权益分类	功能权益	普通用户	{{item.name}}会员
{{category.name}}	{{benefitItem.name}}

Population genomic tests for mechanisms of ecological speciation in bdelloid rotifers

蛭形轮虫生态物种形成机制的群体基因组测试

基本信息

批准号：
NE/M01651X/1
负责人：
Timothy Barraclough
金额：
$ 49.15万
依托单位：
Imperial College London
依托单位国家：
英国
项目类别：
Research Grant
财政年份：
2015
资助国家：
英国
起止时间：
2015 至无数据
项目状态：
已结题

来源：
https://gtr.ukri.org/projects?ref=NE%2FM01651X%2F1
关键词：
Population genomic tests mechanisms ecological

项目摘要

Sex is nearly ubiquitous among animals. Most animals have a stage in their life-cycle when genes from different individuals are shuffled to produce genetically mixed offspring. By doing so, natural selection acts more efficiently both to remove harmful mutations from populations and to allow beneficial combinations of genes to spread. Sex also has profound implications for speciation, namely how an ancestral species diverges into separate descendent species. Adaptation to different habitats and isolation in separate geographical areas can promote speciation, but a key step for sexual organisms is to acquire genetic or behavioural traits that prevent gene exchange. As a result, most speciation research has focused on reproductive isolating mechanisms that restrict gene exchange between diverging populations. Some organisms defy the general ubiquity of sexual reproduction. Bdelloid rotifers are microscopic animals that live in freshwater, such as ponds and the water film on mosses. No males or cellular signs of sex have ever been found, and recent genomic evidence indicates that their chromosome structure is incompatible with the normal pairing of chromosomes associated with sex. Despite the presumed costs of such a lifestyle, bdelloids comprise hundreds of morphologically distinct species. Our previous work confirmed that bdelloids have diversified into independently evolving groups akin to species and found evidence for morphological adaptation to different habitats. But what mechanisms led to divergence? Have bdelloids really evolved as asexuals or do they have hidden mechanisms for gene exchange?One recent discovery found another weird feature of bdelloids that might contribute to adaptation to different environments. Bdelloids harbour thousands of genes that appear to derive from bacteria, protists, plants and fungi and have been taken up into the bdelloid genome where they provide new functions. Some of those functions are previously unknown in the metabolic repertoire of animals. It is believed that uptake occurs (rarely) when bdelloids repair their DNA following damage caused by desiccation - another weird feature of bdelloids is their ability to survive desiccation, a stress that kills most other animals. The uptake of foreign DNA is well known in bacteria, where it contributes to specialisation to different niches (e.g. to cause disease in a new host), but the levels in bdelloids are unprecedented among animals. Might the uptake of foreign genes provide a way for bdelloids to acquire new functions and adapt to different environments, as in bacteria? Or perhaps there are other hidden mechanisms of gene exchange between bdelloids? We will use genome sequencing to test the importance of gene exchange and the uptake of foreign DNA in 4 closely related bdelloid species living in different habitats: 2 species in habitats that desiccate regularly and 2 that are fully aquatic and cannot recover from desiccation. Our prior work found that most foreign genes are shared, but a significant remainder appear to be unique to each species. We will sequence whole genomes to verify or refute the status of these genes. We will also sample genomic variation within each species to test whether shuffling of genes has occurred, and if so whether that conforms to hidden sexual exchange (unlikely) or other mechanisms. We will test whether gene exchange has shaped the pattern of natural selection across genes. The results will reveal the contribution of strictly asexual evolution versus gene exchange in bdelloid adaptation and speciation. Findings for these intriguing animals will contribute new knowledge of mechanisms that promote adaptation and speciation, in comparison to organisms with more conventional lifestyles.

性在动物中几乎无处不在。大多数动物在其生命周期中都有一个阶段，不同个体的基因被打乱，产生基因混合的后代。通过这样做，自然选择可以更有效地从种群中去除有害的突变，并允许有益的基因组合传播。性对物种形成也有深刻的影响，即祖先物种如何分化成独立的后代物种。对不同生境的适应和在不同地理区域的隔离可以促进物种形成，但有性生物的一个关键步骤是获得防止基因交换的遗传或行为特征。因此，大多数物种形成研究都集中在限制不同种群之间基因交换的生殖隔离机制上。有些生物无视普遍存在的有性生殖。蛭形轮虫是生活在淡水中的微小动物，如池塘和苔藓上的水膜。没有发现雄性或细胞的性别迹象，最近的基因组证据表明，他们的染色体结构与正常配对的染色体与性别有关。尽管这种生活方式的成本很高，但蛭形目生物包括数百种形态上不同的物种。我们以前的工作证实，蛭类动物已经分化成独立进化的群体，类似于物种，并发现了形态适应不同栖息地的证据。但是，是什么机制导致了分歧呢？蛭形动物真的是无性进化的吗？还是它们有隐藏的基因交换机制？最近的一项发现发现了蛭形类动物的另一个奇怪的特征，这可能有助于适应不同的环境。蛭形虫携带着数千个基因，这些基因似乎来自细菌、原生生物、植物和真菌，并已被吸收到蛭形虫基因组中，在那里它们提供了新的功能。其中一些功能在动物的代谢库中是以前未知的。据信，当蛭类动物在干燥造成的损伤后修复它们的DNA时，会发生吸收（很少）-蛭类动物的另一个奇怪的特征是它们在干燥中生存的能力，这种压力会杀死大多数其他动物。细菌对外源DNA的吸收是众所周知的，它有助于专门化到不同的生态位（例如在新宿主中引起疾病），但蛭形类的水平在动物中是前所未有的。吸收外来基因是否能为蛭类生物提供一种获得新功能和适应不同环境的方法，就像细菌一样？又或者，蛭类生物之间还有其他隐藏的基因交换机制？我们将使用基因组测序来测试基因交换的重要性和外来DNA的吸收在4密切相关的蛭形虫物种生活在不同的栖息地：2种栖息地，定期干燥和2是完全水生的，不能从干燥中恢复。我们先前的工作发现，大多数外源基因是共享的，但其余的重要基因似乎是每个物种所独有的。我们将对整个基因组进行测序，以验证或反驳这些基因的状态。我们还将对每个物种的基因组变异进行采样，以测试是否发生了基因改组，如果是的话，这是否符合隐藏的性交换（不太可能）或其他机制。我们将测试基因交换是否塑造了跨基因的自然选择模式。研究结果将揭示严格的无性进化与基因交换在蛭形虫适应和物种形成中的作用。这些有趣的动物的发现将有助于促进适应和物种形成机制的新知识，与具有更传统生活方式的生物体相比。

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）

Evolutionary dynamics of transposable elements in bdelloid rotifers.

DOI：
10.7554/elife.63194
发表时间：
2021-02-05
期刊：
eLife
影响因子：
7.7
作者：
Nowell RW;Wilson CG;Almeida P;Schiffer PH;Fontaneto D;Becks L;Rodriguez F;Arkhipova IR;Barraclough TG
通讯作者：
Barraclough TG

Comparative genomics of bdelloid rotifers: Insights from desiccating and nondesiccating species.

DOI：
10.1371/journal.pbio.2004830
发表时间：
2018-04
期刊：
PLoS biology
影响因子：
9.8
作者：
Nowell RW;Almeida P;Wilson CG;Smith TP;Fontaneto D;Crisp A;Micklem G;Tunnacliffe A;Boschetti C;Barraclough TG
通讯作者：
Barraclough TG

Whole-genome analyses converge to support the Hemirotifera hypothesis within Syndermata (Gnathifera)