RNA-Seq analysis and WGCNA reveal dynamic molecular responses to air exposure in the hard clam Mercenaria mercenaria

Differential toxic effects of nano-titanium dioxide on clams (Meretrix meretrix) with various individuality

Nano-TiO2 is inevitably released into aquatic environment with increasing of nanotechnology industries. Study pointed that different individuality showed divergent behavioral and physiological response when facing environmental stress. However, the effects of nano-TiO2 on tolerance of bivalves with different individualities remain unknown. In the study, clams were divided into two types of individuality - proactive and reactive by post-stress recovery method. It turned out that proactive individuals had quicker shell opening level, stronger burrowing behavior, faster feeding recovery, higher standard metabolic rate and more rapid ammonia excretion ability than reactive individuals after exposed to air. Then, the survival rate, hemocytes response and oxidase activity of classified clams were evaluated after nano-TiO2 exposure. Results showed that after 30 d exposure, proactive individuals accelerated burrowing behavior with higher survival rate. Moreover, proactive clams had better adaptability and less hemocytes response and oxidative damage than reactive clams. The study highlights the individualities of marine shell fish determine individual capacity to adapt to environmental changes, play important roles in aquaculture and coastal ecosystem health.

Multi-omics reveals largely distinct transcript- and protein-level responses to the environment in an intertidal mussel

Organismal responses to stressful environments are influenced by numerous transcript- and protein-level mechanisms, and the relationships between expression changes at these levels are not always straightforward. Here, we used paired transcriptomic and proteomic datasets from two previous studies from gill of the California mussel, Mytilus californianus, to explore how simultaneous transcript and protein abundance patterns may diverge under different environmental scenarios. Field-acclimatized mussels were sampled from two disparate intertidal sites; individuals from one site were subjected to three further treatments (common garden, low-intertidal or high-intertidal outplant) that vary in temperature and feeding time. Assessing 1519 genes shared between the two datasets revealed that both transcript and protein expression patterns differentiated the treatments at a global level, despite numerous underlying discrepancies. There were far more instances of differential expression between treatments in transcript only (1451) or protein only (226) than of the two levels shifting expression concordantly (68 instances). Upregulated expression of cilium-associated transcripts (likely related to feeding) was associated with relatively benign field treatments. In the most stressful treatment, transcripts, but not proteins, for several molecular chaperones (including heat shock proteins and endoplasmic reticulum chaperones) were more abundant, consistent with a threshold model for induction of translation of constitutively available mRNAs. Overall, these results suggest that the relative importance of transcript- and protein-level regulation (translation and/or turnover) differs among cellular functions and across specific microhabitats or environmental contexts. Furthermore, the degree of concordance between transcript and protein expression can vary across benign versus acutely stressful environmental conditions.

Molecular evidence for the adaptive evolution in euryhaline bivalves

Marine bivalves inhabiting intertidal and estuarine areas are frequently exposed to salinity stress due to persistent rainfall and drought. Through prolonged adaptive evolution, numerous bivalves have developed eurysalinity, which are capable of tolerating a wide range of salinity fluctuations through the sophisticated regulation of physiological metabolism. Current research has predominantly focused on investigating the physiological responses of bivalves to salinity stress, leaving a significant gap in our understanding of the adaptive evolutionary characteristics in euryhaline bivalves. Here, comparative genomics analyses were performed in two groups of bivalve species, including 7 euryhaline species and 5 stenohaline species. We identified 24 significantly expanded gene families and 659 positively selected genes in euryhaline bivalves. A significant co-expansion of solute carrier family 23 (SLC23) facilitates the transmembrane transport of ascorbic acids in euryhaline bivalves. Positive selection of antioxidant genes, such as GST and TXNRD, augments the capacity of active oxygen species (ROS) scavenging under salinity stress. Additionally, we found that the positively selected genes were significantly enriched in KEGG pathways associated with carbohydrates, lipids and amino acids metabolism (ALDH, ADH, and GLS), as well as GO terms related to transmembrane transport and inorganic anion transport (SLC22, CLCND, and VDCC). Positive selection of MCT might contribute to prevent excessive accumulation of intracellular lactic acids during anaerobic metabolism. Positive selection of PLA2 potentially promote the removal of damaged membranes lipids under salinity stress. Our findings suggest that adaptive evolution has occurred in osmoregulation, ROS scavenging, energy metabolism, and membrane lipids adjustments in euryhaline bivalves. This study enhances our understanding of the molecular mechanisms underlying the remarkable salinity adaption of euryhaline bivalves.

