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 (Ctenopharyngodon idella and Megalobrama amblycephala) and two carnivorous (Elopichthys bambusa and Culter alburnus), 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 (|log₂FC| ≥ 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 oard1 exhibited Ka/Ks > 1 in the E. bambusa vs. C. idella 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.

Ongoing urbanization continuously reshapes water quality, habitat structure, and biological communities in river ecosystems; however, its impacts on host-associated microbial communities remain poorly documented. The fish gut microbiota, a critical interface between the aquatic environment and host physiology, is widely recognized as an integrative indicator of both environmental change and host ecological traits. This study established a continuous urbanization gradient along Shanghai’s Suzhou River, spanning from suburban areas through the outer and inner ring roads to the city center. Five common wild fish species (Coilia nasus, Hemiculter bleekeri, Culter alburnus, Acheilognathus macropterus, and Pseudorasbora parva) were collected, and their gut microbiota were characterized via high-throughput 16S rRNA gene sequencing. Significant variation in OTU richness, alpha diversity, and community structure was observed across urbanization gradients and among fish species. Principal coordinate analysis revealed that samples from suburban areas were structurally distinct from those collected in other zones, whereas inner-ring and urban-core areas exhibited substantial compositional overlap. Taxonomic analysis revealed that Firmicutes and Pseudomonadota dominated all samples; however, their relative abundances and genus-level composition varied considerably among fish species and across the urbanization gradient. PICRUSt-based functional prediction indicated that metabolic pathways predominated, particularly those involved in global and overview maps, carbohydrate metabolism, amino acid metabolism, energy metabolism, and metabolism of cofactors and vitamins. Collectively, these findings demonstrate that fish gut microbial communities exhibit spatial structuring along the urbanization gradient, with species-specific responses linked to ecological traits. This study provides valuable data on host-associated microbial communities in urban rivers and offers a reference for incorporating microbial indicators into urban water ecological assessments.