Wormbase ParaSite

寄生虫蠕虫

• 批准号: BB/P024610/1
• 负责人: Matthew Berriman
• 金额: $ 30.06万
• 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: 2018
• 资助国家: 英国
• 起止时间: 2018 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=BB%2FP024610%2F1
• 关键词: Wormbase; ParaSite

Parasitic worms (helminths) cause a massive economic burden, with agricultural losses in the UK exceeding £100 million per annum. Across the globe helminths are also responsible for long term, chronic diseases in humans. The UK is a leader in research and development targeting helminths, despite global investment being disproportionately low compared with the impact of infections. Helminth are diverse - the term covers both round worms and flatworms - and no single model species can capture the range of disease-causing mechanisms involved. Researchers are therefore inherently interested in making comparisons between species. The genomes of more than 30 species are now published and many more available. Alongside their genomes, large scale functional genomics datasets have been produced describing key life cycle transitions for more than 10 species. To drive helminth research into the genomic era, we established WormBase ParaSite in 2014. The resource now contains more than 100 draft genomes of helminths. Genes and genomes can be explored, enabling a greater understanding of helminth biology to accelerate the development of new strategies for helminth control.In its first two years, there have been 8 public releases of the resource and in 2015 the website was accessed by 29000 unique users. In addition to accessing gene structures and functional annotation for draft genomes, users are able to examine evolutionary relationships between genes and look for the differences and similarities between species that may underpin differences and similarities in helminth biology. The resource provides fast and intuitive interfaces for browsing and searching and contains an interface for extracting custom datasets. Several workshops have been organised to provide training in its use.This proposal will fund the maintenance and improvement of WormBase ParaSite. We intend to incorporate all publicly available nematode and flatworm genome assemblies as they become available. Due to changes in sequencing technology, research groups will produce new and better versions of existing gene sequences. However, these sequences will in many cases not be annotated, so we will provide an automated way to annotate naked genomes with consistent gene structures and functional descriptions. Defining gene families will remain a critically important activity. However, we will increase the speed, accuracy and scalability in which evolutionary histories can be inferred. We will also greatly improve the way in which data from large-scale studies on gene expression or genome variation are included into the resource. In particular, a new Gene Expression Atlas will be included for interactive exploration of gene expression data. To help identify new drug targets or to identify re-use possibilities for existing drugs, WormBase ParaSite will include links to targets and chemistry data (by linking to the ChEMBL database). We will also enable users to query available phenotypic data.In addition to the new features, we will frequently update the site to provide rapid access to new data. We will continue to provide training on the use of the resource and maintain a live and responsive helpdesk.

寄生蠕虫（蠕虫）造成巨大的经济负担，英国每年的农业损失超过 1 亿英镑。在全球范围内，蠕虫也是人类长期慢性疾病的罪魁祸首。英国在针对蠕虫的研究和开发方面处于领先地位，尽管与感染的影响相比，全球投资过低。蠕虫是多种多样的——该术语涵盖了圆虫和扁虫——并且没有单一的模型物种能够捕获所涉及的致病机制的范围。因此，研究人员本质上对物种之间的比较感兴趣。现已公布 30 多个物种的基因组，并且还有更多物种的基因组可供使用。除了基因组之外，还生成了大规模功能基因组数据集，描述了 10 多个物种的关键生命周期转变。为了推动蠕虫研究进入基因组时代，我们于 2014 年建立了 WormBase ParaSite。该资源现在包含 100 多个蠕虫基因组草案。可以探索基因和基因组，从而更好地了解蠕虫生物学，从而加速蠕虫控制新策略的开发。在最初两年内，该资源已公开发布 8 次，2015 年该网站有 29000 名独立用户访问。除了访问基因组草案的基因结构和功能注释之外，用户还能够检查基因之间的进化关系，并寻找物种之间的差异和相似之处，这些差异和相似之处可能是蠕虫生物学差异和相似之处的基础。该资源提供快速直观的浏览和搜索界面，并包含用于提取自定义数据集的界面。已经组织了多个研讨会来提供其使用培训。该提案将资助 WormBase ParaSite 的维护和改进。我们打算整合所有公开可用的线虫和扁虫基因组组件。由于测序技术的变化，研究小组将生产现有基因序列的新的、更好的版本。然而，这些序列在许多情况下不会被注释，因此我们将提供一种自动化的方法来注释具有一致的基因结构和功能描述的裸基因组。定义基因家族仍将是一项至关重要的活动。然而，我们将提高推断进化历史的速度、准确性和可扩展性。我们还将大大改进将大规模基因表达或基因组变异研究的数据纳入资源的方式。特别是，将包括一个新的基因表达图谱，用于基因表达数据的交互式探索。为了帮助确定新的药物靶标或确定现有药物重复使用的可能性，WormBase ParaSite 将包含靶标和化学数据的链接（通过链接到 ChEMBL 数据库）。我们还将允许用户查询可用的表型数据。除了新功能之外，我们还将经常更新网站以提供对新数据的快速访问。我们将继续提供有关资源使用的培训，并维护实时响应的帮助台。

项目成果

Extensive genomic and transcriptomic variation defines the chromosome-scale assembly of Haemonchus contortus , a model gastrointestinal worm

广泛的基因组和转录组变异定义了捻转血矛线虫（一种胃肠道蠕虫模型）的染色体规模组装

• DOI: 10.1101/2020.02.18.945246
• 发表时间: 2020
• 作者: Doyle S

Accelerated variant curation from scientific literature using biomedical text mining.

• DOI: 10.17912/micropub.biology.000578
• 发表时间: 2022
• 期刊: microPublication biology
• 作者: Mallick, Rishab;Arnaboldi, Valerio;Davis, Paul;Diamantakis, Stavros;Zarowiecki, Magdalena;Howe, Kevin
• 通讯作者: Howe, Kevin

Genomic and transcriptomic variation defines the chromosome-scale assembly of Haemonchus contortus, a model gastrointestinal worm.

• DOI: 10.1038/s42003-020-01377-3
• 发表时间: 2020-11-09
• 期刊: Communications biology
• 影响因子: 5.9
• 作者: Doyle SR;Tracey A;Laing R;Holroyd N;Bartley D;Bazant W;Beasley H;Beech R;Britton C;Brooks K;Chaudhry U;Maitland K;Martinelli A;Noonan JD;Paulini M;Quail MA;Redman E;Rodgers FH;Sallé G;Shabbir MZ;Sankaranarayanan G;Wit J;Howe KL;Sargison N;Devaney E;Berriman M;Gilleard JS;Cotton JA
• 通讯作者: Cotton JA

Complete representation of a tapeworm genome reveals chromosomes capped by centromeres, necessitating a dual role in segregation and protection.

• DOI: 10.1186/s12915-020-00899-w
• 发表时间: 2020-11-09
• 期刊: BMC biology
• 影响因子: 5.4
• 作者: Olson PD;Tracey A;Baillie A;James K;Doyle SR;Buddenborg SK;Rodgers FH;Holroyd N;Berriman M
• 通讯作者: Berriman M

Comparative genomics of the major parasitic worms.

• DOI: 10.1038/s41588-018-0262-1
• 发表时间: 2019-01
• 期刊: Nature genetics
• 影响因子: 30.8
• 作者: International Helminth Genomes Consortium