The Yangtze finless porpoise (Neophocaena asiaeorientalis asiaeorientalis, YFP) and the East Asian finless porpoise (Neophocaena asiaeorientalis sunameri, EFP) are 2 subspecies of the narrow-ridged finless porpoise that live in freshwater and saltwater, respectively. The main objective of this study was to provide contiguous chromosome-level genome assemblies for YFP and EFP. Here, we generated and upgraded the genomes of YFP and EFP at the telomere-to-telomere level through the integration of PacBio HiFi long reads, ultra-long ONT reads, and Hi-C sequencing data with a total size of 2.48 Gb and 2.50 Gb, respectively. The scaffold N50 of 2 genomes was 125.12 Mb (YFP) and 128 Mb (EFP) with 1 contig for 1 chromosome. The telomere repeat and centromere position were clearly identified in both YFP and EFP genomes. In total, 5,480 newfound genes were detected in the YFP genome, including 56 genes located in the newly identified centromere regions. Additionally, synteny blocks, structural similarities, phylogenetic relationships, gene family expansion, and inference of selection were studied in connection with the genomes of other related mammals. Our research findings provide evidence for the gradual adaptation of EFP in a marine environment and the potential sensitivity of YFP to genetic damage. Compared to the 34 cetacean genomes sourced from public databases, the 2 new assemblies demonstrate superior continuity with the longest contig N50 and scaffold N50 values, as well as the lowest number of contigs. The improvement of telomere-to-telomere gap-free reference genome resources supports conservation genetics and population management for finless porpoises.

The Yangtze finless porpoise (Neophocaena asiaeorientalis asiaeorientalis; YFP) is the only freshwater cetacean species that remains in the Yangtze River, China. Poyang Lake is connected to the main stream of the Yangtze River, and the number of YFPs in Poyang Lake constitutes approximately half of the total species population. To implement effective conservation measures and formulate scientific genetic management strategies for the YFPs in Poyang Lake, we conducted population genetic analyses on 125 blood samples from the Poyang population and 46 tissue samples from the Anqing population, utilizing mitochondrial DNA D-loop and microsatellite loci. The genetic diversity analysis revealed two haplotypes in the Poyang population, with mitochondrial genetic diversity indices of Hd = 0.481 ± 0.020 and Pi = 0.00078 ± 0.00030. Microsatellite markers further demonstrated indices of Ho = 0.610 and He = 0.655. The genetic differentiation analysis indicated that the two populations exhibited moderate genetic differentiation (0.05 < Fst < 0.15). Upon excluding the dead samples from the Anqing population, the genetic differentiation between the two populations increased and the gene flow diminished. This indicated that certain dead samples from the Anqing population might have originated from Poyang Lake or had a background of Poyang Lake–Yangtze River migration and gene exchange. This finding was further corroborated by STRUCTURE analysis, which revealed genetic admixture between the two populations. We assessed the current genetic diversity of the Poyang population and its genetic differentiation from the Anqing population. This study provides fundamental data for formulating a conservation program for YFPs in Poyang Lake.

The Yangtze finless porpoise (Neophocaena asiaeorientalis asiaeorientalis, YFP) is the only freshwater cetacean species currently found in China’s Yangtze River. To accurately evaluate its genetic diversity and provide reliable molecular markers for population genetic studies, this study developed a highly efficient and reproducible method for identifying polymorphic microsatellite loci using whole-genome sequencing data. Using this method, we identified and validated a set of highly polymorphic microsatellite markers, which were then used to analyze the genetic diversity of the YFP populations in Poyang Lake to evaluate their effectiveness. Our results demonstrated that the screening pipeline successfully identified 220 tetranucleotide repeat microsatellite loci. Based on the principle of uniform chromosomal distribution, 190 loci were randomly selected for experimental validation, of which 19 exhibited stable amplification, high polymorphism, and a low genotyping error rate. Genetic diversity analysis based on these markers revealed significant genetic variation among YFP populations in Poyang Lake, confirming the effectiveness of the developed markers. The polymorphic microsatellite molecular marker system developed in this study demonstrates high reliability and applicability for assessing YFP genetic diversity. This system provides a critical technical foundation for future research in conservation genetics, genetic resource preservation, and the development of genetic management strategies for the species.

Cryopreservation of semen is an important interdisciplinary field at the intersection of reproductive biotechnology and cryobiology, and holds significant value for the genetic rescue of endangered species, long-term preservation of germplasm resources, and management of reproduction in livestock and aquaculture. Although this technology is relatively well established in fish and terrestrial mammals, it still faces numerous challenges in marine mammals, particularly cetaceans. The Yangtze finless porpoise (Neophocaena asiaeorientalis asiaeorientalis), a rare and endemic freshwater porpoise of China, remains at an early stage of research regarding semen cryopreservation, and there is an urgent need to develop a technical system tailored to its unique physiological characteristics. Literature was searched in PubMed, Web of Science, and CNKI from database inception to May 2025. This structured narrative review was based on 77 core publications, including eight original studies on cetacean semen cryopreservation. This structured narrative review synthesizes evidence from cetacean semen cryopreservation research, with particular emphasis on technical insights from the bottlenose dolphin (Tursiops truncatus), Pacific white-sided dolphin (Lagenorhynchus obliquidens), killer whale (Orcinus orca), and beluga (Delphinapterus leucas). Additionally, it incorporates advances in extender formulations and cryoprotectants from studies on other species to summarize key technical parameters suitable for the cryopreservation of Yangtze finless porpoise semen, aiming to provide a theoretical basis and practical framework for establishing an efficient and safe cryopreservation system for this species.

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.

The Yangtze finless porpoise (Neophocaena asiaeorientalis asiaeorientalis) is the only extant freshwater cetacean species inhabiting the Yangtze River in China. Facing significant threats from habitat degradation and human activities, this critically endangered species requires urgent conservation efforts. A thorough understanding of its genetic diversity is fundamental for informing effective conservation strategies. To address the need for stable and reliable molecular markers, this study aimed to develop and validate a set of highly polymorphic single nucleotide polymorphism (SNP) markers. Candidate SNPs were initially identified based on chromosome-level genome and whole-genome resequencing data, yielding a total of 1070 candidate loci. Following the principle of even distribution across chromosomes, 50 SNPs were randomly selected for Sanger sequencing validation, from which 35 polymorphic SNPs were preliminarily confirmed. These 35 SNPs were subsequently genotyped using the Kompetitive allele-specific PCR (KASP) assay, which successfully validated 19 highly polymorphic markers. Genetic diversity analysis using these SNPs successfully captured moderate-to-high polymorphism in the Poyang Lake population, demonstrating the capability of these markers in detecting genetic variation. The SNP markers developed in this study show promising applicability for genetic diversity assessment in the Yangtze finless porpoise. Further validation across broader geographic and demographic samples will be essential to confirm their potential efficiency for detecting spatial heterogeneity and informing region-wide management strategies.