Siniperca roulei is primarily distributed in the eastern waters of China, with its population being both scarce and vulnerable. Research on this species remains limited, with few studies conducted on its biology and genetics, which hampers efforts to conserve its germplasm resources. To support breeding and conservation efforts, we generated a gap-free genome assembly using a combination of DNBSeq short reads, PacBio HiFi long reads, Nanopore ultra-long reads, and Hi-C data. The nearly telomere-to-telomere (T2T) genome of S. roulei spans 717.34 Mb, with a contig N50 of 30.25 Mb, and each chromosome is represented by a single contig. A total of 26,596 genes were predicted, with 87.97% functionally annotated. These high-precision genomic data provide valuable insights into the germplasm resources of S. roulei, offering crucial information for clarifying the taxonomic status and evolutionary history of sinipercids. These findings are significant for the conservation and sustainable use of its germplasm resources.

Coilia nasus, a typical species with migratory–sedentary polymorphism, shows different intestinal microbiota characteristics among its different ecotypes. This is attributed to differences in feeding habits and habitat environments (such as water temperature, salinity, etc.). This study constructed a database of intestinal microbiota for three ecological types of C. nasus, namely migratory type (comprising marine populations and freshwater populations), sedentary type and aquaculture-reared type, through 16S rRNA amplicon sequencing technology. This study investigates the ecological mechanisms underlying microbiota differentiation, focusing on three key drivers: environmental selection, host nutritional metabolism requirements, and host life history strategies. The results showed that the core flora of C. nasus consisted of Firmicutes, Proteobacteria, and Actinobacteria. Both the depletion of microbial taxa and the enrichment of marine-adapted bacterial lineages—including Proteobacteria and Psychrobacter—are associated with elevated salinity in the migratory marine population of C. nasus. In contrast, the elevated relative abundance of Actinobacteria in aquaculture-reared C. nasus is likely attributable to dietary supplementation with protein- and lipid-rich artificial feed. Functional correlation analysis holds promise for partially predicting the microbiota’s metabolic functional succession patterns. The dominance of Pseudomonas_E in the migratory freshwater population is consistent with its well-documented physiological versatility and adaptive capacity in dynamically fluctuating aquatic habitats. The elevated abundance of Cyanobacteria in the sedentary population C. nasus coincides with the water bloom in their habitat, suggesting that the structure of the microbiota may serve as a novel biomarker for indicating the ecosystem. In conclusion, this study identifies potential molecular markers for tracing genetic resources and distinguishing ecological types of C. nasus, while establishing a theoretical foundation for elucidating the co-evolutionary dynamics between fish hosts and their associated microbiota—and thereby informing both conservation strategies for wild populations and microbiota-informed aquaculture practices.