Integrated transcriptomic and metabolomic analysis reveals the response of pearl oyster (Pinctada fucata martensii) to long-term hypoxia

The frequency at which organisms are exposed to hypoxic conditions in aquatic environments is increasing due to coastal eutrophication and global warming. To reveal the effects of long-term hypoxic stress on metabolic changes of pearl oyster, commonly known as Pinctada (Pinctada fucata martensii), the present study performed the integrated analysis of transcriptomics and metabolomics to investigate the global changes of genes and metabolites following 25 days hypoxia challenge. Transcriptome analysis detected 1108 differentially expressed genes (DEGs) between the control group and the hypoxia group. The gene ontology (GO) analysis of DEGs revealed that they are significantly enriched in functions such as "microtubule-based process", "histone (H3-K4, H3-K27, and H4-K20) trimethylation", "histone H4 acetylation", "kinesin complex", and "ATPase activity", and KEGG pathway functions, such as "DNA replication", "Apoptosis", and "MAPK signaling pathways". Metabolome analysis identified 68 significantly different metabolites from all identified metabolites, and associated with 25 metabolic pathways between the control and hypoxia groups. These pathways included aminoacyl-tRNA biosynthesis, arginine and proline metabolism, and phenylalanine metabolism. Our integrated analysis suggested that pearl oysters were subject to oxidative stress, apoptosis, immune inhibition, and neuronal excitability reduction under long-term hypoxic conditions. We also found a remarkable depression in a variety of biological functions under long-term hypoxia, including metabolic rates, biomineralization activities, and the repression of reorganization of the cytoskeleton and cell metabolism. These findings provide a basis for elucidating the mechanisms used by marine bivalves to cope with long-term hypoxic stress.

ROS-induced moderate autophagy of haemocytes confers resistance of Mercenaria mercenaria to air exposure stress

Air exposure (AE) is a significant environmental stressor that can lead to desiccation, hypoxia, starvation, and disruption of cellular homeostasis in marine bivalves. Autophagy is a highly conserved catabolic pathway that facilitates the degradation of damaged macromolecules and organelles, thereby supporting cellular stress responses. To date, autophagy-mediated resistance mechanisms to AE stress remain largely elusive in bivalves. In this study, we performed a multi-tool approach to investigate the autophagy-related physiological regulation in hard clams (Mercenaria mercenaria) under different duration of AE (T = 0, 1, 5, 10, 20, 30 days). We observed that autophagy of haemocytes was significantly activated on day 5. However, autophagy activity began to significantly decline from day 10 to day 30. Autophagy was significantly inhibited after antioxidant treatment, indicating that reactive oxygen species (ROS) was an endogenous inducer of autophagy. A significant decline in the survival rate of hard clams was observed after injection of ammonium chloride or carbamazepine during AE stress, suggesting that moderate autophagy was conducive for clam survival under AE stress. We also observed DNA breaks and high levels of apoptosis in haemocytes on day 10. Activation of apoptosis lagged behind autophagy, and the relationship between autophagy and apoptosis might shift from antagonism to synergy with the duration of stress. This study provides novel insights into the stress resistance mechanisms in marine bivalves.

Comparison of the flavor qualities between two varieties of Mercenaria mercenaria

The saltwater hard clam Mercenaria mercenaria (M. mercenaria) as a representative of low-value shellfish, enhancing its flavor quality, is the key to enter the high-end market. Nevertheless, there has not been reported research on the flavor quality of M. mercenaria. This study compared the flavor quality of selective and non-selective saltwater hard clams of M. mercenaria by using various indicators: proximate component, free amino acids, nucleotides, and metabolomic analysis. The results indicated that selective breeding contributed to the significant improvement contents of crude protein, flavor-associated free amino acids (glutamic acid, aspartic acid, proline, etc.), and nucleotides (AMP) (P < 0.05). Then, the metabolome was utilized to assess the metabolite changes in the pre/post-selective breeding of M. mercenaria and further understand the flavor characteristics and metabolic status. In the metabolomics assay, among the 3143 quantified metabolites, a total of 102 peaks were identified as significantly different metabolites (SDMs) between the selective and non-selective varieties of M. mercenaria (VIP > 1 and P < 0.05). These results can provide new insights for future research on improving the quality of saltwater bivalves through selective breeding.

