Population Genomics of Daphnia pulex

描述(由申请人提供)： 该项目的目标是获得微甲壳动物Paphnia Pulex约150个分离物的高质量基因组序列，以及用于种群遗传分析的约5000个地理分布的低覆盖率数据。研究物种是一个大型国际生命科学家联盟研究中采用的主要模式系统。由于被检测的基因类型将以克隆的方式无限期地保留，结果数据集将作为研究界的永久资源。该项目的创新特征包括通过分离精子的全基因组扩增直接测序和组装单倍型，以及应用最大似然法估计个体内和个体之间的变异模式和连锁不平衡。对所有待研究的主要谱系中从头突变的速率和分子谱的直接估计的可用性，为解释分子群体遗传数据提供了一种能力水平，这在以前的工作中是不可能的，例如，估计每个研究群体中的遗传漂移的力量。除了提供社区资源，这将利用许多其他实验室的额外工作，这项调查的抽样方案旨在产生与进化遗传学中几个长期存在的问题有关的结果。首先，研究物种拥有大量永久的无性血统，这是由于一种不寻常的性别限制减数分裂抑制系统，该系统通过雄性与有性种的回交促进了新的无性克隆的循环产生。对不同年龄的无性世系的分析将提供一个前所未有的机会来评估重组丧失的全基因组原因和后果，而且由于存在两条永远不会重组的染色体，即使是通过男性传播，这种分析也会得到进一步加强。其次，D.Pulex含有大量新的内含子。收集数百个新内含子，分析它们的分子特征，阐明它们的谱系分布，将为未来内含子起源机制的功能工作奠定基础，内含子起源是进化基因组学中最大的谜团之一。第三，一个广泛的普氏杜鹃世系经历了漫长的种群瓶颈，将这个种群与~50个其他种群进行比较，基本上将涵盖后生动物物种中已知的所有有效种群大小，为随机遗传漂移强度的变异后果提供独特的全基因组分析。最后，由于只有大约一半的待测序基因能够产生雄性，比较分析将提供对该系统中性别决定机制的洞察，澄清提出的非重组交配系统染色体的存在，并评估这种遗传环境对原本自由重组的遗传背景的影响。

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.