Wormbase-ParaSite

蠕虫基地-ParaSite

基本信息

  • 批准号:
    BB/K020048/1
  • 负责人:
  • 金额:
    $ 29.47万
  • 依托单位:
  • 依托单位国家:
    英国
  • 项目类别:
    Research Grant
  • 财政年份:
    2014
  • 资助国家:
    英国
  • 起止时间:
    2014 至 无数据
  • 项目状态:
    已结题

项目摘要

Flatworms and roundworms are diverse groups of organisms and include those responsible for serious human, veterinary and plant diseases. Their global impact is hard to measure but annual human morbidity is estimated to be equivalent to at least 50 million productive years of life (c.f. 85M for HIV/AIDS), and agricultural losses from plant parasitic nematodes can be measured in hundreds of millions of dollars. Despite their impact on human health, a recent report highlighted that parasitic helminths attract only $77M per annum in research expenditure (cf. $1.1billion for HIV/AIDS). Due to the wide range of pathology caused in various host species, no single model species can capture the range of disease-causing mechanisms involved. Parasitologists are therefore inherently interested in making comparisons between many different species. Access to genomic-scale datasets has revolutionized molecular and cell biological studies of protozoan pathogens, advancing basic and applied research, but this is only now starting to happen for parasitic worms. Major sequencing programmes are now underway and large scale functional genomics datasets are beginning to emerge (e.g. RNA-Seq is becoming commonplace). Studies of genomic variation in multiple isolates, to address clinical, epidemiological or applied agricultural questions, are the obvious next steps. While the emergence of new genome-scale datasets is immensely exciting, genomes are often produced in a relatively poor states of assembly and annotation compared to existing reference genomes. Moreover, the prevailing paradigm for organising genomic information (essentially, the genome browser and the underlying data models that support this) are relatively poorly fitted to the exploration of hundreds of highly fragmented genomes with limited functional characterisation. In this application, we propose the creation of a new resource to organise, classify and allow the exploration hundreds of worm genomes, facilitating the exploitation of sequence-based data for understanding and ultimately controlling worm-induced pathology.The propose resource will be called WormBase-ParaSite, and will be strategically aligned with WormBase (the main resource for the model nematode Caenorhadbitis elegans). Specifically the resource will provide: (a) Gene structures and functional annotation for unannotated worm genomes. (b) Comparative genomic analysis, visualisation and querying. (c) Methods for exploration and data mining the complete data set, through an intuitive query-building interface accessible to research scientists. (d) A platform for the visualisation of the results of high-throughput sequencing experiments in the context of other annotation that enables functional genomics and variation studies. (e) An infrastructure for accepting and integrating functional annotation submitted from the community engaged in worm research.The project will complement the existing scope (and leverage the existing content) of WormBase, which has supplied biologists working on the model worm Caenorhabditis elegans with an invaluable information resource since the genome of this species was one of the first to be deciphered. It will provide additional capacity and tools for the handling of a massively increased quantity of genomes, with a clear focus on the information that is most relevant to parasitologists. The resource will also provide a home for data from the flatworms, such as flukes and tapeworms, which are outside the scope of WormBase.
扁虫和蛔虫是不同的生物群体,包括那些负责严重的人类,兽医和植物疾病。它们的全球影响难以衡量,但据估计,人类每年的发病率至少相当于5000万个生产生命年(参见图1)。8500万人感染艾滋病毒/艾滋病),植物寄生线虫造成的农业损失可以以数亿美元计。尽管寄生蠕虫对人类健康有影响,但最近的一份报告强调,寄生蠕虫每年仅吸引7700万美元的研究支出(参见11亿美元用于艾滋病毒/艾滋病)。由于在各种宿主物种中引起的广泛的病理学,没有单一的模型物种可以捕获所涉及的致病机制的范围。因此,寄生虫学家天生对许多不同物种之间的比较感兴趣。获得基因组规模的数据集已经彻底改变了原生动物病原体的分子和细胞生物学研究,推进了基础和应用研究,但这只是现在才开始发生在寄生蠕虫。主要的测序计划正在进行中,大规模的功能基因组学数据集开始出现(例如RNA-Seq正在变得司空见惯)。对多个分离株的基因组变异进行研究,以解决临床、流行病学或应用农业问题,是显而易见的下一步。虽然新的基因组规模数据集的出现非常令人兴奋,但与现有的参考基因组相比,基因组通常在相对较差的组装和注释状态下产生。此外,组织基因组信息的流行范式(基本上是基因组浏览器和支持这一点的基础数据模型)相对不适合探索数百个功能特征有限的高度碎片化的基因组。在这个应用程序中,我们建议创建一个新的资源来组织,分类和允许探索数以百计的蠕虫基因组,促进利用基于序列的数据来理解和最终控制蠕虫诱导的病理学。拟议的资源将被称为WormBase-ParaSite,并将与WormBase(模式线虫秀丽隐杆线虫的主要资源)进行战略性对齐。具体而言,该资源将提供:(a)未注释的蠕虫基因组的基因结构和功能注释。(b)比较基因组分析、可视化和查询。(c)探索和数据挖掘完整数据集的方法,通过一个直观的查询界面,研究科学家可以访问。(d)在其他注释的背景下可视化高通量测序实验结果的平台,支持功能基因组学和变异研究。(e)该项目将补充WormBase的现有范围(并利用现有内容),该项目为研究模式蠕虫秀丽隐杆线虫(Caesophylhabditis elegans)的生物学家提供了宝贵的信息资源,因为该物种的基因组是最早被破译的物种之一。它将为处理大量增加的基因组提供额外的能力和工具,并明确侧重于与寄生虫学家最相关的信息。该资源还将为来自扁虫(如吸虫和绦虫)的数据提供一个家,这些数据不在WormBase的范围内。

