Ocean and coastal acidification (OCA) poses a significant and rapidly emerging threat to mollusks. The physiological resilience of mollusks to OCA varies considerably; however, the underlying molecular mechanisms remain poorly understood. Seawater in estuaries, being more susceptible to acidification than that in open coastal zones, may enhance the tolerance of resident mollusks to low pH levels. Here, we conducted a comparative analysis between estuarine oysters (Crassostrea ariakensis) and Pacific oysters (Crassostrea gigas) using physiological phenotype and transcriptomic analyses to reveal differential acid-tolerance mechanisms in response to constant pH of 7.8. Our findings indicated that survival and respiration rates of C. ariakensis, which inhabits estuaries with fluctuating pH levels, were higher than those of C. gigas, which inhabits open coastal zones with relative stable pH conditions. Acid-responsive genes identified in C. gigas, including molecular chaperones and immune-related genes, exhibited higher constitutive expression in C. ariakensis under control conditions. Co-expression analyses revealed that C. ariakensis mitigated the effects of low pH by expressing genes involved in ion transporter activity and translation control. C. gigas activated genes associated with glycolipid metabolism while inhibiting cell division during acid stress. These findings suggested that C. ariakensis has evolved into a more energy-efficient regulatory network than C. gigas, incorporating both front-loading and responsive mechanisms to maintain acidbase homeostasis. This study is the first to investigate acid-tolerance differences between mollusks inhabiting estuarine and open coastal environments and provides critical insights into the resilience of mollusks in increasingly acidified oceans.

Low-coverage whole-genome sequencing (lcWGS) followed by imputation is emerging as a cost-effective method for generating a substantial number of single nucleotide polymorphism (SNP) in aquatic species with highly heterozygous and complex genomes. This study represents the first systematic investigation into the application of low-coverage whole-genome sequencing (lcWGS) combined with imputation for genotyping in Pacific abalone (Haliotis discus hannai) without a reference panel. We utilized 1059 Pacific abalone individuals sequenced at an average depth of 7.86×, as well as 16 individuals sequenced at 20×, as sample materials. To assess the genotype imputation accuracy for lcWGS without a reference panel, we simulated data with varying sequencing depths (0.5–4×) and examined the effects of sample size, chromosome length, and minor allele frequency (MAF) using BaseVar and STITCH strategies. Results showed that STITCH achieved high accuracy when the sample size exceeded 400, with a genotype correlation (R²) of 0.98 ± 0.002 and genotype concordance (GC) of 0.99 ± 0.001. Imputation accuracy plateaued when the sample size exceeded 400 and sequencing depth surpassed 1×. Chromosome length had minimal effects, with all three chromosomes achieving an accuracy of approximately 0.98. However, the accuracy for rare MAF (<0.05) was lower, falling below 0.99. A second imputation with Beagle significantly increased SNP detection by 3.9–8.3 folds for a sequencing depth of 0.5–4×, apparently without sacrificing accuracy. To our knowledge, this is the first study of lcWGS analysis conducted in abalone. The findings demonstrate that lcWGS with imputation can achieve high accuracy with moderate sample sizes (n ≥ 400) in Pacific abalone, offering a cost-effective approach for genotyping in aquaculture species.

Mussels’ byssus and their adhesion ability play a crucial role in their attachment and artificial cultivation of mussels. In this study, transcriptomic and proteomic analyses were performed to identify byssogenesis-associated genes in the Mediterranean mussel Mytilus galloprovincialis Lamarck, 1819, seeking to advance our knowledge of the molecular basis of byssal secretion in mussels. Transcriptomic analysis identified 1742 and 1498 differentially expressed genes in the foot tissue of M. galloprovincialis at 9 h and 24 h post-byssal ablation, respectively. Meanwhile, proteomic analysis revealed 1254 and 484 differentially expressed proteins at the same two time points. Integrated analysis identified 121 genes differentially expressed at both transcript and protein levels. Among these genes, 44 were significantly upregulated, and they may constitute high-confidence gene sets associated with mussel byssogenesis. Notably, they included genes encoding tyrosinase-like protein, low affinity immunoglobulin epsilon Fc receptor, and O-methyltransferase MdmC. They were enriched in KEGG pathways, including metabolism of amino acids, lipid metabolism, nucleotide metabolism, and immune system. Quantitative real-time PCR was performed on seven selected genes, confirming that their expression patterns were consistent with those observed in transcriptomic and proteomic sequencing. This study provides novel data and insights for understanding the molecular basis involved in byssus development of M. galloprovincialis.

This study was designed to evaluate the genetic parameters of growth, meat yield and foot color in Pacific abalone (Haliotis discus hannai) to support the development of a quality-oriented breeding program. Using data from 141 pedigreed full-sib families, heritabilities and genetic correlations among these traits were estimated. The results indicated that shell length at varying ages (0.45–0.71) and total wet weight (0.48) exhibited moderate-to-high heritabilities, suggesting substantial potential for genetic improvement in growth traits. The heritabilities for foot color (0.26) and meat weight (0.31) were moderate and statistically significant (p < 0.05), whereas the heritability for meat yield (0.14) was low and not statistically significant (p > 0.05). Strong positive genetic correlations were observed between shell length and total wet weight at harvest (0.90), as well as between total wet weight and meat weight at harvest (0.92). In contrast, the genetic correlations between total wet weight and foot color, and between total wet weight and meat yield, were low and not statistically significant (p > 0.05). These findings suggest that direct selection can effectively improve the growth and meat weight of Pacific abalone. However, improving foot color and meat yield may require independent or multi-trait selection approaches. Overall, this study provides crucial data for formulating a comprehensive breeding strategy that integrates both production efficiency and product quality in Pacific abalone aquaculture.