Background: Oriental river prawnMacrobrachium nipponenseis an economically important aquaculture species in China, Japan, and Vietnam. In commercial prawn farming, feed cost constitutes about 50 to 65% of the actual variable cost. Improving feed conversion efficiency in prawn culture will not only increase economic benefit, but also save food and protect the environment. The common indicators used for feed conversion efficiency include feed conversion ratio (FCR), feed efficiency ratio (FER), and residual feed intake (RFI). Among these, RFI is much more suitable than FCR and FER during the genetic improvement of feed conversion efficiency for aquaculture species.Results: In this study, the transcriptome and metabolome of hepatopancreas and muscle ofM. nipponensefrom high RFI low RFI groups, which identified after culture for 75 days, were characterized using combined transcriptomic and metabolomic analysis. A total of 4540 differentially expressed genes (DEGs) in hepatopancreas, and 3894 DEGs in muscle were identified, respectively. The DEGs in hepatopancreas were mainly enriched in KEGG pathways including the metabolism of xenobiotics by cytochrome P450 (down-regulated), fat digestion and absorption (down-regulated) and aminoacyl-tRNA biosynthesis (up-regulated), etc. The DEGs in muscle were mainly enriched in KEGG pathways including the protein digestion and absorption (down-regulated), glycolysis/gluconeogenesis (down-regulated), and glutathione metabolism (up-regulated), etc. At the transcriptome level, the RFI ofM. nipponensewas mainly controlled in biological pathways such as the high immune expression and the reduction of nutrients absorption capacity. A total of 445 and 247 differently expressed metabolites (DEMs) were identified in the hepatopancreas and muscle, respectively. At the metabolome level, the RFI ofM. nipponensewas affected considerably by amino acid and lipid metabolism.Conclusions: M. nipponensefrom higher and lower RFI groups have various physiological and metabolic capability processes. The down-regulated genes, such as carboxypeptidase A1, 6-phosphofructokinase, long-chain-acyl-CoA dehydrogenase, et. al., in digestion and absorption of nutrients, and the up-regulated metabolites, such as aspirin, lysine, et. al., in response to immunity could be potential candidate factors contributed to RFI variation forM. nipponense. Overall, these results would provide new insights into the molecular mechanism of feed conversion efficiency and assist in selective breeding to improve feed conversion efficiency inM. nipponense.

The Manila clam (Ruditapes philippinarum) is an economically important bivalve widely cultured in coastal aquaculture systems of China. However, the genome-wide genetic background and germplasm differentiation of geographically distinct populations remain unclear, which constrains germplasm conservation and the development of selective breeding programs. In this study, 50 individuals from five representative coastal populations (QZ, ZZ, ZP, CL, and NH) in China were subjected to whole-genome resequencing, producing 126.67 Gb of clean data and 92,593,087 SNPs after stringent filtering. Genetic diversity analyses showed that nucleotide diversity (π) ranged from 0.2453 to 0.2588, observed heterozygosity (Ho) from 0.1316 to 0.1492, and expected heterozygosity (He) from 0.2303 to 0.2435, with the CL population exhibiting relatively lower diversity. Population differentiation was low to moderate, with pairwise F_ST values ranging from 0.0454 to 0.0557. Principal component analysis, neighbor-joining phylogenetic analysis, and Admixture clustering consistently indicated limited population structure and extensive genetic admixture. TreeMix analysis further revealed directional gene flow among populations. Rapid linkage disequilibrium decay and predominantly positive Tajima’s D values suggested relatively stable demographic histories. Despite low genome-wide differentiation, combined F_ST and nucleotide diversity ratio analyses identified localized selective sweep signals in specific genomic regions. These results provide preliminary genome-wide insights into genetic diversity, population connectivity, and candidate localized differentiation signals in R. philippinarum. Given the low sequencing depth, the findings should be interpreted as population-level observations that require further validation using higher-depth genomic datasets before being applied to germplasm conservation and selective breeding programs.

This study explored the physiological responses and gene expression profiles of the Manila clam (Ruditapes philippinarum) and the hard clam (Mercenaria mercenaria) under heat and hyposaline stress. Experimental conditions involved increasing the temperature from 25 °C to 35 °C and decreasing salinity from 25 ppt to 15 ppt over a 6 h acclimation period, followed by 72 h exposure. Key physiological and immune indicators, including filtration rate, oxygen consumption rate, ammonia excretion rate, and the expression of related genes, were measured. Under heat stress, R. philippinarum exhibited higher filtration, oxygen consumption, and ammonia excretion rates than M. mercenaria at most sampling time points. The expression of fatty acid desaturase (Δ6FAD) and heat shock protein (HSP70) genes increased and then decreased for both species, whereas superoxide dismutase (Cu/Zn SOD) gene expression gradually decreased over time. Furthermore, the expression levels of all three genes were generally significantly higher in M. mercenaria compared to R. philippinarum. Under hyposaline stress, R. philippinarum exhibited significantly higher filtration, oxygen consumption, and ammonia excretion rates than M. mercenaria between 24 h and 72 h. Expression levels of the Na⁺-K⁺-ATPase (NKAα), HSP70, and Cu/Zn SOD genes remained higher in M. mercenaria compared to R. philippinarum. Overall, the present study indicates that M. mercenaria maintains relative stability and R. philippinarum exhibits greater physiological fluctuation under both heat and hyposaline stress. This study highlights bivalve species-specific responses to environmental stressors and provides valuable insights for aquaculture planning and ecological management in different environmental regions, particularly in the context of global climate change.

This study employed an artificial greenhouse-based system to enhance gonadal development in the Manila clam, Ruditapes philippinarum. The dynamics of gonadal development and expression patterns of five regulatory genes were analyzed through histological sections and quantitative PCR. Under the controlled conditions (Chlorophyll a: 18.61 ± 1.36 μg/L; temperature: 27.3 ± 2.0 °C), the clams’ gonads reached full maturity within approximately one month, underscoring the critical importance of appropriate food availability and temperature. Gene expression analysis revealed sex- and stage-specific patterns. The gonadotropin-releasing hormone (GnRH) gene was more expressed in males at day 7, reaching a significant peak at day 7. In contrast, females exhibited synchronized expression peaks for both estrogen-related receptor (ERR) and 17β-hydroxysteroid dehydrogenase (17β-HSD) at day 14 (p < 0.05). Cytochrome P450 17 (CYP17) exhibited a dynamic, sex-specific profile, with significantly higher levels in males at day 7 but elevated expression in females at day 14 and day 21. Furthermore, doublesex and mab-3-related transcription factor 4-like (Dmrt4-like) showed clear sex-dependent temporal patterns: it peaked early during maturation in males, while in females, the peak occurred significantly later, at day 21 (p < 0.05). These dynamic changes in gene expression were closely synchronized with histological alterations, providing mechanistic insights into the regulation of gonadal maturation in R. philippinarum.