项目成果

期刊论文数量(6)
专著数量(0)
科研奖励数量(0)
会议论文数量(0)
专利数量(0)
Comparative genomics of the major parasitic worms.
  • DOI:
    10.1038/s41588-018-0262-1
  • 发表时间:
    2019-01
  • 期刊:
  • 影响因子:
    30.8
  • 作者:
    International Helminth Genomes Consortium
  • 通讯作者:
    International Helminth Genomes Consortium
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:
  • 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
WormBase 2016: expanding to enable helminth genomic research.
  • DOI:
    10.1093/nar/gkv1217
  • 发表时间:
    2016-01-04
  • 期刊:
  • 影响因子:
    14.9
  • 作者:
    Howe KL;Bolt BJ;Cain S;Chan J;Chen WJ;Davis P;Done J;Down T;Gao S;Grove C;Harris TW;Kishore R;Lee R;Lomax J;Li Y;Muller HM;Nakamura C;Nuin P;Paulini M;Raciti D;Schindelman G;Stanley E;Tuli MA;Van Auken K;Wang D;Wang X;Williams G;Wright A;Yook K;Berriman M;Kersey P;Schedl T;Stein L;Sternberg PW
  • 通讯作者:
    Sternberg PW
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
  • 期刊:
  • 影响因子:
    0
  • 作者:
    Doyle S
  • 通讯作者:
    Doyle S
WormBase ParaSite - a comprehensive resource for helminth genomics.
  • DOI:
    10.1016/j.molbiopara.2016.11.005
  • 发表时间:
    2017-07
  • 期刊:
  • 影响因子:
    1.5
  • 作者:
    Howe KL;Bolt BJ;Shafie M;Kersey P;Berriman M
  • 通讯作者:
    Berriman M
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Matthew Berriman其他文献

Hatching of parasitic nematode eggs: a crucial step determining infection
  • DOI:
    10.1016/j.pt.2021.08.008
  • 发表时间:
    2022-02-01
  • 期刊:
  • 影响因子:
  • 作者:
    Tapoka T. Mkandawire;Richard K. Grencis;Matthew Berriman;María A. Duque-Correa
  • 通讯作者:
    María A. Duque-Correa
Genomic-scale prioritization of drug targets: the TDR Targets database
药物靶点的基因组规模优先级排序:TDR 靶点数据库
  • DOI:
    10.1038/nrd2684
  • 发表时间:
    2008-10-17
  • 期刊:
  • 影响因子:
    101.800
  • 作者:
    Fernán Agüero;Bissan Al-Lazikani;Martin Aslett;Matthew Berriman;Frederick S. Buckner;Robert K. Campbell;Santiago Carmona;Ian M. Carruthers;A. W. Edith Chan;Feng Chen;Gregory J. Crowther;Maria A. Doyle;Christiane Hertz-Fowler;Andrew L. Hopkins;Gregg McAllister;Solomon Nwaka;John P. Overington;Arnab Pain;Gaia V. Paolini;Ursula Pieper;Stuart A. Ralph;Aaron Riechers;David S. Roos;Andrej Sali;Dhanasekaran Shanmugam;Takashi Suzuki;Wesley C. Van Voorhis;Christophe L. M. J. Verlinde
  • 通讯作者:
    Christophe L. M. J. Verlinde
Correction: A manually curated annotation characterises genomic features of P. falciparum lncRNAs
  • DOI:
    10.1186/s12864-023-09164-0
  • 发表时间:
    2023-04-06
  • 期刊:
  • 影响因子:
    3.700
  • 作者:
    Johanna Hoshizaki;Sophie H. Adjalley;Vandana Thathy;Kim Judge;Matthew Berriman;Adam J. Reid;Marcus C. S. Lee
  • 通讯作者:
    Marcus C. S. Lee

Matthew Berriman的其他文献

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{{ truncateString('Matthew Berriman', 18)}}的其他基金

BBSRC-NSF/BIO Next generation collaborative annotation of genomes and synteny
BBSRC-NSF/BIO 下一代基因组和同线性协作注释
  • 批准号:
    BB/T016299/1
  • 财政年份:
    2022
  • 资助金额:
    $ 29.47万
  • 项目类别:
    Research Grant
WormBase: expanding the reference resource for helminth research
WormBase:扩展蠕虫研究的参考资源
  • 批准号:
    MR/S000453/2
  • 财政年份:
    2022
  • 资助金额:
    $ 29.47万
  • 项目类别:
    Research Grant
WormBase: expanding the reference resource for helminth research
WormBase:扩展蠕虫研究的参考资源
  • 批准号:
    MR/S000453/1
  • 财政年份:
    2018
  • 资助金额:
    $ 29.47万
  • 项目类别:
    Research Grant
Wormbase ParaSite
寄生虫蠕虫
  • 批准号:
    BB/P024610/1
  • 财政年份:
    2018
  • 资助金额:
    $ 29.47万
  • 项目类别:
    Research Grant
WormBase: an evolving resource for nematode biology
WormBase:线虫生物学的不断发展的资源
  • 批准号:
    MR/L001020/1
  • 财政年份:
    2013
  • 资助金额:
    $ 29.47万
  • 项目类别:
    Research Grant

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用多尺度蛋白质组学研究宿主-寄生虫相互作用组
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    2024
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