OPUS: CRS - Developing a Synthetic Understanding of Programmed DNA Elimination in Eukaryotes and the Evolution of Genome Size in Copepods

在大多数生物体中，个体内的所有细胞都含有相同的DNA序列。生殖细胞（精子和卵子）含有体细胞一半的DNA（例如，皮肤，肺细胞），但仍然包含相同的DNA序列。这种序列同一性有助于基因组的稳定性和正常功能。某些无脊椎动物和脊椎动物物种是这个规则的例外，因为在它们的一生中，它们从体细胞中消除了大部分生殖细胞基因组。这种程序化的淘汰是精确的，每一代都会发生。切除的DNA序列中有基因、遗传寄生虫和功能未知的重复序列。切除的DNA在某些物种中相似，但在其他物种中不同。解释这种现象的假设包括：1）控制体细胞的大小，从而控制发育速率和身体大小，2）消除寄生DNA的基因组，3）控制基因表达，4）产生新的基因组合，5）提供发育期间DNA复制所需的分子。理解体细胞基因组的“缩小”和重组的作用对于理解基因组如何组织的基本问题以及它们在多大程度上可以通过自然过程改变但仍然正常发挥功能至关重要。这项研究将综合30年来对桡足类、微型甲壳类浮游动物基因组生物学的研究，其中一些物种切除了50 - 99%的生殖系DNA。基于桡足类的理解将与原生动物、蠕虫、盲鳗和七鳃鳗中通过类似过程发生的情况相结合。 来自DNA序列、细胞组织学制备和生物体水平的生活史特征的数据将用于推断从基因组到整个生物体水平的适应。产品将包括（1）桡足类DNA消除的全面描述和解释，以及与其他具有类似性状的类群的比较，（2）基因组大小的模式及其与桡足类适应性性状的相关进化，如使用系统发育比较方法推断的，（3）关于桡足类DNA消除研究方法的教学论文，（4）批判性思维练习，使用特质DNA消除来评估使用科学方法的技能从一个学科到另一个学科、规模或背景的转移。此外，由于大部分工作是由本科生研究人员完成的，因此该综合研究将展示研究经验在培养下一代科学家和推进科学知识方面所发挥的作用。该奖项反映了NSF的法定使命，并被认为值得通过使用基金会的智力价值和更广泛的影响审查标准进行评估来支持。

In most organisms, all cells within an individual contain identical DNA sequences. Germ cells (sperm and eggs) contain half the amount of DNA as somatic cells (e.g., skin, lung cells) but still contain identical DNA sequences. This sequence identity contributes to stability and normal functioning of the genome. Certain invertebrate and vertebrate species are exceptions to this rule because during their liftime they eliminate large portions of their germline genome from somatic cells. This programmed elimination is precise and occurs in every generation. Among the excised DNA sequences are genes, genetic parasites, and repetitive sequences of unknown function. The excised DNA is similar among some species but different in others. Hypotheses to explain this phenomenon include 1) controlling the size of somatic cells and thus development rate and body size, 2) ridding the genome of parasitic DNA, 3) controlling gene expression, 4) generating new combinations of genes, and 5) providing molecules needed for DNA replication during development. Understanding the role of “downsizing” and reorganization of the somatic genome is critical for understanding the fundamental question of how genomes are organized and the extent to which they can be altered through natural processes but still function normally. This study will synthesize 30 years of research on the genome biology of copepods, microcrustacean zooplankton of which some species excise 50 – 99% of their germline DNA. Understanding based on copepods will be integrated with what occurs via similar processes in protozoans, nematode worms, hagfish and lamprey. Data derived from DNA sequences, histological preparations of cells, and life history traits at the organismal level will be used to infer adaptation at levels from the genome to the whole organism. Products will include (1) a comprehensive description and interpretation of DNA elimination in copepods and comparisons with other taxa that possess a similar trait, (2) patterns of genome size and its correlated evolution with fitness traits in copepods, as inferred using phylogenetic comparative methods, (3) an instructional paper with videos on methods unique to studying DNA elimination in copepods, and (4) critical thinking exercises that use the trait DNA elimination to assess the transfer of skills in using the scientific method from one discipline to another discipline, scale, or context. Additionally, as a large body of the work was conducted with undergraduate researchers, the synthesis will demonstrate the role that research experiences play in training the next generation of scientists and advancing scientific knowledge.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.