Yafei Duan

While female heterogamety in black tiger shrimp (Penaeus monodon) is consistent with a ZW/ZZ system, the sequence organization of its sex-associated region remains unclear. In this study, we examined the candidate sex-determining region on chromosome 19 (2.71–2.89 Mb) using PacBio HiFi reads from a marker-supported ZW female, genotypes from 200 full-sib offspring, local assembly, and public long reads. Three phase blocks overlapped this interval. Sex-associated SNPs assigned W-like and Z-like alleles in two blocks, while the central block remained unoriented. The first block contained gene24, a partial dmd-3-related gene model, and a 54 bp insertion in gene25 intron 1 (INS00000105; INS54). This insertion, supported by 17 W-like HiFi reads and two local assemblers, was called in 100/100 female offspring and 1/99 called males; one male was uncalled. Sanger reads confirmed the insertion and both flanks in three selected market-sourced females and the no-insertion junction in three selected males. Public reads from a Thai female reproduced the insertion-bearing structure, whereas Australian male reads supported the alternative structure. Separate Thai and Chinese long reads crossed the two phase gaps in their respective samples. Together, these results define local female-associated sequence differences and targets for functional investigation, rather than complete W and Z chromosome sequences.

Fish exhibit a high degree of susceptibility to shifts in thermal conditions within the water. The liver is central to metabolic homeostasis and immune defense, and its physiological stability is critical for fish health. The present study evaluated the hepatic physiological responses of Trachinotus ovatus following a 7-day exposure to high-temperature (HT) stress, including alterations in histology, oxidative stress, iron homeostasis, inflammation, immunity, apoptosis, and bile acid (BA) metabolism. HT stress induced alterations in liver histology and disrupted redox homeostasis, accompanied by enhanced Nrf2-mediated antioxidant signaling and changes in antioxidant defense enzyme activities and peroxide levels. Iron homeostasis and lipid peroxide defense exhibited complex alterations, including Fe levels and NCOA4 expression were increased, accompanied by compensatory upregulation of iron-homeostasis genes ( FTH1 , FPN1 , and NFS1 ) and antioxidant defense genes ( GPx4 , SLC7A11 , and p53 ). However, reduced lipid peroxidation products (LPO and MDA) suggested that these changes reflected regulatory adaptation rather than the execution of ferroptosis. HT stress induced hepatic inflammatory and immune responses, characterized by activation of pro-inflammatory signaling, dysregulated anti-inflammatory regulation, downregulation of IL-8 expression, and downregulation of the immunoglobulin genes IgM and IgT . Apoptosis-related genes showed divergent expression patterns, with CHOP , Casp-9 , and Casp-3 being upregulated, whereas CytC was downregulated. Furthermore, BA metabolism was affected, as shown by reductions in total BA pool size and free BA levels, along with the upregulated expression of BA metabolism-related genes ( FXR , SULT1 , and UGT8 ). Three metabolites, cholic acid, chenodeoxycholic acid, and 7-ketolithocholic acid were identified as potential biomarkers. Collectively, these findings suggest that HT stress impaired hepatic physiological homeostasis in T. ovatus , accompanied by tissue architecture disruption, redox imbalance, inflammatory responses, immune suppression, BA metabolic remodeling, and coordinated changes in iron homeostasis and apoptosis-related regulatory pathways.

