Transcriptome and Gene Coexpression Network Analyses of Two Wild Populations Provides Insight into the High-Salinity Adaptation Mechanisms of Crassostrea ariakensis

LncRNA-Mediated Tissue-Specific Plastic Responses to Salinity Changes in Oysters

Salinity is a key environmental factor influencing the survival of aquatic organisms, and transcriptional plasticity is a crucial emergency response to environmental changes. However, most transcriptomic studies on salinity responses have not explored the expression patterns and regulatory mechanisms across different tissues. The Suminoe oyster (Crassostrea ariakensis), a sessile estuarine species that inhabits fluctuating salinity environments, provides an excellent model for studying the molecular basis of salinity response divergence. All eight tissues responded to acute salinity stresses and exhibited distinct tissue-specific expression patterns in both mRNA and long non-coding RNA (lncRNA) profiles across three salinity conditions. The hepatopancreas and striated muscle were identified as tissues specifically sensitive to hyper- and hypo-saline stress, respectively, based on the number, expression pattern, and plasticity of differentially expressed genes (DEGs). We established lncRNA-mRNA regulatory relationships that environmentally responsive lncRNAs enhanced DEGs' expression and underpinning tissue-specific responses. Under moderate stress, the hepatopancreas and striated muscle initiated positive responses related to water transport and shell closure, respectively. Under severe stress, the hepatopancreas activated cellular resistance pathways, while the striated muscle experienced significant cell death. Our findings provide insights into lncRNA-mediated, tissue-specific environmental responses and lay the foundation for further research into the adaptive evolution of tissue-specific regulation.

Chromosome-level genome assembly of the Suminoe oyster Crassostrea ariakensis in south China

The Suminoe oyster Crassostrea ariakensis (Fujita, 1913) is one of the most important ecological and fishery bivalve mollusks with a worldwide distribution. Here, we reported an improved high-quality chromosomal-level genome assembly of C. ariakensis inhabiting the South China Sea, using Nanopore technology, Illumina sequencing, and high-throughput chromosomal conformation capture analysis. The assembled genome size is 631.73 Mb, with contig N50 length of 5.36 Mb and scaffold N50 length of 61.15 Mb, and is assigned to 10 chromosomes. A total of 29,357 protein-coding genes are predicted, 96.68% of which are functionally annotated. The genome contains 347.11 Mb (54.94%) of repetitive elements and 1130 noncoding RNAs. This improved genome assembly of south C. ariakensis is an important resource for understanding oyster diversity and evolution, and provides insights into genetic improvement, protection and management of oyster resource.

Effects of medium- and long-term high-salinity environments on free amino acid content and related genes of Sinonovacula constricta

Introduction

The razor clam, Sinonvacula constricta, one of the important mariculture bivalves in China, has unique flavor and wide salinity adaptability. The unique flavor mainly depends on the content of free amino acids and other umami substances in vivo. However, the flavor divergence of razor clam caused by the variable salinity breeding environment, while the mechanisms remain unclear.

Methods

Here, the razor clams were cultured in high salinity (30 ppt) and normal salinity (20 ppt) for eight weeks, and the effects of salinity on free amino acids and related genes expression in S. constricta were investigated by transcriptomics and metabolomics method.

Results

The results showed the free amino acid content under high salinity environment was significantly higher than normal salinity environment through the duration of the experiment (P < 0.05). The combination of transcriptomic and metabolomic data also indicated that high salinity environment resulted in enhanced metabolism of free amino acids. Furthermore, eight genes such as RALDH2, ACOX1, ALDH-E2 were potentially important for enhancing free amino acids metabolism under high salinity environment.

Discussion

This study preliminarily explained the regulation processes of high salinity environment on the metabolism of free amino acids in razor clams, providing a reference for the flavor regulation mechanism.

