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农作物受损的主要原因，对粮食安全具有相当大的经济影响和后果。由于人口增长、富裕程度的提高和饮食结构的改变，全球对食品的需求正在上升。在典型的种植年中，由于病原微生物感染引起的田间产量损失很少低于 5%，更常见的是 10-15%。近年来，通过应用高通量技术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。 PhytoPath 是一种资源，旨在捕获来自植物病原物种的广泛分子信息，并将其与有关感染过程的描述性信息相结合，包括更具体的分子信息，例如关于感染过程中相互作用的病原体和宿主蛋白以及相互作用结果的表型。以前关于病原体基因组、基因表达模式和潜在相互作用伙伴的新知识是使用 Ensembl 平台存储的。 Ensembl 包含一套用于管理和显示基因组规模数据的综合软件。后者关于每个致病物种致病能力所需的实验验证基因的新表型知识由科学界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 资金更新的申请（于 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菌植物病原体（以及有关人群范围多态性的相关数据），部署新的社区管理工具，并改进资源内进行比较分析的设施。例如，已发布的 RNA seq 数据将用于预测新的基因模型并修改现有的基因模型，但通过部署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。用户将使用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，该项目涉及具有不同致病能力、宿主基因型范围和/或产生不同有害物质的能力的单一物种的其他菌株霉菌毒素/代谢物。对表型信息的新管理将增加有关病原体产生的小效应蛋白库与其在作物宿主内的初始目标之间的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。还将提供简单的可视化工具来显示蛋白质伙伴关系以及新兴的路径部分和本地网络“中心”。我们打算捕获大约 200 种致病物种的分子和表型信息，这些物种在谷物和非谷物物种中具有广泛的致病生活方式。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）术语的使用将逐渐引入管理过程。我们将继续与该领域大型活跃的英国研究界合作，了解他们的新要求，并通过特定 PhytoPath 团队成员的重点研讨会和大学/研究所访问来满足他们当前的需求。该资源还将服务于日益关注相同科学和社会问题的更大的全球学术界、工业界和政府界。

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: http://dx.10.1093/gbe/evx030
• 发表时间: 2017
• 期刊: Genome biology and evolution
• 作者: Derbyshire M

RNAseq reveals hydrophobins that are involved in the adaptation of Aspergillus nidulans to lignocellulose.

RNAseq 揭示了参与构巢曲霉对木质纤维素的适应的疏水蛋白。

• DOI: http://dx.10.1186/s13068-016-0558-2
• 发表时间: 2016
• 期刊: Biotechnology for biofuels
• 作者: Brown NA

Fungal Biomolecules - Sources, Applications and Recent Developments

真菌生物分子 - 来源、应用和最新进展

• DOI: http://dx.10.1002/9781118958308.ch19
• 发表时间: 2015
• 作者: Brown N

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: http://dx.10.1016/j.foodchem.2017.06.113
• 发表时间: 2018
• 期刊: Food chemistry
• 影响因子: 8.8
• 作者: Curtis TY

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

天然植物胁迫诱导子顺式茉莉酮会导致臭虫生长的品种依赖性减少，以及大豆中黄酮类化合物浓度的相关变化

• DOI: 10.1016/j.phytochem.2016.08.013
• 发表时间: 2016-11-01
• 期刊: Phytochemistry
• 影响因子: 3.8
• 作者: J. P. da Graça;T. E. Ueda;T. Janegitz;S. S. Vieira;Mariana C. Salvador;M. D. de Oliveira;S. Zingaretti;S. Powers;J. Pickett;M. Birkett;C. B. Hoffmann
• 通讯作者: C. B. Hoffmann