Cardiac performance and heart gene network provide dynamic responses of bay scallop Argopecten irradians irradians exposure to marine heatwaves

The increased frequency of marine heat waves (MHWs) caused by global climate change is predicted to threaten the survival of economic bivalves, therefore having severely adverse effects on local ecological communities and aquaculture production. However, the study of scallops facing MHWs is still scarce, particularly in the scallop Argopecten irradians irradians, which has a significant share of "blue foods" in northern China. In the present study, bay scallop heart was selected to detect its cardiac performance, oxidative impairment and dynamic molecular responses, accompanied by assessing survival variations of individuals in the simulated scenario of MWHs (32 °C) with different time points (0 h, 6 h, 12 h, 24 h, 3 d, 6 d and 10 d). Notably, cardiac indices heart rate (HR), heart amplitude (HA), rate-amplitude product (RAP) and antioxidant enzyme activities superoxide dismutase (SOD) and catalase (CAT) all peaked at 24 h but sharply dropped on 3 d, coinciding with mortality. Transcriptome analysis revealed that the heart actively defended against heat stress at the acute stage (<24 h) via energy supply, misfolded proteins correction and enhanced signal transduction, whereas regulation of the defense response and apoptotic process combined with twice transcription initiation were the dominant responses at the chronic stage (3-10 d). In particular, HSP70 (heat shock protein 70), HSP90 and CALR (calreticulin) in the endoplasmic reticulum were identified as the hub genes (top 5 %) in the HR-associated module via WGCNA (weighted gene co-expression network analysis) trait-module analysis, followed by characterization of their family members and diverse expression patterns under heat exposure. Furthermore, RNAi-mediated knockdown of CALR expression (after 24 h) significantly weakened the thermotolerance of scallops, as evidenced by a drop of 1.31 °C in ABT (Arrhenius break temperature) between the siRNA-injected group and the control group. Our findings elucidated the dynamic molecular responses at the transcriptome level and verified the cardiac functions of CALR in bay scallops confronted with stimulated MHWs.

Integrated transcriptomic and metabolomic analysis sheds new light on adaptation of Pinctada fucata martensii to short-term hypoxic stress

Analyses of the transcriptome and metabolome were conducted to clarify alterations of key genes and metabolites in pearl oysters following exposure to short-term hypoxic treatment. We totally detected 209 DEGs between the control and hypoxia groups. Enrichment analysis indicated the enrichment of GO terms including "oxidation-reduction process", "ECM organization", "chaperone cofactor-dependent protein refolding", and "ECM-receptor interaction" KEGG pathway by the DEGs. In addition, between the two groups, a total of 28 SDMs were identified, which were implicated in 13 metabolic pathways, such as "phenylalanine metabolism", "D-amino acid metabolism", and "aminoacyl-tRNA biosynthesis". Results suggest that pearl oysters are exposed to oxidative stress and apoptosis under short-term hypoxia. Also, pearl oysters might adapt to short-term hypoxic treatment by increasing antioxidant activity, modulating immune and biomineralization activities, maintaining protein homeostasis, and reorganizing the cytoskeleton. The results of our study help unveil the mechanisms by which pearl oysters respond adaptively to short-term hypoxia.

Genome-wide transcriptome analysis reveals the regulatory network governing terpene trilactones biosynthesis in Ginkgo biloba

