RIG: Genome Size and Karyotype Evolution in Esociform Fishes

本研究的目的是确定在形成所观察到的基因组大小和核型变异中发挥作用的因素，其中包括广泛认可的北方梭子鱼的谱系。 经典的细胞遗传学研究表明，在这组鱼类的物种的基因组特征的广泛多样性。 这种变异性，加上对群体进化关系的共识，使其成为染色体和基因组水平上进化的潜在机制和后果的新兴思想的理想试验场。 该项目将产生的知识，数据和材料将为更广泛地研究鱼类染色体和基因组进化的模式和克里思提供基础，鱼类是物种最丰富的脊椎动物谱系。 该研究有两个具体目标：a）确定esociform属Umbra基因组扩增的特征;和B）产生esociforms及其近亲的分子细胞遗传学研究所需的方案和试剂。 从长远来看，这些方案可能适用于表现出独特的基因组组织特征的其他谱系。 三个种中的两个种的基因组包含的DNA大约是在其他esociform属中观察到的DNA的两倍。 确定有助于这种基因组扩增的因素是显着的，在最近重新的兴趣，在假设的生物体进化和基因组大小之间的关系。 初步数据表明，一些转座因子（TE）群体的扩增是导致Umbra基因组扩增的主要力量。 目前的项目旨在使用几种互补的证据来检验这一假设。 Southern和斑点杂交实验将揭示不同基因组组分对基因组扩增的相对贡献。 PCR靶向克隆实验的深度测序和系统发育分析将用于表征代表性esociform基因组中TE群体的多样性和相对年龄。 最后，荧光原位杂交观察将有助于确定基因组大小和核型排列变化之间任何假定关系的特征。 另一个有趣的方面，基因组变异之间的esociforms是明显的变化，在染色体的稳定性，在该组的核型多样性的基础。 具体而言，经典的细胞遗传学研究和化石证据表明，Esox属成员的核型在6000多万年内几乎保持不变;而在另一个极端，不同种群的esociform Dallia pectoralis显示出不同的核型。 总的来说，esociforms的二倍体染色体数目从22到78不等。 核型和核型稳定性的这种变异性突出了研究esociforms中染色体进化的价值，以揭示形成基因组变异的机制的特征。 本项目通过开发和应用染色体特异性DNA探针，启动了确定esociforms染色体进化模式和速率的任务。 这项工作也将有助于确定细胞遗传学数据在鱼类遗传学中的用途。本项目将研究在染色体和基因组尺度上形成遗传变异的过程。 这项研究的重点是一组鱼类，这是众所周知的，拥有广泛的和有趣的多样性，在他们的染色体和基因组特征。 从这项工作中获得的见解将导致更多地了解负责产生一些遗传多样性的机制，这些遗传多样性是生命的特征，并构成生物进化的燃料。 这项研究将有助于促进一个开始的调查员的专业发展，他是一个在科学和研究生中代表性不足的群体的成员，他将获得一套科学工具的实践经验，这些工具目前在美国的进化生物学家中没有广泛使用。有关结果会即时及方便地向公众公布。

The goal of this research is to determine factors that played a role in shaping the observed variation in genome size and karyotype among the fishes of the order Esociformes, a lineage that includes the widely recognized Northern Pike. Classical cytogenetic studies have demonstrated extensive diversity in the genomic characteristics of the species in this group of fishes. This variability, coupled with emerging consensus on the evolutionary relationships of the group makes it an ideal testing ground for emerging ideas on the underlying mechanisms and consequences of evolution at the chromosome and genome levels. The knowledge, data and materials that this project will generate will provide the foundation for broader investigations of the mode and tempo of chromosome and genome evolution in fishes, the most species-rich vertebrate lineage. The research has two specific goals: a) to determine the characteristics of the expansion of the genome in the esociform genus Umbra; and b) to produce protocols and reagents necessary for molecular cytogenetic studies of esociforms and their closest relatives. In the long term, these protocols may be applied to other lineages that exhibit unique features of genomic organization. The genome of two of the three species of Umbra comprise approximately two times as much DNA as those observed in other esociform genera. Determining the factors that contribute to this genome expansion is significant in light of the recently renewed interest in hypothesized relationships between organismal evolution and genome size. Preliminary data point to the amplification of some transposable element (TE) populations as a primary force leading to genome expansion in Umbra. The current project is designed to test that hypothesis using several complementary lines of evidence. Southern and dot blot experiments will reveal the relative contributions of different genomic components to genome expansion. Deep sequencing of PCR-targeted cloning experiments and phylogenetic analyses will be used to characterize the diversity and relative age of TE populations in representative esociform genomes. Finally, fluorescence in situ hybridization observations will help define features of any putative relationships between changes in genome size and karyotypic arrangement. Another interesting aspect of genomic variation among esociforms is the apparent change in chromosomal stability that underlies the diversity of karyotypes in the group. Specifically, classical cytogenetic studies and fossil evidence indicate that the karyotypes of members of the genus Esox have remained virtually unchanged for more than 60 million years; while at the other extreme, different populations of the esociform Dallia pectoralis show divergent karyotypes. Overall, diploid chromosome numbers among esociforms range from 22 to 78. This variability in karyotype and karyotypic stability highlights the value of the study of chromosome evolution in esociforms to uncover characteristics of the mechanisms that shape genome variation. This project initiates the task of determining the mode and rate of chromosomal evolution in esociforms through the development and application of chromosome specific DNA probes. This effort will also help determine the utility of cytogenetic data in fish phylogenetics.This project will examine processes that shape genetic variability at the scale of chromosomes and genomes. The research focuses on one group of fishes that is known to possess extensive and interesting diversity in their chromosomal and genomic characteristics. The insights gained from this work will lead to increased understanding of the mechanisms that are responsible for generating some of the genetic diversity that characterizes life and that constitutes the fuel for biological evolution. This research will help foster the professional development of a beginning investigator who is a member of a group underrepresented in science and a graduate student, who will gain hands-on experience with a set of scientific tools that currently are not in widespread use among evolutionary biologists in the U.S. Thanks to the investigator's affiliation with a natural history museum and his participation in its educational activities, the project's results will be made promptly and conveniently available to the general public.