体高通量数据的增加。PhytoPath将由欧洲领先的生物信息服务中心EBI管理，但将从英国植物病原体研究社区成员那里获得科学指导，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界面访问宿主、病原体（和载体）基因组的令人兴奋的前景。特别地，这将促进新型资源的开发，将宿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）相关联。目前植物病害表型的主要资源是由Rothamsted Research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接口，用于监督PHI-基地的社区管理，并将PHI-基地紧密整合到PhytoPath中，以确保可以在其基因组背景下研究病原体表型。

项目成果

PHI-base in 2022: a multi-species phenotype database for Pathogen-Host Interactions.

• DOI: 10.1093/nar/gkab1037
• 发表时间: 2022-01-07
• 期刊: Nucleic acids research
• 影响因子: 14.9
• 作者: Urban M;Cuzick A;Seager J;Wood V;Rutherford K;Venkatesh SY;Sahu J;Iyer SV;Khamari L;De Silva N;Martinez MC;Pedro H;Yates AD;Hammond-Kosack KE
• 通讯作者: Hammond-Kosack KE

Ribosomic DNA intergenic spacer 1 region is useful when identifying Candida parapsilosis spp. complex based on high-resolution melting analysis

核糖体 DNA 基因间间隔区 1 区域在鉴定近平滑念珠菌属时非常有用。

• DOI: 10.1093/mmy/myu009
• 发表时间: 2014
• 期刊: Medical Mycology
• 影响因子: 2.9
• 作者: Gago S

Ensembl Genomes 2013: scaling up access to genome-wide data.

• DOI: 10.1093/nar/gkt979
• 发表时间: 2014-01
• 期刊: Nucleic acids research
• 影响因子: 14.9
• 作者: Kersey PJ;Allen JE;Christensen M;Davis P;Falin LJ;Grabmueller C;Hughes DS;Humphrey J;Kerhornou A;Khobova J;Langridge N;McDowall MD;Maheswari U;Maslen G;Nuhn M;Ong CK;Paulini M;Pedro H;Toneva I;Tuli MA;Walts B;Williams G;Wilson D;Youens-Clark K;Monaco MK;Stein J;Wei X;Ware D;Bolser DM;Howe KL;Kulesha E;Lawson D;Staines DM
• 通讯作者: Staines DM

Ensembl Genomes: an integrative resource for genome-scale data from non-vertebrate species.

• DOI: 10.1093/nar/gkr895
• 发表时间: 2012-01
• 期刊: Nucleic acids research
• 影响因子: 14.9
• 作者: Kersey PJ;Staines DM;Lawson D;Kulesha E;Derwent P;Humphrey JC;Hughes DS;Keenan S;Kerhornou A;Koscielny G;Langridge N;McDowall MD;Megy K;Maheswari U;Nuhn M;Paulini M;Pedro H;Toneva I;Wilson D;Yates A;Birney E
• 通讯作者: Birney E

Ensembl BioMarts: a hub for data retrieval across taxonomic space.

• DOI: 10.1093/database/bar030
• 发表时间: 2011
• 期刊: Database : the journal of biological databases and curation
• 作者: Kinsella RJ;Kähäri A;Haider S;Zamora J;Proctor G;Spudich G;Almeida-King J;Staines D;Derwent P;Kerhornou A;Kersey P;Flicek P
• 通讯作者: Flicek P