Nitrite nitrogen is a prevalent environmental stressor in intensive shrimp aquaculture that impairs growth and health, yet its chronic effects and underlying molecular mechanisms in Penaeus monodon remain incompletely understood. To address this, we exposed juvenile P. monodon (initial body weight 2.06–2.34 g) to 0, 4, and 8 mg/L nitrite nitrogen for 30 days, measuring survival, growth performance, hepatopancreas enzyme activities (ACP, AKP, T-AOC, T-SOD), and conducting transcriptomic profiling of gill and hepatopancreas tissues. Chronic nitrite exposure significantly reduced weight gain rate from 82.98% in the control to 39.33% (4 mg/L) and 33.86% (8 mg/L), with survival declining from 58.89% to 51.11% and 38.89%, respectively. ACP activity and antioxidant capacities (T-AOC and T-SOD) were markedly suppressed, indicating impaired immune and oxidative stress defenses. Transcriptomic analysis revealed tissue-specific responses: gills primarily adjusted nitrogen/amino-acid metabolism at 4 mg/L and mitochondrial oxidative phosphorylation at 8 mg/L, whereas the hepatopancreas showed broader reprogramming involving cell junction integrity, tryptophan–kynurenine metabolism, cofactor/vitamin metabolism, lipid remodeling, cytochrome P450-mediated detoxification, and melanization-related immune pathways at higher stress. These findings demonstrate that chronic nitrite stress progressively erodes shrimp homeostasis through tissue-specific transcriptional reprogramming, forcing resource allocation toward maintenance and defense at the expense of growth, thereby providing a mechanistic basis for nitrite risk assessment and threshold management in aquaculture.

High carbonate alkalinity (CA) is a major constraint on shrimp culture in saline–alkaline waters. The hepatopancreas is central to shrimp immunity and metabolic regulation. Litopenaeus vannamei underwent a 7-day exposure period to 5 mmol/L CA, followed by a subsequent 7-day recovery phase after removal of the stressor. The physiological regulatory mechanism of the hepatopancreas during CA stress and recovery was investigated by integrating multiple biological levels including histomorphology, antioxidant and immune indices, energy metabolism, and metabolite profiles. Results showed that CA stress induced structural changes in the hepatopancreas and triggered stress responses. Specifically, a significant upregulation was observed in genes involved in antioxidation (romo1, nrf2, gpx, hsp70), apoptosis (casp-9, casp-3), endoplasmic reticulum (ER) stress (ire1, xbp1), immune defense (alf, crus, pen-3, lys, propo), and detoxification (cyp450). CA stress also increased osmoregulatory genes (ccp, nhe, ca, aqp, vatp, nka-β, nka-α), whereas clc and tip4 were suppressed. CA stress reduced the levels of energy-metabolism-related biochemical indicators, including glucose (GLU), pyruvic acid (PYR), lactic acid (LAC) and triglycerides (TG), while markedly inducing the expression of genes involved in carbohydrate metabolism (ldh, pdh, hk, pk), lipid metabolism (ampk, srebp, fas), the tricarboxylic acid (TCA) cycle (mdh, cs, idh, odh, sdh, fh), and the electron transport chain (ETC) (ndh, cytc, coi, cco, atph). Moreover, the hepatopancreatic metabolic profile was remodeled, especially “phenylalanine, tyrosine and tryptophan biosynthesis” and the metabolism of β-alanine, arachidonic acid, linoleic acid, and sphingolipids being substantially altered during both the stress and recovery phases. Several functional metabolites linked to stress responses were further pinpointed. Following stress relief, some physiological parameters partially recovered, yet overall function failed to return to normal. Collectively, CA stress compromised hepatopancreatic homeostasis by damaging morphological integrity, eliciting stress and immune responses, and perturbing energy metabolism and metabolite homeostasis; these adverse effects were not readily reversible in the short term.

