BBR GenomeHubs - agile genome databasing for neglected organisms of agricultural, development and biodiversity importance

BBR GenomeHubs - 针对农业、发展和生物多样性重要性的被忽视生物体的敏捷基因组数据库

• 批准号: BB/R015325/2
• 负责人: Mark Blaxter
• 金额: $ 39.75万
• 依托单位: Wellcome Sanger Institute
• 依托单位国家: 英国
• 项目类别: Research Grant
• 财政年份: 2020
• 资助国家: 英国
• 起止时间: 2020 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=BB%2FR015325%2F2
• 关键词: BBR; GenomeHubs; agile; genome; databasing

Building the first draft of the human genome cost around £2.5 billion. New sequencing technologies mean the cost of resequencing a human has reduced over a million-fold. This reduction in cost also transforms genomics approaches to many other biological questions. Genomics is now commonly applied to diverse goals from crop and livestock improvement, through pathogen and parasite surveillance, to biodiversity assessment. Many research communities are now able to generate reference genomes for their target species, compare genomes across suites of related species and sequence many individuals of the same species to investigate how variation between genome sequences affects biology.With these benefits come the challenges of managing a deluge of data, of analysing the data to answer questions, and of making the data and results available to others. For raw sequence data deposition in "databases of record" (internationally-supported systems that collect, collate and store for posterity) is standard. However, many discoveries are based on intensively analysed data - raw sequence is "assembled" to predict the whole genome sequence, genes are predicted in this genome sequence, and their functions are inferred by a range of annotation tools. Capturing these analyses in databases of record is strongly encouraged, but is technically difficult. For a few species, researchers have developed dedicated genome exploration databases that collect and collate not only sequence but also annotation and functional data, and present it in a way that facilitates integration. These databases require considerable expertise and effort to set up, maintain and keep current with the latest scientific developments. Thus, for the majority of species, and especially species of interest to the developing world, dedicated databases do not exist and communities lack the resources to plug this gap.During a previous BBR project, we developed an approach to genome databasing, named GenomeHubs, that removes the barriers to creating and maintaining a dedicated genomics resource for any species group. We do this by greatly simplifying the process of importing data into, and hosting an instance of, the most comprehensive genome database platform, Ensembl. Using the carefully-engineered Ensembl system, we have developed tools that standardise data from diverse sources, run automated analyses, import analysis results back into the database and visualise the genome and annotations through a web interface. In this proposal we will develop GenomeHubs further to make it straightforward for researchers to run all the steps to assemble, annotate and run standard analyses on any genome or set of genomes and share these results with the wider community. We will add new analyses and visualisations and we will help users through collaboration and training in the setup and use of GenomeHubs.This application is being made in tandem with one to the BBSRC BBR Global Challenges Research Funding call, which will work with Lower and Middle Income Country (LMIC) scientists to develop and exploit GenomeHubs for their needs. Genomics is being increasingly applied to problems of the developing world, in particular improvement of crop plants and local farm animals, understanding and combating infectious disease, and biodiversity conservation. This project will work very closely with the GCRF GenomeHubs outreach project, bringing the technology to LMIC researchers and supporting their use of GenomeHubs. We will link research communities, promote data sharing and enhance the pooling of resources and understanding to solve shared problems. We will develop collaborations with key scientists in LMICs who will act as Ambassadors for GenomeHubs, and collaborate closely with LMIC researchers to develop new code, new visualisations and new analytic tools for GenomeHubs to meet their requirements.

