BBSRC Institute Strategic Programme: Decoding Biodiversity (DECODE) - Partner Grant

BBSRC 研究所战略计划：解码生物多样性 (DECODE) - 合作伙伴资助

• 批准号: BB/X020037/1
• 负责人: Daniel Read
• 金额: $ 62.97万
• 依托单位: UK CENTRE FOR ECOLOGY & HYDROLOGY
• 依托单位国家: 英国
• 项目类别: Research Grant
• 财政年份: 2023
• 资助国家: 英国
• 起止时间: 2023 至 无数据
• 项目状态: 未结题
• 来源: https://gtr.ukri.org/projects?ref=BB%2FX020037%2F1
• 关键词: BBSRC; Institute; Strategic; Programme; Decoding

The start of the 21st Century saw the landmark publication of the human genome, changing the way we do biology and having a huge impact on medicine. This heralded a new era of genomics that was initially dominated by the generation and analysis of genomes of model organisms and more economically important species. Concurrently, genome technologies have enabled advances in microbiology, such as disentangling complex communities or, as has been seen in the pandemic, identifying new emerging variants of SARS-CoV-2. These rapid advances have been driven by innovation in high-throughput sequencing technologies and software to assemble and analyse genomes. Recently, step changes in these areas enable the generation of high-quality genomes at scale, making ambitious projects like the Earth Biogenome Project, with the goal of generating genomes for all eukaryotic life, feasible. Furthermore, it means that rather than being limited to a single genome for a species, it is now possible to generate multiple genomes, helping to capture the diversity of the species. However, the scale and complexity of this genomic data presents an analytical challenge and there is a pressing need across the public and private sectors (our stakeholders) for tools, expertise and capacity to translate genomes and long-read technologies into discoveries. The outputs of the Decoding Biodiversity (DECODE) research programme will deliver to this need, to the BBSRC Transformative Technologies theme, and to the government prioritization of investment and innovation in genomics and bioinformatics (UK Innovation Strategy).DECODE brings together expertise in computational biology, mathematics and genomics. It builds on innovations from our previous core strategic programme "Genomics for Food Security", the cross Institute Strategic Programme (ISP) "Designing Future Wheat", and the Quadram ISP "Gut Microbes and Health". In addition, it draws on the experience and networks gained through the research capacity-building programme "Grow Colombia", and as a partner in the Darwin Tree of Life (DToL) consortium. DECODE is delivered through three interconnected work packages:Work package 1 will develop tools and techniques to investigate biodiversity. Specifically, this includes developing methods for: comparing multiple genomes within and across species to identify structural changes; using multiple genomes to improve annotation of coding and regulatory regions in the genome; resolving complexity of bacteria communities and biological roles within those communities; the deployment of sequences as real-time sensors of environmental communities. With our partners IBM and Eagle genomics, we will make the software and workflows developed are robust, deployable and scalable.Work package 2 will use the tools developed in WP1 to investigate biodiversity in publicly available genomes. We will use multiple analytical approaches to: assign function to genomic "dark matter"-genes of currently unknown function; investigate mechanisms underpinning chemical diversity in plants; and identify mechanisms driving genetic diversity in key agricultural crops and aquaculture species.Work Package 3 will use long read sequencing technologies and the tools developed in WP1 to uncover and explore biodiversity. Specifically, how community structures change over time in increasingly complex systems (the gut, anaerobic digesters and soil) will be investigated. Furthermore, through quantifying gene content changes, WP3 will aim to identify how biological functions change in a community and link these to community health.To deliver this programme, we have established four key strategic partnership: RBG Kew will provide expertise in plant metabolism, pangenomics and crop wild relatives, IBERS brings expertise in UK orphan crops, the UK Center for Ecology & Hydrology will provide soil samples and access to contextual datasets, and IBM Research will support deployment and scalability of tools.

21世纪初，人类基因组的具有里程碑意义的出版物，改变了我们进行生物学的方式并对医学产生巨大影响。这预示着一个新的基因组学时代，该时代最初由模型生物和更经济重要的物种的基因组的产生和分析主导。同时，基因组技术已使微生物学的进步，例如解开复杂社区，或者，如大流行中所见，识别了SARS-COV-2的新出现变体。这些快速进步是由高通量测序技术和软件的创新驱动的，以组装和分析基因组。最近，这些区域的步骤变化使得能够大规模地产生高质量的基因组，从而使诸如Earth Biogeogeme项目之类的雄心勃勃的项目旨在为所有真核生命产生基因组，可行。此外，这意味着现在有可能产生多个基因组，而不是仅限于一个物种的单个基因组，有助于捕获物种的多样性。但是，该基因组数据的规模和复杂性提出了一个分析挑战，并且在公共和私营部门（我们的利益相关者）迫切需要将基因组和长阅读技术转化为发现的工具，专业知识和能力。解码生物多样性（解码）研究计划的产出将为这一需求，BBSRC变革技术主题以及政府优先考虑基因组学和生物信息技术的投资和创新的优先级（英国创新策略）。Decode在计算生物学，数学，数学和种类学方面汇集了专业知识。它基于我们以前的核心战略计划“粮食安全基因组学”，跨学院战略计划（ISP）“设计未来小麦”和Quadram ISP“肠道微生物与健康”的创新。此外，它借鉴了通过研究能力建设计划“ Grow Colombia”获得的经验和网络，并作为达尔文生命之树（DTOL）财团的合作伙伴。解码是通过三个互连工作包进行的：工作包1将开发工具和技术来研究生物多样性。具体而言，这包括开发用于以下方法：比较物种内部和整个物种内部的多个基因组以识别结构变化；使用多个基因组改善基因组中编码和调节区域的注释；解决这些社区内细菌群落和生物作用的复杂性；序列作为环境社区的实时传感器的部署。借助我们的合作伙伴IBM和Eagle基因组学，我们将使开发的软件和工作流程可靠，可部署和可扩展。WorkPackage 2将使用WP1中开发的工具来研究公开可用的基因组中的生物多样性。我们将使用多种分析方法来：将功能分配给基因组“暗物质” - 当前未知功能的基因基因；研究植物中化学多样性支撑的机制；并确定在关键农作物和水产养殖物种中推动遗传多样性的机制。工作包3将使用长阅读的测序技术以及WP1中开发的工具来揭示和探索生物多样性。具体而言，将研究越来越复杂的系统（肠道，厌氧消化园和土壤）的社区结构如何随时间变化。 Furthermore, through quantifying gene content changes, WP3 will aim to identify how biological functions change in a community and link these to community health.To deliver this programme, we have established four key strategic partnership: RBG Kew will provide expertise in plant metabolism, pangenomics and crop wild relatives, IBERS brings expertise in UK orphan crops, the UK Center for Ecology & Hydrology will provide soil samples and access to contextual datasets, and IBM研究将支持工具的部署和可扩展性。