Genome-wide temporal gene expression reveals a post-reproductive shift in the nematode C. briggsae

C. briggsae offers a robust system for comparative investigations of genetic pathways that affect physiological processes. One of these, namely reproduction, directly impacts longevity due to its significant energetic demands. Long-lived mutants often exhibit reproductive impairments, and studies in C. elegans have demonstrated that removal of the germline can promote longevity, underscoring the link between reproduction and aging. Our study focuses on identifying gene expression changes during reproductive and post-reproductive phases in C. briggsae. We conducted whole-genome transcriptome profiling at various adult stages and found that the majority of differentially expressed (DE) genes were downregulated during the reproductive period. Interestingly, this trend reversed post-reproduction, with three-quarters of the genes upregulated—a phenomenon we termed the 'post-reproductive shift'. A similar analysis in C. elegans also showed a downregulation bias during the reproductive period, but the post-reproductive shift was absent. 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 of the reproductive status of animals 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. RNA-seq profiling of C. briggsae AF16 hermaphrodites at day 1, 3, 6, and 9 of adulthood.

拟秀丽隐杆线虫（Caenorhabditis briggsae）是开展影响生理过程的遗传通路比较研究的成熟模型体系。其中繁殖过程因极高的能量消耗，直接关联个体寿命。长寿突变体通常伴随生殖功能受损；此前对秀丽隐杆线虫（Caenorhabditis elegans）的研究已证实，生殖系移除可延长寿命，进一步凸显了生殖与衰老之间的紧密联系。本研究聚焦于拟秀丽隐杆线虫繁殖期与繁殖后期的基因表达变化鉴定。我们对不同成虫阶段的样本开展全基因组转录组分析，结果显示繁殖期的多数差异表达（differentially expressed, DE）基因均呈现下调趋势。有趣的是，这一趋势在繁殖后期发生逆转：四分之三的基因呈现上调，我们将这一现象命名为“繁殖后表达偏移”。对秀丽隐杆线虫的同类分析同样观察到繁殖期的基因下调偏倚，但未发现繁殖后表达偏移现象。在拟秀丽隐杆线虫中，繁殖期的差异表达基因显著富集于基质组（matrisome）、肌肉发育及功能相关的生物学过程；繁殖后期下调的基因则显著富集于DNA损伤修复、应激反应及免疫应答相关通路。此外，脂肪酸代谢、分解代谢及转录调控相关的基因表达模式呈现出更为复杂的变化特征。通过实验操控线虫的生殖状态，可预见性地改变其基因表达谱，为繁殖后表达偏移现象提供了体内实验证据。综上，本研究揭示了拟秀丽隐杆线虫在繁殖期与繁殖后期的全新基因表达模式。本研究数据可为线虫及其他动物模型的跨物种比较研究提供宝贵资源，助力解析影响生殖与衰老的遗传通路的演化机制。本数据集包含拟秀丽隐杆线虫AF16品系雌雄同体成虫在成年第1、3、6、9天的RNA-seq转录组分析结果。