Population genomics of Daphnia: mapping the 'arms-race genome'

水蚤群体基因组学：绘制“军备竞赛基因组”图谱

• 批准号: NE/J010790/1
• 负责人: Darren Obbard
• 金额: $ 44.29万
• 依托单位: University of Edinburgh
• 依托单位国家: 英国
• 项目类别: Research Grant
• 财政年份: 2012
• 资助国家: 英国
• 起止时间: 2012 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=NE%2FJ010790%2F1
• 关键词: Population; genomics; Daphnia; mapping; arms

We aim to measure the impact of conflict on the way genomes evolve. For example, what fraction of the differences between two genomes are a consequence of the arms-race between hosts and parasites? Is it a tiny amount, or do such conflicts dominate evolution at the molecular level? There is already some evidence that immune-system genes do show high rates of evolution, but it is not clear how general the effect is, or how big it is compared to other causes. We will answer this question by comparing the evolution of genes involved in host-parasite interaction (potential 'arms-race' genes), to the evolution of other genes. We will do this using the genome of an ecological and evolutionary model species - the water flea (Daphnia magna). It is only possible to address such questions by studying many genes simultaneously - i.e. whole genomes. Until recently, such an approach was untenable: a 'genome project' was complete when it had sequenced the genome of a single individual. Now, new advances in technology make it possible to examine full genome sequences for tens (or even hundreds) of individuals, and the price has fallen to the point at which such 'population genomic' studies fall well within the range of a single project. Daphnia are small freshwater crustaceans found in ponds throughout the UK and the world. Daphnia are well studied in terms of their ecology, so we know a great deal about the diversity of Daphnia and how this diversity arises when they interact with their environment. For example, Daphnia are used to assess the ecological impact of toxins in the environment; they adapt physiologically to a wide range of pH, food, oxygen, and temperature variation; and they exhibit specialised behaviour or morphology in response to predators. Daphnia are also interesting from a genetic perspective, for example they alternate between sexual and asexual reproduction, and they have nearly 50% more genes than humans - possibly because they have evolved to respond to such a wide range of environmental conditions. Most importantly for our study, Daphnia pathogens are widely studied in the lab and the field, so that we can identify which of their genes respond to pathogens, and to which pathogens those genes respond.We will sequence the genomes of 50 Daphnia magna from ponds all across Europe, and after sequencing, we will use statistical methods based on population-genetic theory to ask how important conflict is in determining the genome-wide rate of adaptive evolution. Our data will be made freely available to everyone, both academics and the public, over the web. This will provide a vital resource for interpreting population-genomic studies in laboratory organisms, such as the fruit fly (Drosophila). It will also provide a spring-board for future genetic studies of ecology, conservation, epidemiology and ecotoxicology that use Daphnia as a study system.

我们的目标是衡量冲突对基因组进化方式的影响。例如，两个基因组之间的差异有多大比例是宿主和寄生虫之间军备竞赛的结果？这是一个很小的量，还是这样的冲突在分子水平上主导着进化？已经有一些证据表明，免疫系统基因确实显示出高进化率，但尚不清楚这种影响有多普遍，或者与其他原因相比有多大。我们将通过比较宿主-寄生虫相互作用中涉及的基因（潜在的“军备竞赛”基因）的进化与其他基因的进化来回答这个问题。我们将使用一个生态和进化模式物种的基因组-水蚤（大型蚤）。只有通过同时研究多个基因，即整个基因组，才有可能解决这些问题。直到最近，这种方法都是站不住脚的：当一个人的基因组测序完成时，“基因组计划”就完成了。现在，技术的新进步使得研究数十（甚至数百）个个体的全基因组序列成为可能，并且价格已经下降到这样的“群体基因组”研究完全落入单个项目的范围内。水蚤是小型淡水甲壳类动物，在英国和世界各地的池塘中发现。水蚤在生态学方面得到了很好的研究，所以我们对水蚤的多样性以及当它们与环境相互作用时这种多样性是如何产生的了解很多。例如，水蚤被用来评估环境中毒素的生态影响;它们在生理上适应广泛的pH值、食物、氧气和温度变化;它们表现出专门的行为或形态来应对捕食者。从遗传学的角度来看，水蚤也很有趣，例如，它们在有性生殖和无性生殖之间交替，它们的基因比人类多近50%-可能是因为它们已经进化到对如此广泛的环境条件做出反应。对我们的研究来说，最重要的是，水蚤病原体在实验室和野外都得到了广泛的研究，这样我们就可以确定它们的哪些基因对病原体有反应，以及这些基因对哪些病原体有反应。我们将对来自欧洲各地池塘的50只大型水蚤的基因组进行测序，测序后，我们将使用基于群体遗传理论的统计方法来探讨冲突在决定适应性进化的全基因组速率方面的重要性。我们的数据将通过网络免费提供给每个人，包括学术界和公众。这将为解释实验室生物（如果蝇）的种群基因组研究提供重要资源。它还将为未来使用水蚤作为研究系统的生态学、保护、流行病学和生态毒理学的遗传研究提供一个跳板。

项目成果

The genetics of host-virus coevolution in invertebrates.

• DOI: 10.1016/j.coviro.2014.07.002
• 发表时间: 2014-10
• 期刊: CURRENT OPINION IN VIROLOGY
• 影响因子: 5.9
• 作者: Obbard, Darren J.;Dudas, Gytis
• 通讯作者: Dudas, Gytis

Mitogenome phylogeographic analysis of a planktonic crustacean

浮游甲壳动物的线粒体基因组系统地理学分析

• DOI: 10.5451/unibas-ep68911
• 发表时间: 2018
• 作者: Fields, Peter D.

Balancing Selection for Pathogen Resistance Reveals an Intercontinental Signature of Red Queen Coevolution.

• DOI: 10.1093/molbev/msab217
• 发表时间: 2021-10-27
• 期刊: Molecular biology and evolution
• 影响因子: 10.7
• 作者: Bourgeois Y;Fields PD;Bento G;Ebert D
• 通讯作者: Ebert D

Novel insights into the insect trancriptome response to a natural DNA virus.

关于昆虫转录组对天然 DNA 病毒反应的新见解。

• DOI: 10.1186/s12864-015-1499-z
• 发表时间: 2015-04-17
• 期刊: BMC genomics
• 影响因子: 4.4
• 作者: McTaggart SJ;Hannah T;Bridgett S;Garbutt JS;Kaur G;Boots M
• 通讯作者: Boots M

Population-Genomic Analysis Identifies a Low Rate of Global Adaptive Fixation in the Proteins of the Cyclical Parthenogen Daphnia magna.

• DOI: 10.1093/molbev/msac048
• 发表时间: 2022-03-02
• 期刊: Molecular biology and evolution
• 影响因子: 10.7
• 作者: Fields PD;McTaggart S;Reisser CMO;Haag C;Palmer WH;Little TJ;Ebert D;Obbard DJ
• 通讯作者: Obbard DJ