Chenyang Yue

Taurine (Tau) is a major organic osmolyte in marine bivalves, yet how its biosynthesis is regulated during salinity stress remains poorly understood. Here, we investigated the coordinated regulation of Tau homeostasis in the estuarine oyster Crassostrea hongkongensis by integrating salinity-responsive gene and protein expression analyses, free amino acid (FAA) profiling, in-situ hybridisation and in vivo RNA interference. We characterized four Tau-related genes—two cysteine sulfinic acid decarboxylase paralogs (ChCSAD1 and ChCSAD2), cysteine dioxygenase 1 (ChCDO1), and glutamate decarboxylase 1 (ChGAD1). The paralogs exhibited reciprocal, salinity-polarized regulation: ChCSAD1 transcript and protein peaked at low salinity, whereas ChCSAD2 peaked at high salinity, and both were enriched in gill epithelial cells. ChCDO1 remained comparatively stable across the salinity gradient, with modest induction under low salinity and predominant localization in gill epithelial cells, whereas ChGAD1 responded to both salinity extremes and was enriched in interlamellar junction cells and muscle fibres. Silencing ChCSAD1 suppressed ChCSAD2 and ChGAD1 while activating ChCDO1; silencing ChCSAD2 activated ChCDO1 and transiently upregulated both ChCSAD1 and ChGAD1, indicating that duplicated CSAD genes form a coupled regulatory module rather than redundant duplicates. Knockdown of either CSAD paralog elevated Tau in the gill while depleting it in the hemolymph, with limited effects on the other measured free amino acids. Our results establish that Tau biosynthesis in C. hongkongensis is governed by an adaptive network integrating CSAD cross-talk and compensatory homolog activation during salinity stress. This work will enrich the knowledge about Tau homeostasis and provides molecular framework for salinity resilience in marine invertebrates.

The Pacific oyster (Crassostrea gigas) and the Fujian oyster (Crassostrea angulata) are both high-yielding farmed oysters. The two are sister subspecies that are difficult to distinguish reliably by appearance and show no reproductive isolation. Owing to their overlapping distribution ranges, the inter-regional transfer of seed and the large-scale use of hybrids, the risk of germplasm admixture has become increasingly prominent. However, accurate and efficient molecular markers capable of distinguishing the two species and their hybrid offspring have long been lacking, which has substantially hampered the conservation of the pure germplasm of each species and the exploitation of heterosis between them. In the present study, marker development was based on whole-genome resequencing data totalling 4916.96 GB from 480 individuals, comprising 24 C. angulata populations and 15 C. gigas populations collected from all coastal provinces of China. An ancestry-informative marker (AIM) set comprising 1085 loci was first constructed and used to identify and exclude recent hybrid individuals. Subsequently, 988 highly differentiated indel loci with FST ≥ 0.9 between the two species were screened, and an ARMS-PCR marker based on the canscf7_5489896 locus was developed for the rapid identification of C. angulata, C. gigas and their hybrids. Validation in six C. angulata populations, four C. gigas populations and one hybrid population yielded an identification accuracy higher than 92%. These results provide a reference workflow for the pure-line identification of closely related species and for the development of nuclear molecular markers, and offer a practical molecular tool for monitoring seed purity, identifying hybrid offspring and conserving the germplasm resources of C. angulata and C. gigas.

