Purpose: To identify the differences in gut bacterial community of Parabramis pekinensis under different growth conditions, and the effect of the diet in a controlled habitat on the community structure, aiming to provide a comprehensive survey of how the gut microbiota in P. pekinensis varies depending on habitat. Methods: A total of 73 P. pekinensis from Yangtze River (W), rivers in the outskirts of Jingjiang (Jiangsu province, China, R), and farms (C) were collected to analyze the intestinal microbiota using high-throughput sequencing of the V3-V4 16S ribosomal RNA gene. We also subdivided the gut into the foregut (F), midgut (M), and hindgut (B) to analyze the differences between them. Results: The dominant bacterial phyla in P. pekinensis were Fusobacteria, Firmicutes, Proteobacteria, and Actinobacteria; meanwhile, Cyanobacteria, Bacteroidetes, Chloroflexi, and Verrucomicrobia were also highly abundant. It is worth noting that the abundance of Fusobacteria Cetobacterium was also very high. The abundance and diversity of the intestinal microbiota structure of fish taken from breeding farm were significantly lower than those taken from Yangtze river and Suburban river, and the abundance of Aeromonas in the gut of fish taken from Yangtze river was much higher than that of fish taken from Suburban river. Compared to midgut, foregut and hindgut have similar microbiota structures, but did not differ significantly in them. Conclusions: The core intestinal microbiota of P. pekinensis is the same to other herbivorous and partially omnivorous fish. There were significant differences in the intestinal microbiota structure of P. pekinensis from different habitats, but no significant differences in the microbiota abundance and diversity between the different parts of the intestine.

Parabramis pekinensis was treated as research object in order to investigate the correlation between morphological traits and body weight. We measured 9 morphological indexes including total length (X₁), body length (X₂), body height (X₃), head length (X₄), snout length (X₅), eye diameter (X₆), eye distance (X₇), caudal stalk length (X₈) and caudal stalk height (X₉). The principal morphological traits affecting body weight were screened out and the regression equation was established. The regression equation of Y1 (age 1 group) shape character (X) and weight (Y) was Y = − 169.183 + 32.544 × ₃ + 10.263 × ₄ + 15.655 × ₇. The regression equation of Y2 (age 2 group) shape character (X) and weight (Y) was Y = − 694.082 + 7.725 × ₁ + 72.822 × ₃ + 77.023 × ₆, the regression equation of Y3 (age 3 group) shape character (X) and weight (Y) was Y = − 1161.512 + 26.062 × ₁ + 22.319 × ₂- 107.218 × ₅ + 83.901 × ₇. Gene expression was consistent with these conclusions. TOR signaling pathway expression raised in Y1 then width increased. And GH-IGF-1 signaling pathway expression raised in Y2 then the length increased. In conclusion, the paper could prove that P. pekinensis showed a growth trend, which was increasing width first and length later. In some sense, the study not only enriched the basic biological data of P. pekinensis, but also provided waiting morphological traits for selective breeding of P. pekinensis artificial breeding in future.

Excessive feed input led to eutrophication and Cyanobacterial blooms in the culture of giant freshwater prawn (GFP, Macrobrachium rosenbergii). In order to improve the water quality and control the Cyanobacterial blooms, we tried the mixed culture of oriental river prawn (ORP, Macrobrachium nipponense), which can feed on plant and organic debris. In this study, the culture trial began on June 20th and ended on September 10th. The control group (CG) was GFPs monoculture, while the experimental group (EG) cultured GFPs and ORPs. Water samples were collected from the ponds for five times to compare the changes of water environmental factors and phytoplankton communities in CG and EG. Phosphate, nitrite, sulfide, and ammonia nitrogen in CG were significantly higher than those in EG at the end of culture (p < 0.05). In the middle stage of culture, the Margalef index, Pielou index, and Shannon–Wiener index of EG were significantly higher than those of CG (p < 0.05). The biomass and density of phytoplankton in EG were lower than those in CG, and the occurrence of Cyanobacterial blooms in EG was later. The results indicated that ORPs in the mixed culture model effectively transformed and stored part of the energy by consuming the residual bait, which reduced the degree of eutrophication and Cyanobacterial blooms.

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.

White bream Parabramis pekinensis is an omnivorous fish belong to Cyprinidae that is widespread in Asia. In this study, we presented chromosome-level genome assemblies of P. pekinensis by using PacBio HiFi long reads and Hi-C technology. We assembled high-quality genome of 1.03 Gb with scaffold N50 length of 40.04 Mb, and a total of 98.31% of the assembled sequences were anchored to 24 chromosomes. BUSCO analysis revealed that the genome assembly has a high-level completeness of 98.35% gene coverage. A total of 26,542 protein-coding genes were predicted, of which 92.61% were functionally annotated. The phylogenetic analysis indicated that the lineage leading to P. pekinensis was diverged from the lineage to Megalobrama amblycephala approximately 7.6 million years ago. The high-quality genome assembly provide valuable resources for evolutionary study and genetic breeding of genus Parabramis.