Xue Hua, Gu Hailong, Yang Liu, Chen Jingchen, Tang Wenqiao
Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai Ocean University, Shanghai 201306, China.
Taizhou Institute of Agricultural Science, Jiangsu Academy of Agricultural Sciences, Taizhou 225300, China.
Animals (Basel). 2025 Sep 19;15(18):2741. doi: 10.3390/ani15182741.
Olfaction plays a crucial role in fish feeding behaviors and ecological adaptation. However, systematic studies on its transcriptional regulation and molecular evolutionary mechanisms in herbivorous and carnivorous fishes remain scarce. In this study, we analyzed four Xenocyprididae species: two herbivorous ( and ) and two carnivorous ( and ), using olfactory rosette transcriptome sequencing and cross-species comparisons. The number of unigenes per species ranged from 40,229 to 42,405, with BUSCO completeness exceeding 89.2%. Functional annotation was performed using six major databases. Olfactory-related candidate genes were identified based on Pfam domains (7tm_4) and KEGG pathways (ko04740), revealing 8-19 olfactory receptor genes per species. These candidate genes were predominantly enriched in the olfactory transduction and neuroactive ligand-receptor interaction pathways. A total of 3681 single-copy orthologous genes were identified, and their expression profiles exhibited clear interspecific divergence without forming strict clustering by dietary type. High-threshold differentially expressed trend genes (|logFC| ≥ 4) were enriched in pathways related to RNA processing, metabolite transport, and xenobiotic metabolism, suggesting that the olfactory system may participate in diverse adaptive responses. Ka/Ks analysis indicated that most homologous genes were under purifying selection, with only 0.87-2.07% showing positive selection. These positively selected genes were enriched in pathways related to immune response and neural regulation, implying potential roles in adaptive evolution associated with ecological behavior. Furthermore, the olfactory-related gene exhibited Ka/Ks > 1 in the vs. comparison. qRT-PCR validation confirmed the reliability of the RNA-Seq data. This work is the first to integrate two complementary indicators-expression trends and evolutionary rates-to systematically investigate the transcriptional regulation and molecular evolution of the olfactory system in Xenocyprididae species under the context of dietary differentiation, providing valuable reference data for understanding the perceptual basis of dietary adaptation in freshwater fish.
嗅觉在鱼类摄食行为和生态适应中起着至关重要的作用。然而，关于草食性和肉食性鱼类嗅觉转录调控及分子进化机制的系统研究仍然匮乏。在本研究中，我们对四种鲤科鱼类进行了分析：两种草食性鱼类（ 和 ）以及两种肉食性鱼类（ 和 ），采用嗅叶转录组测序和跨物种比较的方法。每个物种的单基因数量在40,229至42,405之间，BUSCO完整性超过89.2%。使用六个主要数据库进行功能注释。基于Pfam结构域（7tm_4）和KEGG通路（ko04740）鉴定嗅觉相关候选基因，每个物种发现8至19个嗅觉受体基因。这些候选基因主要富集在嗅觉转导和神经活性配体-受体相互作用通路中。共鉴定出3681个单拷贝直系同源基因，其表达谱呈现出明显的种间差异，并未按食性类型形成严格聚类。高阈值差异表达趋势基因（|logFC|≥4）富集在与RNA加工、代谢物运输和异生物质代谢相关的通路中，表明嗅觉系统可能参与多种适应性反应。Ka/Ks分析表明，大多数同源基因受到纯化选择，只有0.87 - 2.07%表现出正选择。这些正选择基因富集在与免疫反应和神经调节相关的通路中，暗示其在与生态行为相关的适应性进化中可能发挥的作用。此外，嗅觉相关基因 在 与 的比较中表现出Ka/Ks>1。qRT-PCR验证证实了RNA-Seq数据的可靠性。本研究首次整合表达趋势和进化速率这两个互补指标，系统地研究鲤科鱼类在食性分化背景下嗅觉系统的转录调控和分子进化，为理解淡水鱼食性适应的感知基础提供了有价值的参考数据。