Whether marine bivalves, as osmoconformers, actively transport inorganic ions to counter osmotic stress remains unclear due to insufficient direct evidence. The estuarine bivalve Crassostrea hongkongensis offers an ideal model to address this issue, as our previous ultrastructural study hinted at the existence of ionocyte‑like cells in the gill. Here, single‑cell RNA sequencing revealed that the homologs of key ion transporters in oyster gill, Na⁺/K⁺-ATPase α subunit (CHNKAα), Na⁺/K⁺/2Cl⁻ cotransporter 1 (CHNKCC1) and Na⁺/H⁺ exchanger 3 (CHNHE3), lack the cluster‑specific expression typical of teleost homologs. Instead, their transcripts are broadly distributed across multiple gill epithelial cells, confirmed by RNA fluorescence in situ hybridization. At 8 h post‑salinity exposure, CHNKAα and CHNHE3transcripts increased at salinity 30 (positively correlated with gill Na⁺, K⁺ and Cl⁻ contents), whereas CHNKCC1 was upregulated at salinity 6 (negatively correlated), implicating their involvement in active ion transport. Multiplex immunofluorescence revealed an interesting membrane distribution: CHNKAα retained a conserved basal membrane pattern in gill epithelial cells, CHNKCC1 showed an unusual apical localization, and CHNHE3 displayed a cell‑type‑specific dual (apical and basal) membrane distribution. RNA interference-mediated knockdown further indicated that CHNKAα drives Cl⁻ uptake while CHNKCC1 mediates Cl⁻ secretion, directly linking their active transport to salinity‑induced ion content changes. Notably, these observations, particularly membrane distribution and functional contribution to ion transport, do not completely conform to any existing ion transport model in aquatic animals. Our findings provide direct evidence for active ion transport in a euryhaline bivalve under salinity stress and indicate a potential ion transport system distinct from that observed in most teleosts, opening new avenues for understanding osmoregulation in marine invertebrates.

Whether marine bivalves, as osmoconformers, actively transport inorganic ions to counter osmotic stress remains unclear due to insufficient direct evidence. The estuarine bivalve Crassostrea hongkongensis offers an ideal model to address this issue, as our previous ultrastructural study hinted at the existence of ionocyte‑like cells in the gill. Here, single‑cell RNA sequencing revealed that the homologs of key ion transporters in oyster gill, Na⁺/K⁺-ATPase α subunit (CHNKAα), Na⁺/K⁺/2Cl⁻ cotransporter 1 (CHNKCC1) and Na⁺/H⁺ exchanger 3 (CHNHE3), lack the cluster‑specific expression typical of teleost homologs. Instead, their transcripts are broadly distributed across multiple gill epithelial cells, confirmed by RNA fluorescence in situ hybridization. At 8 h post‑salinity exposure, CHNKAα and CHNHE3 transcripts increased at salinity 30 (positively correlated with gill Na⁺, K⁺ and Cl⁻ contents), whereas CHNKCC1 was upregulated at salinity 6 (negatively correlated), implicating their involvement in active ion transport. Multiplex immunofluorescence revealed an interesting membrane distribution: CHNKAα retained a conserved basal membrane pattern in gill epithelial cells, CHNKCC1 showed an unusual apical localization, and CHNHE3 displayed a cell‑type‑specific dual (apical and basal) membrane distribution. RNA interference-mediated knockdown further indicated that CHNKAα drives Cl⁻ uptake while CHNKCC1 mediates Cl⁻ secretion, directly linking their active transport to salinity‑induced ion content changes. Notably, these observations, particularly membrane distribution and functional contribution to ion transport, do not completely conform to any existing ion transport model in aquatic animals. Our findings provide direct evidence for active ion transport in a euryhaline bivalve under salinity stress and indicate a potential ion transport system distinct from that observed in most teleosts, opening new avenues for understanding osmoregulation in marine invertebrates.

Aquaculture has witnessed excellent growth in recent decades, with significant potential for protein nutrition security and jobs. Genomics has significantly enhanced aquaculture technologies across various species and culture processes, improving production efficiency and profitability. With the continuous advances in next-generation sequencing technologies and bioinformatics, substantial genomic resources have been obtained for dozens of aquaculture species. These include the development of high-quality whole-genome sequences, transcriptome databases, and molecular markers, mainly single nucleotide polymorphisms (SNPs), followed by the discovery of high-density linkages and physical maps. This review presents an overview of recent advancements in aquaculture genomics, including genome sequencing and assembly, molecular breeding, genetic characterization of traits, health and biodiversity assessments, and conservation biology of fish and shellfish. The review further examines the challenges impeding the effective implementation of genomics in aquaculture research, as the full potential remains underexploited within this sector. Finally, we highlight the available opportunities, including discussing the future priorities for technologies, auspicious science, and governmental policies for realizing the fullest benefit of genomic advancement in improving the aquaculture industry. The suggestions proposed in this review will facilitate using genomic-informed data to manage valuable aquaculture resources.

