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（如皮肤、肺细胞）一半的DNA，但仍然含有相同的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系基因组。这种程序化的消除是精确的，每一代都会发生。在被切除的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在一些物种中是相似的，但在另一些物种中是不同的。解释这一现象的假说包括：1)控制体细胞的大小，从而控制发育速度和体型；2)清除寄生DNA的基因组；3)控制基因表达；4)产生新的基因组合；5)提供发育过程中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，对于理解基因组是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，但仍能正常运作，是至关重要的。本研究将综合30年来对桡足类这类浮游微甲壳类动物基因组生物学的研究，其中一些物种的生殖系DNA丢失了50 - 99%。基于桡足类动物的理解将与原生动物、线虫、盲鳗和七鳃鳗的类似过程相结合。从DNA序列、细胞的组织学准备和生物体水平的生活史特征中获得的数据将用于推断从基因组到整个生物体水平的适应性。产品将包括(1)对桡足类DNA消除的全面描述和解释，以及与具有类似特征的其他类群的比较；(2)通过系统发育比较方法推断出的桡足类基因组大小模式及其与适应性特征的相关进化；(3)一篇关于研究桡足类DNA消除的独特方法的教学论文和视频。(4)批判性思维练习，使用特征DNA消除来评估使用科学方法从一个学科到另一个学科、规模或背景的技能转移。此外，由于大部分工作是由本科生研究人员进行的，综合研究将证明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。该奖项反映了美国国家科学基金会的法定使命，并通过使用基金会的知识价值和更广泛的影响审查标准进行评估，被认为值得支持。

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.