Fenneropenaeus merguiensis is one of the largest species of penaeid shrimp. It has a wide distribution of germplasm resources in the South China Sea and the southeastern coastal regions of China, yet its germplasm characteristics remain insufficiently understood. Therefore, we conducted analyses of basic nutritional components, amino acids, fatty acids, antioxidant indices, and genetic diversity in three F. merguiensis populations (FmRP, FmSZ, FmSY). The results showed a significant difference in ash content, with FmSZ having the highest ash content (1.77 g/100 g) (p < 0.05). A total of 17 amino acids were detected, and FmSZ exhibited higher concentrations of most amino acids, especially essential amino acids (p < 0.05). The analysis of fatty acid composition revealed significant differences between the populations, with FmSY potentially having a nutritional advantage overall (p < 0.05). In terms of antioxidant capacity and genetic diversity, there were no significant differences in total antioxidant capacity (T-AOC), catalase (CAT), or superoxide dismutase (SOD) among the populations (p > 0.05). However, genetic analysis indicated that FmSZ had the lowest inbreeding coefficient and relatively higher genetic diversity. In conclusion, among the three F. merguiensis populations, FmSZ has relatively higher nutritional quality and genetic diversity, and F. merguiensis is a high-quality aquatic product worth promoting. The analysis and characterization of various aspects of F. merguiensis from the three locations provide important information and data support for germplasm resources and genetic breeding efforts.

Due to its high tolerance to salinity and temperature, as well as its strong adaptability, Metapenaeus ensis holds an important position in the Chinese aquaculture industry. However, studies on the evaluation of its germplasm resources remain insufficient. This research conducted an in-depth comparative evaluation of M. ensis from three representative farming regions in China: Sanya, Zhuhai, and Raoping. The nutritional analysis of muscle tissue showed no statistically significant differences in crude ash, moisture, and crude protein content among the populations (p > 0.05). However, significant differences were observed in crude fat and total sugar content (p < 0.05). The MeSY and MeRP populations had higher crude fat content than the MeZH population (p < 0.05), while the MeZH population exhibited the highest total sugar content. In terms of amino acid composition, the MeSY population had relatively higher total essential amino acid content and proportion, as well as higher total amino acid content, both of which were statistically significant (p < 0.05). A fatty acid composition analysis further highlighted the advantages of the MeRP population in several key fatty acids (p < 0.05). Physiological and biochemical analyses showed no significant differences among the three populations in total antioxidant capacity, superoxide dismutase activity, or catalase activity (p > 0.05). A genetic diversity analysis indicated that M. ensis has relatively low diversity, with the MeSY population showing higher SNP density and nucleotide diversity. A genetic differentiation analysis revealed significant genetic differentiation between the MeSY and MeZH populations, while differentiation between the MeZH and MeRP populations was relatively smaller. This comprehensive assessment of nutritional components, amino acids, fatty acids, antioxidant capacity, and genetic diversity highlights the advantages of germplasm resources from different regions. These findings provide valuable insights for future research on the genetic characteristics and breeding potential of M. ensis.

Penaeus semisulcatus, a commercially valuable aquaculture species, is widely distributed along the southeastern coast of China and throughout the South China Sea. Despite its economic importance, the comprehensive understanding of its germplasm characteristics remains limited. This investigation evaluated nutrient profiles, amino acid composition, lipid constituents, antioxidant capacity, and genomic variability across three farmed aquaculture populations maintained under standardized environmental parameters to discern divergence in nutritive attributes and hereditary characteristics. The results revealed significant interpopulation variation in ash content (p < 0.05), while other proximate components showed comparable levels. Among 17 detected amino acids, glutamic acid was the most abundant (2.07–2.30 g/100 g), while cysteine had the lowest concentration (0.10–0.11 g/100 g). Notably, the PsHK population had a relatively higher amino acid content, indicating superior nutritional value. Fatty acid analysis detected 13 fatty acids, with C18:0 (88.27–108.00 mg/100 g) being the most abundant, and C20:2 (3.40–4.70 mg/100 g) the least. The PsHK population exhibited significantly higher levels of all fatty acids compared to the other two populations (p < 0.05). Antioxidant enzyme activity assays revealed no significant differences in antioxidant capacity across the three populations, indicating a similar overall antioxidant status. Genetic diversity analysis indicated that the PsHK population had the highest genetic diversity, with a relatively pronounced genetic differentiation between the PsHK and PsRP populations. In conclusion, the comparative analysis of these three cultured populations highlights that the PsHK population excels in both nutritional composition and genetic diversity. With its superior nutritional profile and rich genetic background, P. semisulcatus shows great potential for aquaculture development. These findings provide valuable insights for future germplasm improvement and aquaculture optimization efforts, offering a scientific basis for refining breeding strategies and enhancing the nutritional evaluation of P. semisulcatus. Additionally, the comparative analysis of genetic diversity and biochemical composition contributes to a better understanding of population variation, which is essential for the sustainable management and utilization of this species in aquaculture.

Penaeus monodon is one of the world’s most important aquaculture species, with its host-associated microbial community playing a crucial role in its growth, metabolism, immune response, and adaptation. In our study, we utilized Illumina high-throughput sequencing to investigate the composition, structure, and function of the intestinal microbial communities of P. monodon from two different regions in Guangdong. Our results identified 176 phyla across both populations, with Proteobacteria and Firmicutes being predominant. Furthermore, we identified 3095 genera, with Photobacterium, Vibrio, and Aliiroseovarius being the most dominant. Functional gene analysis based on KEGG data indicated that the carbohydrate metabolism and amino acid metabolism were significant at the secondary metabolic pathway level. The eggNOG functional annotation revealed that the genes involved in replication, recombination, and repair are of paramount importance. The CAZy annotation results indicated that Glycoside Hydrolases (GH) have the highest abundance. The Pfam annotation analysis showed that the two most prevalent domains are P-loop NTPase and NADP Rossmann. Our investigation provides a reference for species-level and functional-level analyses of the intestinal microbiota of P. monodon, contributing valuable insights into its microbial ecology.