Intestinal health is crucial for the growth and stress resistance of shrimp. Butyrate, a beneficial metabolite of intestinal microbiota and the primary energy substrate for enterocytes, exerts regulatory effects on intestinal health. Butyrates exist in various chemical forms, yet their application in shrimp remains limited. Therefore, in this study, Penaeus monodon were fed diets supplemented with 1% four types of butyrate (monobutyrin, MB; tributyrin, TB; sodium butyrate, SB; poly-β-hydroxybutyrate, PHB) for 56 days, followed by 48 h of acute nitrite stress. A systematic investigation into their influences on the shrimp growth, intestinal health and nitrite stress resistance was conducted. The results showed that the four butyrate types significantly increased the weight gain rate of the shrimp by more than 25% and improved the survival rate under nitrite stress by more than 28% when compared with the control group (p < 0.05). They also improved intestinal mucosal integrity, and enhanced intestinal antioxidant and immune capacities through the activation of the Nrf2 pathway and the upregulation of immune gene expression. Specifically, T-AOC and SOD activities, as well as the expression levels of Nrf2, GPx, Trx, ALF, Pen3, and serP genes, were significantly upregulated in all four butyrate groups, while MDA content was significantly decreased (p < 0.05). In addition, LPO content, CAT and ASC activities, and the expression of HO1, SOD, Crus, and proPO genes exhibited differential changes among the four butyrate groups. Furthermore, the intestinal microflora structure was reshaped by all four butyrate variants, with notable reductions in pathogenic Vibrio alongside elevated abundances of advantageous taxa including Rhodobacteraceae. In conclusion, butyrate can facilitate the growth and anti-stress capacity of P. monodon by improving intestinal health, with the overall efficacy ranked as TB, PHB, MB and SB under the present study conditions.

Ammonia acts as a key environmental pollutant in fish farming. Elevated ammonia concentrations can induce stress responses in fish, threatening their survival and growth. As a vital metabolic organ, the fish liver plays key roles in detoxification and immune defense. In the present study, juvenile hybrid groupers (Epinephelus fuscoguttatus ♀ × Epinephelus lanceolatus ♂) were subjected to ammonia stress at 4 mg/L (A4) and 8 mg/L (A8) over a 7-day period. Subsequently, multiple physiological aspects of the liver were assessed across several biological levels, encompassing histomorphology, oxidative stress, inflammatory factors, and metabolic profiles. The results showed that ammonia stress caused hepatic morphological alterations and triggered oxidative stress and inflammatory responses. In detail, MDA content and T-AOC and SOD activities were increased in the A4 and A8 groups (P < 0.05), and LPO content was increased in the A8 group (P < 0.05). Meanwhile, the mRNA expression levels of nrf2, trx, tnfα, and il1β genes were upregulated in the A4 and A8 groups (P < 0.05); gpx and il8 genes were upregulated but il10 gene was downregulated in the A8 group (P < 0.05); nqo1 gene was downregulated in the A4 group (P < 0.05). Furthermore, the hepatic metabolite profiles were perturbed, particularly “histidine metabolism” and “biosynthesis of valine, leucine, and isoleucine” pathways. Additionally, several functional metabolites, including l-tryptophan, indole, carnosine, citric acid, sphingosine, pantothenic acid, and inositol, were emerged as potential candidate biomarkers. These findings demonstrated that ammonia stress could induce physiological dysfunction in the liver of groupers through a cascade of tissue damage, activated oxidative stress, disrupted inflammatory responses and altered metabolic profiles, and such adverse effects were markedly aggravated with the increase in ammonia concentration. Future research should focus on long-term ammonia exposure, concentration–time dose effects, and multi-omics integration to clarify the underlying response mechanisms.

Stocking density plays an important role in P. monodon aquaculture. However, its underlying molecular mechanisms remain unknown. In this work, after a 40-day culture period, we studied the effects of different stocking densities (G1: 50, G2: 100, G3: 150 ind/m³) on P. monodon, assessing their growth performances, physiological indexes, and transcriptome profiles. It was found that increased stocking density greatly decreased the growth performance and survival rate as well as the level of immune enzymes (alkaline phosphatase, acid phosphatase) and antioxidant component (total antioxidant capacity, superoxide dismutase, reduced glutathione) activities. Transcriptomic analysis showed that there are 2284 differentially expressed genes in all groups. Enrichment analysis of WGCNA results indicated that the green module associated with G2 was enriched for amino acid metabolism, lipid metabolism and immunity-related pathway. Furthermore, the G3 associated turquoise module was dominated by stress response, detoxification and energy metabolism pathways. Together, high stocking density causes the occurrence of oxidative stress, disturbance to immune system and alteration of metabolism profiles in P. monodon, whereas medium density (G2) is favorable to maintain physiological homeostasis. The results provide theoretical support to optimize aquaculture practice and contribute valuable information for subsequent studies.