建立人类基因组的初稿耗资约25亿英镑。新的测序技术意味着重新配置人的成本已降低了一百万倍以上。成本的降低还将基因组学方法转化为许多其他生物学问题。现在，基因组学通常应用于农作物和牲畜改善，通过病原体和寄生虫监测到生物多样性评估的潜水目标。现在，许多研究群落能够为其靶物种生成参考基因组，比较相关物种套件的基因组和同一物种的许多个体的序列，以研究基因组序列之间的变化如何影响生物学。这些好处带来了管理大量数据的挑战，分析数据以回答问题，以及将数据和结果提供给其他数据。对于“记录数据库”中的原始序列数据沉积（在国际支持的系统中收集，整理和存储后的后代）是标准的。但是，许多发现基于深入分析的数据 - 原始序列被“组装”以预测整个基因组序列，基因在该基因组序列中预测，并且它们的功能是通过一系列注释工具来推断的。强烈鼓励在记录数据库中捕获这些分析，但在技术上很困难。对于一些物种，研究人员开发了专门的基因组探索数据库，这些数据库不仅收集和收集序列，还收集注释和功能数据，并以促进整合的方式呈现它。这些数据库需要考虑专业知识和精力来建立，维护和保持最新的科学发展。对于大多数物种，尤其是发展中国家感兴趣的物种，专用数据库都不存在，社区缺乏填补这一差距的资源。在先前的BBR项目中，我们开发了一种命名为GenomeHubs的基因组数据库的方法，该方法命名为GenomeHubs，从而消除了创建和维持任何物种组的障碍。我们通过极大地简化将数据导入并托管最全面的基因组数据库平台Ensembl的实例的过程来做到这一点。使用精心设计的Ensembl系统，我们开发了工具，这些工具可以从潜水员来源进行标准化数据，运行自动分析，导入分析结果回到数据库中，并通过Web界面可视化基因组和注释。在此提案中，我们将进一步开发基因组知识，使研究人员直接运行对任何基因组或一组基因组组装，注释和进行标准分析的所有步骤，并与更广泛的社区共享这些结果。我们将添加新的分析和可视化，并将通过在基因组族的设置和使用方面协作和培训来帮助用户。这项应用程序与BBSRC BBR全球挑战研究资金呼吁一起进行，这将与中低收入国家（LMIC）科学家（LMIC）科学家合作，以开发和利用基因组的基因组，以满足其需求。基因组学越来越多地应用于发展中国家的问题，尤其是作物植物和当地农场动物的改善，理解和打击传染病以及生物多样性保护。该项目将与GCRF GenomeHubs Outreach项目紧密合作，将技术带给LMIC研究人员并支持他们对GenomeHubs的使用。我们将链接研究社区，促进数据共享并增强资源和理解的汇总，以解决共同的问题。我们将与LMIC的主要科学家建立合作，他们将充当GenomeHubs的大使，并与LMIC研究人员密切合作，以开发新的代码，新的可视化和新的分析工具，以满足基因组人的需求。

项目成果

The genome sequence of the Buff Ermine, Spilarctia lutea (Hufnagel, 1766).

• DOI: 10.12688/wellcomeopenres.19065.1
• 发表时间: 2023
• 期刊: Wellcome open research

The genome sequence of the Common Plume moth, Emmelina monodactyla (Linnaeus, 1758)

普通羽蛾 Emmelina monodactyla 的基因组序列（Linnaeus，1758）

• DOI: 10.12688/wellcomeopenres.19035.1
• 发表时间: 2023
• 期刊: Wellcome Open Research
• 作者: Boyes D

The genome sequence of the Burnished Brass, Diachrysia chrysitis (Linnaeus, 1758).

• DOI: 10.12688/wellcomeopenres.18990.1
• 发表时间: 2023
• 期刊: Wellcome open research

The genome sequence of the Fulvous Clothes Moth, Tinea semifulvella (Haworth, 1828)

黄衣蛾 (Tinea semifulvella) 的基因组序列（Haworth，1828）

• DOI: 10.12688/wellcomeopenres.19079.1
• 发表时间: 2023
• 期刊: Wellcome Open Research
• 作者: Boyes D

The genome sequence of the Coronet, Craniophora ligustri (Denis and Schiffermu¨ller, 1775)

皇冠、女贞冠的基因组序列（Denis 和 Schiffermuller，1775）

• DOI: 10.12688/wellcomeopenres.18987.1
• 发表时间: 2023
• 期刊: Wellcome Open Research
• 作者: Boyes D