Ginkgo biloba L. is currently the only remaining gymnosperm of the Ginkgoaceae Ginkgo genus, and its history can be traced back to the Carboniferous 200 million years ago. Terpene trilactones (TTLs) are one of the main active ingredients in G. biloba, including ginkgolides and bilobalide. They have a good curative effect on cardiovascular and cerebrovascular diseases because of their special antagonistic effect on platelet-activating factors. Therefore, it is necessary to deeply mine genes related to TTLs and to analyze their transcriptional regulation mechanism, which will hold vitally important scientific and practical significance for quality improvement and regulation of G. biloba. In this study, we performed RNA-Seq on the root, stem, immature leaf, mature leaf, microstrobilus, ovulate strobilus, immature fruit and mature fruit of G. biloba. The TTL regulatory network of G. biloba in different organs was revealed by different transcriptomic analysis strategies. Weighted gene co-expression network analysis (WGCNA) revealed that the five modules were closely correlated with organs. The 12 transcription factors, 5 structural genes and 24 Cytochrome P450 (CYP450) were identified as candidate regulators for TTL accumulation by WGCNA and cytoscape visualization. Finally, 6 APETALA2/ethylene response factors, 2 CYP450s and bHLH were inferred to regulate the metabolism of TTLs by correlation analysis. This study is the comprehensive in authenticating transcription factors, structural genes and CYP450 involved in TTL biosynthesis, thereby providing molecular evidence for revealing the comprehensive regulatory network involved in TTL metabolism in G. biloba.

PacBio Full-Length and Illumina Transcriptomes of the Gill Reveal the Molecular Response of Corbicula fluminea under Aerial Exposure

Air exposure is a common stress for Corbicula fluminea, an economically important freshwater shellfish consumed in China, during aquaculture and transportation. However, little is known about its molecular responses to air exposure. Therefore, this study used a combination of PacBio full-length and Illumina transcriptomes to investigate its molecular responses to air exposure. A total of 36,772 transcripts were obtained using PacBio sequencing. Structural analysis identified 32,069 coding sequences, 1906 transcription factors, 8873 simple sequence repeats, and 17,815 long non-coding RNAs. Subcellular localization analysis showed that most transcripts were located in the cytoplasm and nucleus. After 96-h of air exposure, 210 differentially expressed genes (DEGs) in the gill were obtained via Illumina sequencing. Among these DEGs, most of the genes related to glycolysis, tricarboxylic acid cycle, lipid metabolism, and amino acid metabolism were upregulated. Additionally, many DEGs associated with immunity, cytoskeleton reorganization, autophagy, and ferroptosis were identified. These findings indicated that metabolic strategy change, immune response, cytoskeleton reconstruction, autophagy, and ferroptosis might be the important mechanisms that C. fluminea use to cope with air exposure. This study will enrich the gene resources of C. fluminea and provide valuable data for studying the molecular mechanisms coping with air exposure in C. fluminea and other freshwater mollusks.

Dynamic transcriptome and LC-MS/MS analysis revealed the important roles of taurine and glutamine metabolism in response to environmental salinity changes in gills of rainbow trout (Oncorhynchus mykiss)

Recently, the frequent salinity fluctuation has become a growing threat to fishes. However, the dynamic patterns of gene expression in response to salinity changes remain largely unexplored. In the present study, 18 RNA-Seq datasets were generated from gills of rainbow trout at different salinities, including 0 ‰, 6 ‰, 12 ‰, 18 ‰, 24 ‰ and 30 ‰. Based on the strict thresholds, we have identified 63, 1411, 2096, 1031 and 1041 differentially expressed genes in gills of rainbow trout through pairwise comparisons. Additionally, weighted gene co-expression network analysis was performed to construct 18 independent modules with distinct expression patterns. Of them, green and tan modules were found to be tightly related to salinity changes, several hub genes of which are known as the important regulators in taurine and glutamine metabolism. To further investigate their potential roles in response to salinity changes, taurine, glutamine, and their metabolism-related glutamic acid and α-ketoglutaric acid were accurately quantitated using liquid chromatography-tandem mass spectrometry analysis. Results clearly showed that their concentrations were closely associated with salinity changes. These findings suggested that taurine and glutamine play important roles in response to salinity changes in gills of rainbow trout, providing new insights into the molecular mechanism of fishes in salinity adaptation.