Nitrite is a common toxic substance in aquaculture, and microplastics are environmental pollutants capable of adsorbing small molecules/particles. Shrimp rely mainly on the hepatopancreas to accomplish detoxification metabolism. In this study, we investigated the individual and combined effects of nitrite and microplastics on the physiological function of the P. vannamei hepatopancreas. The results demonstrated that both nitrite and microplastics induced morphological damage, with the combined stress exacerbating tissue damage. Oxidative stress biochemical indicators were disrupted, and most enzyme activities and gene expression levels were upregulated to varying degrees in each experimental group. The expression levels of immune genes (cytC, CASP-3, Crus, ALF, and proPO), detoxification metabolism genes (CYP450, EH1, SULT, and UGT), and oxidative-stress-related genes (ROMO1, SOD, GPx, and Trx) exhibited different fluctuations. Nitrite and microplastic stress resulted in altered hepatopancreatic function, mainly involving amino acid biosynthesis and metabolism, ABC transporters, oxidative phosphorylation, and the mTOR pathway. We identified 17 metabolic biomarkers, including 6 lipids (Oleic acid, Prostaglandin G2, Linoleic acid, Palmitic acid, Docosahexaenoic acid, Docosapentaenoic acid), 6 amino acids (L-Leucine, Agmatine, L-Arginine, L-Tyrosine, Ornithine, N-Acetylornithine), and 5 carbohydrates (Glyceric acid, Citric acid, D-Mannose, Sorbitol, Fumaric acid). These findings suggest that nitrite and microplastic stresses cause hepatopancreatic tissue damage and induce oxidative stress, physiological and metabolic dysfunction in the shrimp P. vannamei, thereby impacting its normal physiological functions.

To investigate the effects of supplementing the diet with Caulerpa lentillifera on the growth performance, antioxidant capacity, and intestinal microbiota of Litopenaeus vannamei, a total number of 600 healthy shrimp, each having an average body weight of 2.45 ± 0.12 g, were allocated randomly into five experimental groups. These groups comprised a control group receiving a basal diet (Ctrl) and four treatment groups receiving the basal diet supplemented with varying concentrations of dried C. lentillifera powder: 2.5% (CL1), 5% (CL2), 7.5% (CL3), and 10% (CL4). Each group consisted of four replicates, with 30 shrimp per replicate. The experimental duration was 56 days. The findings demonstrated that supplementing the diet with 5–7.5% C. lentillifera enhanced growth performance and significantly increased the crude protein content in whole shrimp (p < 0.05). Based on the feed conversion ratio (FCR) and protein efficiency ratio (PER) metrics, the optimal inculusion range of C. lentillifera in L. vannamei feed was determined to be 5.25–7.15%. Simultaneously, there was a significant increase in the activities of total superoxide dismutase (T-SOD), glutathione peroxidase (GPx), and peroxidase (POD) enzymes in the hepatopancreas, accompanied by a substantial reduction in malondialdehyde (MDA) levels (p < 0.05). Dietary supplementation with 5–7.5% C. lentillifera induced a numerical elevation of the relative expression levels of antioxidant and protein synthesis genes, although no statistically significant differences were detected among all groups (p > 0.05). Analyses of intestinal microbiota sequencing revealed that the addition of 5–7.5% C. lentillifera improved the intestinal microbiota’s composition and structural characteristics with a focus on metabolic pathways. In conclusion, the inclusion of dietary C. lentillifera positively influenced growth performance, antioxidant capacity, and the intestinal microbiota of L. vannamei. However, excessively high-dose dietary levels may have adverse effects on shrimp; thus, a dietary inclusion level of 5.25–7.15% C. lentillifera is recommended.