Hypoxia frequently triggers mass mortality events in pearl oysters during the summer months. Hypoxic preconditioning (HP), repeated exposure to sublethal low-oxygen conditions, has been proposed as a potential strategy to enhance stress resistance. Here, we investigated how HP affects hypoxia tolerance in the pearl oyster Pinctada fucata martensii, with emphasis on host apoptotic and immune regulation and the gut microbiota. Pearl oysters assigned to HP (experimental group, EG) and to a non-preconditioned control group (CG) were subjected to sustained hypoxic challenge (1.5 ± 0.1 mg/L DO for 15 days). HP significantly increased the expression of apoptosis- and immunity-related genes (MyD88, IκK, NF-κB) while suppressing JNK expression in gills after extended hypoxia (MyD88: EG 2.26 ± 0.65 vs. CG 0.96 ± 0.29, p < 0.05, ~2.3-fold increase; NF-κB: EG 1.50 ± 0.20 vs. CG 0.81 ± 0.31, p < 0.05, ~1.8-fold increase; IκK: EG 1.55 ± 0.38 vs. CG 0.65 ± 0.12, p < 0.05, ~4.0-fold increase; JNK: EG 0.49 ± 0.25 vs. CG 1.44 ± 0.51, p < 0.05, ~0.34-fold), consistent with a pre-activated yet controlled stress response. In parallel, HP markedly reshaped the intestinal microbial community under hypoxia, increasing alpha diversity (Ace, Chao, and Sobs indices) and enriching potentially beneficial bacterial phyla such as Planctomycetota, Nitrospirota, and Fusobacteriota, groups often linked to nutrient cycling and short-chain fatty acid production. Collectively, these results suggest that HP-enhanced hypoxia tolerance in P. f. martensii is associated with coordinated modulation of host apoptotic and immune signaling and concomitant shifts in gut microbiome diversity. These findings highlight the role of the host–microbiota axis in environmental acclimation and suggest that HP may be a practical tool for improving bivalve performance under hypoxic stress in aquaculture.

The innate immunity of marine bivalves is challenged upon exposure to heat stress, especially with increases in the frequency and intensity of heat waves. TLR4 serves a classical pattern recognition receptor in recognizing pathogenic microorganisms and activating immune responses. In this study, three genes, HMTLR4, HMMyD88 and HMTRAF6, were characterized as homologs of genes in the TLR4-MyD88 signaling pathway in the selected scallop strain “Hongmo No. 1”. According to RT-PCR, acute heat stress (32 °C) inhibited genes in the TLR4-MyD88 signaling pathway, and LPS stimulation-induced activation of TLR4-MyD88 signal transduction was also negatively affected at 32 °C. ELISA showed LPS-induced tumor necrosis factor alpha (TNF-α) or lysozyme (LZM) activity, but this was independent of temperature. RNA interference (RNAi) confirmed that HMTLR4 silencing suppressed the expression of its downstream gene, whether at 24 °C or at 32 °C. The level of TNF-α and the activity of LZM also decreased after injection with dsRNA, indicating a negative effect on the innate immunity of scallops. Additionally, acute heat stress affected the suppression of downstream gene expression when compared with that at 24 °C, which led us to the hypothesis that heat stress directly influences the downstream targets of HMTLR4. These results enrich the knowledge of scallop immunity under heat stress and can be beneficial for the genetic improvement of new scallop strains with higher thermotolerance.