PhytoPath, an infrastructure for hundreds of plant pathogen genomes

PhytoPath，数百种植物病原体基因组的基础设施

• 批准号: BB/K020056/1
• 负责人: Kim Hammond-Kosack
• 金额: $ 54.91万
• 依托单位: Rothamsted Research
• 依托单位国家: 英国
• 项目类别: Research Grant
• 财政年份: 2014
• 资助国家: 英国
• 起止时间: 2014 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=BB%2FK020056%2F1
• 关键词: PhytoPath; infrastructure; hundreds; plant; pathogen

Pathogen-mediated disease is a major cause of damage to crops, with considerable economic impact and consequences for food security. Global demand for food is rising because of population growth, increasing affluence and changing diets. In a typical cropping year in each field yield losses through infections caused by pathogenic microbes are rarely below 5% and are more typically in the range 10-15%. In recent years, new possibilities for the study (and ultimately control) of pathogens have opened up through the application of high-throughput technologies for determining the molecular nature of life. These include genome sequencing, which reveals the genetic code that determines inherited properties of cells - and extends to monitoring the varied cellular contents at different stages of life. PhytoPath is a resource designed to capture broad molecular information from plant pathogenic species, and combine it with descriptive information about the process of infection, including more specific molecular information, e.g. about the pathogen and host proteins that interact during infection and the phenotype of the interaction outcome. The former new knowledge on pathogen genomes, patterns of gene expression and potential interacting partner is housed using the Ensembl platform. Ensembl contains a comprehensive suite of software for the management and display of genome-scale data. The latter new phenotypic knowledge on experimentally verified genes required for the disease causing abilities of each pathogenic species is curated by members of the scientific community into the Pathogen Host Interactions (PHI-base) database. New interfaces (within and between) both these resources support the joint querying and visualisation of genomic and phenotypic data.This is an application for a renewal of BBSRC funding (which commenced in late 2010). We propose expanding the resource, scaling it up to handle hundreds of fungal and oomycete phytopathogens (and associated data about population-wide polymorphisms), deploying new tools for community curation, and improving the facilities for comparative analysis from within the resource. For example, published RNA seq data will be used to predict new gene models and modify existing ones, but by deployment of a new tool for community-curation of gene models further expert revisions can be captured. Tools will be in place for the users to compare the reference genome of each species with the datasets arising from genome re-sequencing projects involving additional strains of a single species with different disease causing abilities, host genotype ranges and / or ability to produce different harmful mycotoxins/metabolites. A new curation focus on the phenotypic information will increase the details recorded about the molecular interactions between the repertoires of small effector proteins produced by pathogen and their initial targets within the crop hosts. New links will be provided allowing users to move freely between the genomes of both plant and pathogen. Also simple visualisation tools will be provide to display protein partnerships, and emerging sections of pathways and local network 'hubs'. We intend to capture molecular and phenotypic information on ~200 pathogenic species with a wide range of pathogenic lifestyles in cereal and non-cereal species. This will further increase the power of comparative analyses and evolutionary studies. The use of the existing pathogen associated microbe gene ontology (PAMGO) terms will gradually be introduced into the curation process. We will continue to engage with the large and active UK research community in this field, to find out their new requirements and to address their current needs through focussed workshops and University/Institute visits by specific PhytoPath team members. This resource will also serve the larger, global academic, industry and government based community increasingly concerned by the same scientific and societal problems.

