PhytoBacExplorer: A Phylogenomic Resource for the Phytobacterial Community

感染植物的细菌种类繁多，可以通过空气、水和土壤传播，也可以通过昆虫或线虫等载体（携带它们的生物体）传播。当被引入新的地区时，它们的传播往往是高度侵入性的。细菌很难用化学品控制，而且经常能够感染大量的植物宿主。它们有可能对城乡景观和生态系统造成广泛而严重的经济、环境和社会影响。这些植物细菌可以迅速进化，最近的疫情表明，英国的经济和环境不断受到新出现的菌株的威胁，这些菌株侵染或感染我们的粮食作物、森林、花园、公园和苗圃。气候变化和贸易中可能受污染的植物材料的流动增加进一步加剧了这一情况。理想情况下，我们应该积极主动，及早发现构成风险的新变种，并采取措施限制其传播。然而，目前我们这样做的能力是有限的。对于感染人类的细菌，医学界已经从EnteroBase中受益匪浅，EnteroBase是一种用于处理和分析细菌DNA序列的计算系统。它被世界各地的实验室用于迅速确定疫情的原因，跟踪多国疫情，为迅速做出公共卫生决策提供信息，并随后在日益全球化的食物链中召回受污染的产品。我们将使用EnteroBase平台开发一个专门针对植物细菌的新系统“PhytoBacExplorer”。PhytoBacExplorer将首先针对前6种植物细菌病原体中的5种进行基因组测序，并开发连接以输入其他来源的相关数据。我们将提供策展，以确保丰富，一致和高质量的数据，包括地理信息，宿主范围和致病性基因。该系统将继承EnteroBase的许多有用功能，包括处理原始数据，识别群体中共享的“核心”基因组，基于核心基因组识别系统发育（祖先）树，以及强大的交互式可视化。我们将根据社区用户的参与度添加工具，包括基因家族进化分析工具，检测菌株组和宏基因组学能力之间功能差异的工具。用户可以上传原始测序数据，以便PhytoBacExplorer处理并整合完整的数据集。用户将了解他们的菌株是新物种还是以前观察到的，并可以识别它们可能的功能特征。这将能够监测正在进行的病原体演变，并大大减少花费在数据处理任务上的时间。用户将对系统的开发有投入：每月将有机会在在线会议室与项目团队交谈，访问在线教程，并将有会议演示。该项目有测序预算，以涵盖代表性差的种间分支。我们将在稍后的项目中包括更多的致病菌和有益菌。该系统将能够识别特定菌株的DNA序列，并能够更快地开发更精确的分子测试。这将极大地促进监管机构和植物健康领域的官员跟踪新的威胁环境，并有助于精准农业.PhytoBacExplorer将被设计为与未来的计算基础设施的互操作性.项目完成后，沃里克大学将通过生物信息学研究技术平台在硬件和维护支持方面继续提供支持。该系统将继续通过每日扫描公共数据库来自动扩展其数据库，并将在早期发现新出现的病原体以及未来对粮食安全的威胁方面发挥重要作用。

Bacteria that infect plants are diverse and can be transmitted via air, water, and soil, or via vectors (the organisms that carry them) like insects or nematodes. When introduced to new areas their spread is often highly invasive. Bacteria are difficult to control with chemicals and frequently able to infect a large number of plant hosts. They have the potential to cause widespread and severe economic, environmental and social impacts on landscapes and ecosystems, both rural and urban.These phytobacteria can evolve rapidly, and as is evident from recent outbreaks, the UK economy and environment are continually threatened by emerging strains that infest or infect our food crops, forests, gardens, parks and nurseries. This is further aggravated by climate change and greater movement of potentially contaminated plant materials by trade. Ideally, we should be proactive and identify new variants posing risks early and take measures to limit their spread. However, our ability to do so is currently limited.For bacteria that infect humans, the medical community has benefited immensely from EnteroBase, a computational system for processing and analysis of bacterial DNA sequences. It is used by labs around the world to promptly identify the causes of outbreaks, track multi-country outbreaks, inform prompt public health decision making and subsequent recall of contaminated products in increasingly global food chains. We will use the EnteroBase platform to develop "PhytoBacExplorer", a new system dedicated to plant bacteria.PhytoBacExplorer will initially target genome sequencing for 5 of the top-6 plant bacterial pathogens, and develop connections to feed in related data from other sources. We will provide curation to ensure rich, consistent, and high-quality data including geographic information, host ranges, and genes underlying pathogenicity. The system will inherit many useful features from EnteroBase, including processing of raw data, identification of the shared "core" genome in a population, identification of the phylogenetic (ancestry) tree based on core genomes, and powerful interactive visualisations. We will add tools based on community user engagement including tools for evolutionary analyses of gene families, tools to detect functional differences between groups of strains and metagenomics capacity.Users can upload raw sequencing data for PhytoBacExplorer to process and integrate with the full data set. Users will learn whether their strains are new species or have been previously observed, and can identify their likely functional characteristics. This will enable monitoring of ongoing pathogen evolution, and significantly reduce time spend on data processing tasks.Users will have input into the development of the system: there will be a monthly opportunity to talk with the project team in an online meeting room, access online tutorials, and there will conference presentations. The project has a budget for sequencing to cover poorly represented interspecific clades. We will include further pathogenic bacteria and beneficial bacteria later in the project. The system will enable identification of DNA sequences specific to particular strains and enable faster development of more precise molecular tests. This will greatly facilitate regulatory bodies and Plant Health field officers in tracking new threats to the environment, and contribute to precision agriculture.PhytoBacExplorer will be designed for interoperability with future computational infrastructure. After the project, it will be continually supported by the University of Warwick via the Bioinformatics Research Technology Platform in terms of hardware and maintenance support. The system will continue to grow its databases automatically by daily scans of public databases and will play an important role in enabling early detection of emerging pathogens and thus upcoming threats to food security.