Transcriptional responses of Crassostrea hongkongensis under high and low salinity stress

Salinity, a key limiting factor, affects the distribution and survival of marine species. The Hong Kong oyster (Crassostrea hongkongensis), a euryhaline species found along the coast of the South China Sea, has become a major aquaculture bivalve species. To determine the molecular mechanism by which oysters respond to coastal waters with varying salinity levels, we used RNA-seq to sequence the gill samples of oysters exposed to normal (25 ‰, S25), low (5 ‰, S5) and high (35 ‰, S35) salinity conditions for one month. The results revealed different expression transcriptome levels among oysters living under low and high salinity conditions. Using high-throughput sequencing, we identified 811 up-regulated genes and 769 down-regulated genes. As determined by KEGG pathway mapping, the differentially expressed genes (DEGs) were significantly enriched in the prion diseases, histidine metabolism, arginine and proline metabolism, and beta-alanine metabolism pathways in both the S5 vs. S25 and S35 vs. S25 group comparison. Several DEGs including heat shock 70 kDa protein 12B-like, poly (ADP-ribose) polymerase (PARP), and tripartite motif-containing protein 2 (TRIM2), and low-density lipoprotein receptor-like, as well as KEGG pathways, including arginine and proline metabolism, apoptosis, PPAR signaling pathway, the thyroid hormone signaling pathway, were concerning response to salinity stress. Additionally, eight DEGs involved in salinity adaptation were selected for RT-qPCR validation, and the results confirmed the credibility of the transcriptome sequencing data. Overall, we designed a one-month, medium-term experiment to examine the responses of C. hongkongensis exposed to different levels of salinity stress and performed transcriptome analysis using high-throughput sequencing. Our results enhance current understanding of the molecular mechanisms of salinity stress responses in C. hongkongensis and provided insights into the osmotic biology of oysters.

Whole Transcriptome Analysis Reveals the Global Molecular Responses of mRNAs, lncRNAs, miRNAs, circRNAs, and Their ceRNA Networks to Salinity Stress in Hong Kong Oysters, Crassostrea hongkongensis

The Hong Kong oyster, Crassostrea hongkongensis, is an estuarine bivalve with remarkable commercial value in South China, and the increase of salinity in estuaries during the dry season has posed a major threat to the oyster farming. To explore the global transcriptional response to salinity stress, a whole-transcriptome analysis was performed with the gills of oysters in 6‰, 18‰, and 30‰ filtered seawater. Overall, 2243, 194, 371, and 167 differentially expressed mRNAs (DEmRNAs), differentially expressed long non-coding RNAs (DElncRNAs), differentially expressed circular RNAs (DEcircRNAs), and differentially expressed microRNAs (DEmiRNAs) were identified, respectively. Based on GO enrichment and KEGG pathway analysis, these important DEmRNAs, DElncRNAs, DEcircRNAs, and DEmiRNAs were predicted to be mainly involved in amino acids metabolism, microtubule movement, and immune defense. This demonstrated the complexity of dynamic transcriptomic profiles of C. hongkongensis in response to salinity fluctuation. The regulatory relationships of DEmiRNAs-DEmRNAs, DElncRNAs-DEmiRNAs, and DEcircRNAs-DEmiRNAs were also predicted, and finally, a circRNA-associated competing endogenous RNA (ceRNA) network was constructed, consisting of six DEcircRNAs, eight DEmiRNAs, and five DEmRNAs. The key roles of taurine and hypotaurine metabolism and phenylalanine metabolism were highlighted in this ceRNA network, which was consistent with the major contribution of free amino acids to intracellular osmolality and cell volume regulation. Collectively, this study provides comprehensive data, contributing to the exploration of coding and non-coding RNAs in C. hongkongensis salinity response. The results would benefit the understanding of the response mechanism of bivalves against salinity fluctuation, and provide clues for genetic improvement of C. hongkongensis with hyper-salinity tolerance.

Differential gene expression analysis in the scallop Argopecten purpuratus exposed to altered pH and temperature conditions in an upwelling-influenced farming area

Increased carbon dioxide in the atmosphere and its absorption across the ocean surface will alter natural variations in pH and temperature levels, occurring in coastal upwelling ecosystems. The scallop Argopecten purpuratus, one of the most economically important species farmed in northern Chile, has been shown to be vulnerable to these environmental drivers. However, the regulatory responses at the gene-level of scallops to these climate stressors remain almost unknown. Consequently, we used an orthogonal experimental design and RNAseq approach to analyze the acute effects of variability in pH and temperature on gene expression in the muscle tissue of A. purpuratus. In respect to control conditions (pH ~ 8.0/ 14 °C), the influence of low pH (~ 7.7) and temperature (14 °C) induced the activation of several genes associated with apoptotic signaling pathways and protein localization to plasma membrane. Elevated temperature (18 °C) and pH (~8.0) conditions increased the expression of transcripts associated with the activation of muscle contraction, regulation, and sarcomere organization effects on muscle tissue. In scallops exposed to low pH and elevated temperature, the genes expressed were differentially associated with the oxidation-reduction process, signal translation, and positive regulation of GTPase activity. These results indicated that the differentially expressed genes under the experimental conditions tested are mainly related to the mitigation of cellular damage and homeostasis control. Our results add knowledge about the function of the adductor muscle in response to stressors in scallops. Furthermore, these results could help in the identification of molecular biomarkers of stress necessary to be integrated into the aquaculture programs for the mitigation of climate change.

