Transcriptomics Analysis and Re-sequencing Reveal the Mechanism Underlying the Thermotolerance of an Artificial Selection Population of the Pacific Oyster

Environmental and social framework to protect marine bivalves under extreme weather events

Rising ocean temperatures, a consequence of anthropogenic climate change, are increasing the frequency, intensity, and magnitude of extreme marine heatwaves (MHWs). These persistent anomalous warming events can have severe ecological and socioeconomic impacts, threatening ecologically and economically vital organisms such as bivalves and the ecosystems they support. Developing robust environmental and social frameworks to enhance the resilience and adaptability of bivalve aquaculture is critical to ensuring the sustainability of this crucial food source. This review synthesizes the current understanding of the physiological and ecological impacts of MHWs on commercially important bivalve species farmed globally. We propose an integrated risk assessment framework that encompasses environmental monitoring, farm-level preparedness planning, and community-level social support systems to safeguard bivalve aquaculture. Specifically, we examine heatwave prediction models, local mitigation strategies, and social programs that could mitigate the impacts on bivalve farms and vulnerable coastal communities economically dependent on this fishery. At the farm level, adaptation strategies such as selective breeding for heat-tolerant strains, optimized site selection, and adjustments to culture practices can improve survival outcomes during MHWs. Robust disease surveillance and management programs are essential for early detection and rapid response. Furthermore, we highlight the importance of stakeholder engagement, knowledge exchange, and collaborative governance in developing context-specific, inclusive, and equitable safeguard systems. Proactive measures, such as advanced forecasting tools like the California Current Marine Heat Wave Tracker developed by NOAA's Southwest Fisheries Science Center, enable preemptive action before losses occur. Coordinated preparation and response, underpinned by continuous monitoring and adaptive management, promise to protect these climate-vulnerable food systems and coastal communities. However, sustained research, innovation, and cross-sector collaboration are imperative to navigate the challenges posed by our rapidly changing oceans.

Transcriptomic analysis revealed the dynamic response mechanism to acute ammonia exposure in the ivory shell, Babylonia areolata

The ivory shell (Babylonia areolata) is an economically important shellfish in tropical and subtropical regions, but its intensive culture and biological characteristic of hiding in the sandy substrate make it highly susceptible to ammonia stress. In this study, we investigated the dynamic changes in histopathology, oxidative stress, and transcriptome of the ivory shell at different time points under high concentration (60 mg/L) ammonia exposure. With prolonged exposure to stress, vacuoles appeared in the hepatopancreas while cell volume and intercellular space increased. The activities of superoxide dismutase (SOD) and catalase (CAT) decreased significantly under high concentrations of ammonia-induced stress while malondialdehyde (MDA) levels increased significantly. Integrated analysis of differentially expressed genes (DEGs), weighted gene co-expression network analysis (WGCNA), and quantitative real-time polymerase chain reaction (qRT-PCR) revealed that lipid transport primarily contributed to maintaining cellular homeostasis during the early stage of stress (6 and 12 h). Subsequently, a significant upregulation of oxidation-reduction reactions occurred at the middle stage (24 h), leading to oxidative stress. Finally, during the later stage (48 h), metabolic decomposition provided energy for survival maintenance. Additionally, lysosome and apoptosis were identified as potential key pathways in response to acute ammonia toxicity. Overall, our findings suggest that ivory shells can respond to acute ammonia toxicity via immune and antioxidant defense mechanisms but sustained high concentrations may cause irreversible damage. This study provides valuable insights into the response mechanism of mollusks towards ammonia and serves as a data reference for breeding ammonia-tolerant varieties of ivory shells.

Development of Nanopore sequencing-based full-length transcriptome database toward functional genome annotation of the Pacific oyster, Crassostrea gigas

The Pacific oyster (Crassostrea gigas) is a widely cultivated shellfish in the world, while its transcriptome diversity remains less unexplored due to the limitation of short reads. In this study, we used Oxford Nanopore sequencing to develop the full-length transcriptome database of C. gigas. We identified 77,920 full-length transcripts from 21,523 genes, and uncovered 9668 alternative splicing events and 87,468 alternative polyadenylation sites. Notably, a total of 16,721 novel transcripts were annotated in this work. Furthermore, integrative analysis of 25 publicly available RNA-seq datasets revealed the transcriptome diversity involved in post-transcriptional regulation in C. gigas. We further developed a Drupal based webserver, Cgtdb, which can be used for transcriptome visualization, sequence alignment, and functional genome annotation analyses. This work provides valuable resources and a useful tool for integrative analysis of various transcriptome datasets in C. gigas, which will serve as an essential reference for functional annotation of the oyster genome.

