UK Crop Diversity Bioinformatics Resource

英国作物多样性生物信息学资源

• 批准号: BB/S019669/1
• 负责人: Mario Caccamo
• 金额: $ 75.85万
• 依托单位: National Institute of Agricultural Botany
• 依托单位国家: 英国
• 项目类别: Research Grant
• 财政年份: 2019
• 资助国家: 英国
• 起止时间: 2019 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=BB%2FS019669%2F1
• 关键词: UK; Crop; Diversity; Bioinformatics; Resource

We are requesting a High-Performance Computing (HPC) cluster that will be dedicated to support and expand the work that of a consortium of six leading UK research organisations with a focus on the characterisation and utilisation of novel genetic diversity for both the improvement of current crops as well as the breeding of novel varieties. The platform will be open to researchers at the participating institutions and their extensive network of collaborators. We will also develop and deploy common genomics workflows relevant to the common interests of the partners in crop diversity informatics. Developments in sequencing and genotyping technologies together with advances in environmental monitoring and characterisation are leading to rapid changes in the opportunities that are available to evaluate and utilise genetic diversity in crop plants and their wild relatives to adapt to the changing landscape of agriculture. This is driven by the increasing impact of climate change as well as by evolving agricultural practices and commodity demand. UK Research Organisations host a wide range of key expertise and information resources that have the potential to play a critical role in ensuring that this potential is fully realised. A major factor in developing the research infrastructure to support and nurture such activities is the provision of access to suitable computational resources that are tailored to the key data resources and analytical tools that that play a central role. A consortium of UK Research Organisations including NIAB, Royal Botanic Gardens, Kew (RBGKew), the Natural History Museum (NHM), the James Hutton Institute (JHI), Royal Botanic Gardens, Edinburgh (RBGE), and Scotland's Rural College (SRUC) have identified a need for additional computing resources beyond what they already host individually, centred on BBSRC-funded work around crop diversity. An high-performance computing (HPC) resource focused on the common needs of our organisations and tailored to the software and data resources which are relevant to this mission will deliver efficiencies in the use of resources, both in terms of computing hardware and systems administration. In addition, it will act as a focus for sharing data, developing new methods of analysis and delivering training, and a platform for developing new collaborative programmes of innovative science. Within the partner organisations alone, the platform will support the work of more than 400 scientists including a large proportion of early career researchers and PhD students. We propose to host the facility at JHI's data centre.

我们正在请求一个高性能计算（HPC）集群，该集群将致力于支持和扩展由六个领先的英国研究组织组成的联盟的工作，该联盟的工作重点是描述和利用新的遗传多样性，以改善现有作物以及培育新品种。该平台将向参与机构的研究人员及其广泛的合作者网络开放。我们还将开发和部署与合作伙伴在作物多样性信息学方面的共同利益相关的通用基因组学工作流程。测序和基因分型技术的发展，以及环境监测和特征鉴定方面的进步，正在导致评估和利用作物及其野生近缘种遗传多样性以适应不断变化的农业环境的机会迅速变化。这是由于气候变化的影响越来越大，以及不断变化的农业实践和商品需求。英国研究机构拥有广泛的关键专业知识和信息资源，这些资源有可能在确保充分实现这一潜力方面发挥关键作用。发展研究基础设施以支持和培育此类活动的一个主要因素是提供对适当的计算资源的访问，这些计算资源是根据关键数据资源和发挥核心作用的分析工具量身定制的。包括NIAB、皇家植物园、邱园（RBGKew）、自然历史博物馆（NHM）、詹姆斯·赫顿研究所（JHI）、皇家植物园、爱丁堡（RBGE）和苏格兰农村学院（SRUC）在内的英国研究机构联盟已经确定，除了他们已经单独托管的计算资源之外，还需要额外的计算资源，以bbsrc资助的作物多样性研究为中心。高性能计算（HPC）资源侧重于我们组织的共同需求，并针对与此任务相关的软件和数据资源进行定制，将在计算硬件和系统管理方面提高资源使用效率。此外，它将成为共享数据、开发新的分析方法和提供培训的焦点，以及开发创新科学的新合作项目的平台。仅在合作伙伴组织内，该平台将支持400多名科学家的工作，其中包括很大一部分早期职业研究人员和博士生。我们建议将该设施托管在JHI的数据中心。

项目成果

Selection on the Fly: Short-Term Adaptation to an Altered Sexual Selection Regime in Drosophila pseudoobscura.

• DOI: 10.1093/gbe/evad113
• 发表时间: 2023-07-03
• 期刊: GENOME BIOLOGY AND EVOLUTION
• 影响因子: 3.3
• 作者: Barata, Carolina;Snook, Rhonda R.;Ritchie, Michael G.;Kosiol, Carolin
• 通讯作者: Kosiol, Carolin

HISS: Snakemake-based workflows for performing SMRT-RenSeq assembly, AgRenSeq and dRenSeq for the discovery of novel plant disease resistance genes

HISS：基于 Snakemake 的工作流程，用于执行 SMRT-RenSeq 组装、AgRenSeq 和 dRenSeq，用于发现新型植物抗病基因

• DOI: 10.1101/2022.11.01.514708
• 发表时间: 2022
• 作者: Adams T

Eragrostis curvula, a Model Species for Diplosporous Apomixis.

• DOI: 10.3390/plants10091818
• 发表时间: 2021-08-31
• 期刊: Plants (Basel, Switzerland)
• 作者: Carballo J;Zappacosta D;Selva JP;Caccamo M;Echenique V
• 通讯作者: Echenique V

Differential Methylation Patterns in Apomictic vs. Sexual Genotypes of the Diplosporous Grass Eragrostis curvula.

• DOI: 10.3390/plants10050946
• 发表时间: 2021-05-10
• 期刊: Plants (Basel, Switzerland)
• 作者: Carballo J;Zappacosta D;Marconi G;Gallardo J;Di Marsico M;Gallo CA;Caccamo M;Albertini E;Echenique V
• 通讯作者: Echenique V

Systematics of the avian family Alaudidae using multilocus and genomic data

• DOI: 10.1016/j.avrs.2023.100095
• 发表时间: 2023-03
• 期刊: Avian Research
• 影响因子: 1.8
• 作者: P. Alström;Zeinolabedin Mohammadi;Erik D. Enbody;M. Irestedt;D. Engelbrecht;P. Crochet;A. Guillaumet