Histological, physiological, and transcriptomic responses of hepatopancreas to air exposure in asian freshwater clam Corbicula fluminea

Corbicula fluminea (C. fluminea) is an important freshwater economy shellfish in China, but it often suffers from air exposure during transportation. In this study, we investigated the histological, physiological (mainly including respiratory metabolism, antioxidant capacity, and immune function), and transcriptomic responses of hepatopancreas in C. fluminea to different times of air exposure. At histological level, air exposure caused vacuolation of digestive cells (24-96 h) and enlargement of digestive tubule lumen (6-96 h) in hepatopancreas. At physiological level, the activities of enzymes related to glycolysis (hexokinase and pyruvate kinase) and anaerobic respiration (lactate dehydrogenase) were increased first (6-24 h) of air exposure, then came back to normal level or even decreased. The activity of aerobic respiration-related enzyme (succinic dehydrogenase) began to reduce from 24 h of air exposure. The activities of antioxidant enzymes (superoxide dismutase and catalase) were enhanced during 6-48 h of air exposure and then returned to control level or even inhibited. The content of malondialdehyde (MDA) increased from 96 h of air exposure. The activities of immune-related enzymes (acid phosphatase and alkaline phosphatase) increased during 6-48 h, then returned to normal or began to decline. At transcriptome level, 44 differentially expressed genes (DEGs) in the hepatopancreas were identified after 96-h air exposure. Among these DEGs, 8 were associated with glycolysis, TCA cycle, immune, and antioxidant, and were downregulated after 96-h air exposure. Taken together, these findings illuminated the response of C. fluminea to air exposure at histological, physiological, and transcriptomic levels, which will be beneficial to the aquaculture and transportation of C. fluminea.

Genome-wide analysis of the hard clam mitogen-activated protein kinase kinase gene family and their transcriptional profiles under abiotic stress

Mitogen-activated protein kinase kinase (MAPKK) was the hub component of the Mitogen-activated protein kinase (MAPK) signaling pathway and played an important role in the cellular response to environmental stress. In this study, we identified five MmMAPKK genes in hard clam Mercenaria mercenaria and found that all MmMAPKK genes contain a conserved protein kinase domain. The MmMAPKK genes derived from dispersed duplication were unevenly distributed in three chromosomes. Although the genome size was highly variable among different bivalve mollusks, the number of MAPKK genes was relatively stable. Phylogenetic analysis showed that bivalve MAPKK was divided into five clades, and amino acid sequences of MAPKK from the same clade consisted of similar conserved motifs. The syntenic analysis demonstrated that MmMAPKKs had the highest number of homologous gene pairs with Cyclina sinensis. MmMAPKKs were ubiquitously expressed in all examined tissues, and all MmMAPKK genes were highly expressed in the ovary. MmMAPKK genes showed stress-specific expression under envirionmental stress. MmMAPKK7 showed an upregulated in heat and heat plus hypoxia stress while MmMAPKK1 showed an upregulated in hypoxic stress groups. Dynamic changes of MmMAPKK7, MmMAPKK6 and MmMAPKK1 in hemocytes were observed in response to air exposure. MmMAPKK4 significantly downregulated after air exposure for five days. MmMAPKK7 and MmMAPKK6 might participate in adaptation to low salinity stress. Our results provided useful information about MAPKK and laid a foundation for further studies on MAPKK evolution in the bivalve.

Comparative Transcriptomics of the Northern Quahog Mercenaria mercenaria and Southern Quahog Mercenaria campechiensis in Response to Chronic Heat Stress

The northern quahog (Mercenaria mercenaria) supports lucrative aquaculture industries in the USA. In the southeastern USA, aquacultured M. mercenaria faces increasing risks of summer die-offs from prolonged heat waves. We used a comparative transcriptomic approach to investigate the molecular responses of M. mercenaria and its southern congener, Mercenaria campechiensis, to controlled incremental heat stress over a 4-week period. Mercenaria were exposed to temperatures from 24 to 34 °C with 2.5 °C/week, after which, gill transcriptomes were de novo assembled and annotated. During the 4 weeks of chronic heat exposure, both species had the same survival rate (96%); M. mercenaria experienced body weight gain/loss depending on the originated hatcheries while M. campechiensis experienced an average net weight loss. The upregulated genes in both species included those in chaperone-mediated protein folding and regulation of cell death pathways, while the downregulated genes in both species involved in mRNA processing and splicing pathways. Compared to M. mercenaria, M. campechiensis appears to be more sensitive to prolonged heat stress as indicated by upregulating significantly more genes in coping with oxidative stress and in the protein degradation pathways, while downregulating some inhibitors of apoptosis. We discussed this finding within their ecological and evolutionary context. Our findings highlighted the potential vulnerability of the two quahogs, especially the southern quahog, to continued ocean warming.