Population Genomics of Daphnia pulex

水蚤群体基因组学

• 批准号: 8463285
• 负责人: Michael R LYNCH
• 金额: $ 61.59万
• 依托单位: TRUSTEES OF INDIANA UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2013
• 资助国家: 美国
• 起止时间: 2013-02-01 至 2017-01-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8463285
• 关键词: Age; Arabidopsis; Architecture; Area; Asexual Reproduction; Automobile Driving; Backcrossings; Behavioral; Biological Assay; Biological Models; Biology; Caenorhabditis; Cellular biology; Chromosomes; Code; Collection; Communities; Daphnia; Data; Data Set; Databases; Derivation procedure; Developmental Biology; Developmental Cell Biology; Diploidy; Distant; Drosophila genus; Ecology; Environment; Event; Evolution; Future; Gene Family; Gene Mutation; Genes; Genetic; Genetic Drift; Genetic Polymorphism; Genetic Recombination; Genome; Genomics; Genotype; Goals; Haploidy; Haplotypes; Human; Indiana; Individual; International; Introns; Invertebrates; Knowledge; Laboratories; Letters; Life; Light; Linkage Disequilibrium; Maintenance; Meiosis; Methods; Mitotic; Modeling; Molecular; Molecular Biology; Molecular Evolution; Molecular Genetics; Molecular Profiling; Mutation; Oregon; Organism; Parasitology; Partner in relationship; Pattern; Physiological; Population; Population Genetics; Population Sizes; Population Study; Process; Production; Proteins; Proteomics; Recurrence; Relative (related person); Research; Research Personnel; Resources; Sampling; Scheme; Science; Scientist; Sentinel; Site; Staging; Study models; Surveys; System; Targeted Research; Taxon; Testing; Time; United States National Institutes of Health; Variant; Work; aquatic organism; asexual; base; comparative; design; duplicate genes; environmental toxicology; experience; genetic analysis; genetic evolution; genome sequencing; genome-wide; genome-wide analysis; innovation; insight; knowledge base; male; novel; public health relevance; purge; rapid technique; screening; sex; sex determination; sperm cell; theories; transmission process; web page

DESCRIPTION (provided by applicant): The goal of this project is to obtain high-quality sequence for the genomes of ~150 isolates of the microcrustacean Daphnia pulex, as well as lower-coverage data for ~5000 additional geographically distributed genotypes for population-genetic analysis. The study species is a major model system employed in the research of a large international consortium of life scientists. As the assayed genotypes will be maintained indefinitely in a clonal fashion, the resultant data set will serve as a permanent resource for the research community. Innovative features of the project include the direct sequencing and assembly of haplotypes via whole-genome amplification of isolated sperm, and the application of maximum-likelihood methods for estimating patterns of within- and among-individual variation and linkage disequilibrium. The availability of direct estimates of the rate and molecular spectra of de novo mutations in all major lineages to be studied provides a level of power for the interpretation of molecular population-genetic data that has not been possible in prior work, e.g., estimation of the power of genetic drift in each study population. In addition to providing a community resource, which will leverage additional work from numerous other labs, the sampling scheme for this survey is designed to generate results bearing on several long-standing problems in evolutionary genetics. First, the study species harbors a large number of permanently asexual lineages, resulting from an unusual system of sex-limited meiosis suppression that promotes the recurrent production of novel asexual clones via backcrossing of males to the sexual species. Analyses of asexual lineages with a range of ages will provide an unprecedented opportunity to evaluate the genome-wide causes and consequences of the loss of recombination, and such analyses are further enhanced by the presence of two chromosomes that never recombine, even via male transmission. Second, D. pulex harbors substantial numbers of novel introns. Collection of hundreds of neo-introns, analysis of their molecular features, and elucidation of their genealogical distributions will set the stage for future functional work on the mechanisms of intron origin, one of the great mysteries in evolutionary genomics. Third, one extensive lineage of D. pulex has undergone a prolonged population bottleneck, and comparison of this to ~50 other populations will cover essentially the full range of effective population sizes known in metazoan species, providing a unique genome- wide analysis of the consequences of variation in the strength of random genetic drift. Finally, as only about half of the genotypes to be sequenced are capable of male production, comparative analyses will provide insight into the mechanisms of sex determination in this system, clarifying the proposed existence of a nonrecombining mating-system chromosome, and evaluating the consequences of such a genetic environment on an otherwise freely recombining genetic background.

描述（由申请人提供）： 该项目的目的是获得〜150个Microcrustacean daphnia pulex基因组的高质量序列，以及〜5000个额外地理位置分布的基因型的较低覆盖范围数据，用于人群遗传分析。该研究物种是用于研究大型国际生活科学家联盟研究的主要模型系统。由于测定的基因型将以克隆方式无限期地维护，因此结果数据集将成为研究界的永久资源。该项目的创新特征包括通过隔离精子的全基因组扩增进行单倍型的直接测序和组装，以及最大可能的方法的应用来估计内部和个体内部变化和链接不平衡的模式。在所有主要谱系中，对从头突变的速率和分子光谱的直接估计值的可用性为解释分子种群遗传数据的解释提供了一定程度的能力，例如先前的工作，例如，在每个研究人群中遗传漂移的力量估计。 除了提供社区资源（将利用其他众多实验室的其他工作）外，该调查的抽样方案旨在产生有关进化遗传学中多个长期存在的问题的结果。首先，该研究物种具有大量永久无性谱系，这是由于性别限制的减数分裂抑制系统引起的，从而通过将雄性反向性化为性物种促进了新型无性克隆的复发产生。对具有一系列年龄范围的无性谱系的分析将提供一个前所未有的机会，以评估重组丧失的全基因组原因和后果，并且通过两个从未重新结合的染色体也可以进一步增强这种分析，甚至通过男性传播。其次，D。Pulex拥有大量新型内含子。收集了数百个新内膜，对它们的分子特征的分析以及阐明其家谱分布的收集将为未来的功能性工作奠定基础，这是内含子起源机制的阶段，这是进化基因组学的最大奥秘之一。第三，D。pulex的一个广泛的谱系经历了长时间的种群瓶颈，将其与〜50个其他种群进行比较将涵盖Metazoan物种中已知的各种有效种群大小的全部范围，从而提供了独特的基因组 - 对随机遗传漂移强度变化的后果进行了广泛的分析。最后，由于只有大约一半要测序的基因型能够产生男性，因此比较分析将洞悉该系统中的性别确定机制，阐明了提议的非本质组合式结合系统染色体的存在，并评估了这种遗传环境对其他自由地重新培养的遗传背景的后果。