Genome-Wide Temporal Gene Expression Reveals a Post-Reproductive Shift in the Nematode <i>Caenorhabditis briggsae</i>

The nematodes Caenorhabditis briggsae and its well-known cousin Caenorhabditis elegans offer many features for comparative investigations of genetic pathways that affect physiological processes. Reproduction is one such process that directly impacts longevity due to its significant energetic demands. To study gene expression changes during reproductive and post-reproductive phases in both these nematodes, we conducted whole-genome transcriptome profiling at various adult stages. The results revealed that the majority of differentially expressed (DE) genes were downregulated during the reproductive period in both species. Interestingly, in C. briggsae, this trend reversed during post-reproduction, with three-quarters of the DE genes becoming upregulated. Additionally, a smaller set of DE genes showed an opposite expression trend, i.e. upregulation followed by post-reproductive downregulation. Overall, we termed this phenomenon the "post-reproductive shift". In contrast, the post-reproductive shift was much less pronounced in C. elegans. In C. briggsae, DE genes were enriched in processes related to the matrisome, muscle development and function during the reproductive period. Post-reproductive downregulated genes were enriched in DNA damage repair, stress response, and immune response. Additionally, terms related to fatty acid metabolism, catabolism, and transcriptional regulation exhibited complex patterns. Experimental manipulations in C. briggsae to affect their reproductive status predictably altered gene expression, providing in vivo support for the post-reproductive shift. Overall, our study reveals novel gene expression patterns during reproductive and post-reproductive changes in C. briggsae. The data provide a valuable resource for cross-sectional comparative studies in nematodes and other animal models to understand evolution of genetic pathways affecting reproduction and aging.