病原体介导的疾病是造成作物损害的一个主要原因，对粮食安全具有相当大的经济影响和后果。由于人口增长、财富增加和饮食变化，全球对粮食的需求正在上升。在一个典型的种植年里，每一块田地因病原微生物感染造成的产量损失很少低于5%，更典型的是在10-15%的范围内。近年来，通过应用高通量技术来确定生命的分子性质，为研究（并最终控制）病原体开辟了新的可能性。其中包括基因组测序，它揭示了决定细胞遗传特性的遗传密码，并扩展到监测生命不同阶段的不同细胞内容物。PhytoPath是一种资源，旨在从植物病原物种中获取广泛的分子信息，并将其与感染过程的描述性信息结合起来，包括更具体的分子信息，例如在感染过程中相互作用的病原体和宿主蛋白质以及相互作用结果的表型。前病原体基因组，基因表达模式和潜在的相互作用伙伴的新知识被安置使用Ensembl平台。Ensembl包含一套全面的软件，用于管理和显示基因组规模的数据。后一种新的表型知识，通过实验验证了每个致病物种致病能力所需的基因，由科学界的成员整理到病原体宿主相互作用（PHI-base）数据库中。这些资源内部和之间的新接口支持基因组和表型数据的联合查询和可视化。这是BBSRC基金续期的申请（2010年底开始）。我们建议扩大资源，扩大其规模以处理数百种真菌和卵霉菌植物病原体（以及有关群体范围内多态性的相关数据），部署新的社区管理工具，并改进资源内部的比较分析设施。例如，已发表的RNA序列数据将用于预测新的基因模型并修改现有的基因模型，但是通过部署一个用于基因模型社区管理的新工具，可以捕获进一步的专家修订。将为用户提供工具，将每个物种的参考基因组与基因组重测序项目产生的数据集进行比较，这些数据集涉及具有不同致病能力、宿主基因型范围和/或产生不同有害真菌毒素/代谢物的能力的单一物种的其他菌株。对表型信息的新关注将增加对病原体产生的小效应蛋白及其在作物寄主内的初始靶标之间分子相互作用的详细记录。将提供新的链接，允许用户在植物和病原体的基因组之间自由移动。此外，还将提供简单的可视化工具来显示蛋白质伙伴关系，以及路径和局部网络“枢纽”的新兴部分。我们打算在谷物和非谷物物种中捕获大约200种具有广泛致病生活方式的致病物种的分子和表型信息。这将进一步增强比较分析和进化研究的力量。现有病原体相关微生物基因本体（PAMGO）术语的使用将逐步引入管理过程。我们将继续与该领域的大型和活跃的英国研究团体合作，通过特定PhytoPath团队成员的重点研讨会和大学/研究所访问，找出他们的新需求，并解决他们当前的需求。这一资源也将服务于更大的、全球性的学术界、工业界和以政府为基础的社区，这些社区越来越关注同样的科学和社会问题。

项目成果

The complete genome sequence of the phytopathogenic fungus Sclerotinia sclerotiorum reveals insights into the genome architecture of broad host range pathogens.

植物病原真菌核盘菌的完整基因组序列揭示了对广泛宿主范围病原体的基因组结构的见解。

• DOI: 10.1093/gbe/evx030
• 发表时间: 2017-03
• 期刊: Genome biology and evolution
• 影响因子: 3.3
• 作者: Derbyshire M;Denton-Giles M;Hegedus D;Seifbarghy S;Rollins J;van Kan J;Seidl MF;Faino L;Mbengue M;Navaud O;Raffaele S;Hammond-Kosack K;Heard S;Oliver R
• 通讯作者: Oliver R

Effects of variety, year of cultivation and sulphur supply on the accumulation of free asparagine in the grain of commercial wheat varieties.

品种、种植年份和硫供应量对商品小麦品种籽粒中游离天冬酰胺积累的影响。

• DOI: 10.1016/j.foodchem.2017.06.113
• 发表时间: 2018-01-15
• 期刊: Food chemistry
• 影响因子: 8.8
• 作者: Curtis TY;Powers SJ;Wang R;Halford NG
• 通讯作者: Halford NG

The natural plant stress elicitor cis-jasmone causes cultivar-dependent reduction in growth of the stink bug, Euschistus heros and associated changes in flavonoid concentrations in soybean, Glycine max.

• DOI: 10.1016/j.phytochem.2016.08.013
• 发表时间: 2016-11
• 期刊: Phytochemistry
• 影响因子: 3.8
• 作者: da Graça JP;Ueda TE;Janegitz T;Vieira SS;Salvador MC;de Oliveira MC;Zingaretti SM;Powers SJ;Pickett JA;Birkett MA;Hoffmann-Campo CB
• 通讯作者: Hoffmann-Campo CB

The trans-kingdom identification of negative regulators of pathogen hypervirulence.

• DOI: 10.1093/femsre/fuv042
• 发表时间: 2016-01
• 期刊: FEMS microbiology reviews
• 影响因子: 11.3
• 作者: Brown NA;Urban M;Hammond-Kosack KE
• 通讯作者: Hammond-Kosack KE