Adaptive divergence and underlying mechanisms in response to salinity gradients between two Crassostrea oysters revealed by phenotypic and transcriptomic analyses

Comparing the responses of closely related species to environmental changes is an efficient method to explore adaptive divergence, for a better understanding of the adaptive evolution of marine species under rapidly changing climates. Oysters are keystone species thrive in intertidal and estuarine areas where frequent environmental disturbance occurs including fluctuant salinity. The evolutionary divergence of two sister species of sympatric estuarine oysters, Crassostrea hongkongensis and Crassostrea ariakensis, in response to euryhaline habitats on phenotypes and gene expression, and the relative contribution of species effect, environment effect, and their interaction to the divergence were explored. After a 2-month outplanting at high- and low-salinity locations in the same estuary, the high growth rate, percent survival, and high tolerance indicated by physiological parameters suggested that the fitness of C. ariakensis was higher under high-salinity conditions and that of C. hongkongensis was higher under low-salinity conditions. Moreover, a transcriptomic analysis showed the two species exhibited differentiated transcriptional expression in high- and low-salinity habitats, largely caused by the species effect. Several of the important pathways enriched in divergent genes between species were also salinity-responsive pathways. Specifically, the pyruvate and taurine metabolism pathway and several solute carriers may contribute to the hyperosmotic adaptation of C. ariakensis, and some solute carriers may contribute to the hypoosmotic adaptation of C. hongkongensis. Our findings provide insights into the phenotypic and molecular mechanisms underlying salinity adaptation in marine mollusks, which will facilitate the assessment of the adaptive capacity of marine species in the context of climate change and will also provide practical information for marine resource conservation and aquaculture.

Effects of low salinity on hemolymph osmolality and transcriptome of the Iwagaki oyster, Crassostrea nippona

Crassostrea nippona is a kind of oysters with great development value as it can be edible in summer for its late reproductive period. Salinity is one of the important limiting abiotic factors to the survival and distribution of this stenohaline species. To better understand the physiological and immunological response of C. nippona to varying environmental salinities, the effects of low salinity on the hemolymph osmolality and gill transcriptome were investigated in this study. The osmolality of hemolymph in vivo and surrounding water were assessed regularly over one week at five test salinities ranging from 5 psμ to 30 psμ. They reached osmotic equilibrium within hours above 15 psμ but remained hyperosmotic at 10 and 5 psμ for the whole sampling period. Through comparative transcriptome analysis, there were less differentially expressed genes (DEGs) in pairwise comparison of S1 (10 psμ) vs S3 (30 psμ) than in S2 (20 psμ) vs S3. KEGG enrichment analysis identified ubiquitin-mediated proteolysis and mitochondrial apoptosis pathway specifically enriched at 10 psμ. This study gained comprehensive insights on the low salinity response of C. nippona at the molecular level, which provide a theoretical basis for understanding the immune mechanism under low salinity stress.

Chromosome-level genome and population genomic analysis provide insights into the evolution and environmental adaptation of Jinjiang oyster Crassostrea ariakensis

The Jinjiang oyster Crassostrea ariakensis, naturally distributing in estuarine regions with low salinity, is an important economic and ecological species in China. However, studies on its genomics and population genetics remain lacking. Here, we assembled the chromosome-level genome of a female C. ariakensis and re-sequenced 261 individuals from five locations in China representing three typical habitats. The C. ariakensis genome was 662.9 Mb with contig N50 length of 5.9 Mb using PacBio HiFi-CCS long reads, and 99.83% sequences were anchored onto 10 pseudochromosomes using Hi-C data. A total of 26,354 protein-coding genes were predicted. We identified three significantly expanded gene families which are closely associated with osmotic pressure regulation, including CDO, SLC13 and SDR. Population structure analysis revealed that the C. ariakensis from five locations were clustered into three typical groups (northern, southern and Shanghai) (K = 3) and their phylogenetic relationship was consistently correlated to their geographical distribution. Furtherly, the differentiation between northern and southern groups was clearly demonstrated by estimated population differentiation coefficient (F_ST  = 0.1154), and the PSMC distribution showed the two groups of effective population size separated at 0.1 Ma. Meanwhile gene flow from southern to Shanghai was detected. Selective sweep analysis between northern and southern group detected genes associated with heat response and salinity adaptation. This study could provide valuable genomic resources and information for further research on the molecular evolution, genetic breeding, biological function and evolutionary adaptation of C. ariakensis.

