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

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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.