Insights into the Response in Digestive Gland of Mytilus coruscus under Heat Stress Using TMT-Based Proteomics

Ocean warming can cause injury and death in mussels and is believed to be one of the main reasons for extensive die-offs of mussel populations worldwide. However, the biological processes by which mussels respond to heat stress are still unclear. In this study, we conducted an analysis of enzyme activity and TMT-labelled based proteomic in the digestive gland tissue of Mytilus coruscus after exposure to high temperatures. Our results showed that the activities of superoxide dismutase, acid phosphatase, lactate dehydrogenase, and cellular content of lysozyme were significantly changed in response to heat stress. Furthermore, many differentially expressed proteins involved in nutrient digestion and absorption, p53, MAPK, apoptosis, and energy metabolism were activated post-heat stress. These results suggest that M. coruscus can respond to heat stress through the antioxidant system, the immune system, and anaerobic respiration. Additionally, M. coruscus may use fat, leucine, and isoleucine to meet energy requirements under high temperature stress via the TCA cycle pathway. These findings provide a useful reference for further exploration of the response mechanism to heat stress in marine mollusks.

Transcriptomic identification of key genes in Pacific oysters Crassostrea gigas responding to major abiotic and biotic stressors

Oysters are commercially important intertidal filter-feeding species. Mass mortality events of oysters often occur due to environmental stresses, such as exposure to fluctuating temperatures, salinity, and air, as well as to metal pollution and pathogen infection. Here, RNA-seq data were used to identify shared and specific responsive genes by differential gene expression analysis and weighted gene co-expression network analysis. A total of 18 up-regulated and 10 down-regulated shared responsive genes were identified corresponding to five different stressors. Total 27 stressor-specific genes for temperature, 11 for salinity, 80 for air exposure, 51 for metal pollution, and 636 for Vibrio mediterranei pathogen stress were identified in oysters. Elongin-β was identified as a crucial gene for thermal stress response. Some HSP70s were determined to be shared responsive genes while others were specific to thermal tolerance. The proteins encoded by these stress-related genes should be further investigated to characterize their physiological functions. In addition, the uncharacterized proteins and ncRNAs that were identified may be involved in species-specific stress-response and regulatory mechanisms. This study identified specific genes related to stressors relevant to oyster cultivation. These findings provide useful information for new selective breeding strategies using a data driven method.

Integrated application of transcriptomics and metabolomics provides insights into condition index difference mechanisms in the Pacific oyster (Crassostrea gigas)

The condition index (CI) is an economically important tool for assessing the quality of oysters, such as the Pacific oyster Crassostrea gigas. However, little is known about the mechanisms that underlie differences in CI between different C. gigas populations. In this study, we integrated transcriptomic and metabolomic profiling to investigate the mechanisms that underlie the differences between high- and low-CI groups in one- and two-year-old populations of C. gigas. The results indicate that differences in CI were associated with the regulation of growth-related genes, the FoxO signaling pathway, and the complex regulation of carbohydrate, lipid, amino acid, and energy metabolism. Moreover, the mechanisms underlying these differences differed between the populations. This study is the first to elucidate the molecular and chemical mechanisms associated with CI, and the results will be helpful for breeding higher quality oysters.

Population Genomics, Transcriptional Response to Heat Shock, and Gut Microbiota of the Hong Kong Oyster Magallana hongkongensis

The Hong Kong oyster Magallana hongkongensis, previously known as Crassostrea hongkongensis, is a true oyster species native to the estuarine-coast of the Pearl River Delta in southern China. The species—with scientific, ecological, cultural, and nutritional importance—has been farmed for hundreds of years. However, there is only limited information on its genetics, stress adaptation mechanisms, and gut microbiota, restricting the sustainable production and use of oyster resources. Here, we present population structure analysis on M. hongkongensis oysters collected from Deep Bay and Lantau Island in Hong Kong, as well as transcriptome analysis on heat shock responses and the gut microbiota profile of M. hongkongensis oysters collected from Deep Bay. Single nucleotide polymorphisms (SNPs), including those on the homeobox genes and heat shock protein genes, were revealed by the whole genome resequencing. Transcriptomes of oysters incubated at 25 °C and 32 °C for 24 h were sequenced which revealed the heat-induced regulation of heat shock protein pathway genes. Furthermore, the gut microbe community was detected by 16S rRNA sequencing which identified Cyanobacteria, Proteobacteria and Spirochaetes as the most abundant phyla. This study reveals the molecular basis for the adaptation of the oyster M. hongkongensis to environmental conditions.