Genome of the estuarine oyster provides insights into climate impact and adaptive plasticity

Understanding the roles of genetic divergence and phenotypic plasticity in adaptation is central to evolutionary biology and important for assessing adaptive potential of species under climate change. Analysis of a chromosome-level assembly and resequencing of individuals across wide latitude distribution in the estuarine oyster (Crassostrea ariakensis) revealed unexpectedly low genomic diversity and population structures shaped by historical glaciation, geological events and oceanographic forces. Strong selection signals were detected in genes responding to temperature and salinity stress, especially of the expanded solute carrier families, highlighting the importance of gene expansion in environmental adaptation. Genes exhibiting high plasticity showed strong selection in upstream regulatory regions that modulate transcription, indicating selection favoring plasticity. Our findings suggest that genomic variation and population structure in marine bivalves are heavily influenced by climate history and physical forces, and gene expansion and selection may enhance phenotypic plasticity that is critical for the adaptation to rapidly changing environments.

Integrated analysis of transcriptomic and metabolomic data to evaluate responses to hypersalinity stress in the gill of the razor clam (Sinonovacula constricta)

Salinity is an important ecological factor that affects physiological metabolism, survival, and distribution of marine organisms. Despite changes in the osmolarity and composition of the cytosol during salinity shifts, marine mollusks are able to maintain their metabolic function. The razor clam (Sinonovacula constricta) survives the wide range of salinity in the intertidal zone via changes in behavior and physiology. To explore the stress responses and mechanisms of salinity tolerance in razor clams, we collected transcriptomic and metabolomic data from a control group (salinity 20‰, S20) and a salinity-stress group (salinity 35‰, S35). The transcriptome data showed that genes related to the immune system, cytoskeleton remodeling, and signal transduction pathways dominated in the S35 group to counteract hypersalinity stress in the gill. The metabolomic analysis showed that 142 metabolites were significantly different between the S35 and S20 groups and that amino acid and carbohydrate metabolism were affected by hypersalinity stress. Levels of amino acids and energy substances, such as l-proline, isoleucine, and fructose, were higher in the gill of the S35 group. The combination of transcriptomic and metabolomic data indicated that metabolism of amino acids, carbohydrates, and lipids was enhanced in the gill during adaptation to high salinity. These results clarified the complex physiological processes involved in the response to hyperosmotic stress and maintenance of metabolism in the gill of razor clams. These findings provide a reference for further study of the biological responses of euryhaline shellfish to hyperosmotic stress and a molecular basis for the search for populations with high salinity tolerance.

Transcriptomic Analysis of the Cold-Pretreated Larimichthys crocea Showing Enhanced Growth Fitness in Cold Water

The large yellow croaker Larimichthys crocea is an economically important marine fish species endemic to China and East Asia. Ningde area of Fujian Province is a major L. crocea aquaculture and spawning center in China. L. crocea cultivated at the Zhoushan area appears to be popular but suffered high mortality in cold water during winter seasons. To reduce the mortality rate, we pretreated fish with cold shocks prior to shift to cold water. In this study, we show that cold-pretreated L. crocea 12 days after shift to cold water increase the viability by 5.77-fold compared to the unpretreated (live fish 75 versus 13, p value = 1.775e-06, n = 100). The highest loss of 31 out of 100 fish in the unpretreated group occurred in day 3 after temperature shift. To identify the pretreatment-induced transcriptional changes that may be attributed to cold-resistance and survival, we performed RNA-seq analysis of a total of 48 fish that were prior to and 48 h, 54 h, and 72 h after temperature shift in pretreated and unpretreated groups in sextuplicate. Transcriptomic profiling analysis indicates that pretreatment-induced transcriptional alterations of enzymes involved in FASI, β-oxidation, PUFA synthesis, oxidative phosphorylation, and molecular chaperones persisted after temperature shift, suggesting that these metabolic pathways may play a role in L. crocea cold-resistance and survival. Our study provides insights on how the pretreatment enhances the L. crocea growth fitness in cold water.