Cyclina Sinensis Research Articles

Environmental adaptation, growth performance and nutrient content of the clam Cyclina sinensis from different geographic locations

The clam Cyclina sinensis is an economically important marine species in China. However, overfishing, habitat destruction, and inbreeding have led to the destruction of genetic resources. In this study, five natural populations [Dandong (DD), Dongying (DY), Tianjin (TJ), Wenzhou (WZ), and Yancheng (YC)] from different geographical locations were relocated and cultured homogeneously to study their potential for translocation and environmental adaptation by observing growth performance and nutrient content. There were significant differences in the growth rates of shell length (SL), shell height (SH), and shell width (SW) among the five populations (P<0.05). The DD, TJ, and YC populations exhibited the highest SL and SH growth rates, whereas these were lowest in the WZ population. The survival rate was highest in the YC population and lowest in the WZ population, which was significantly lower than the other four populations (P<0.05). The DD population exhibited superior plumpness and glycogen content, and the overall glycogen content in male C. sinensis was higher compared with that in females (P<0.05). All populations displayed a high total amino acid content and the essential amino acid/Total Amino Acid (EAA/TAA) and Non-essential amino acid/Total Amino Acid (NEAA/TAA) ratios in the soft tissue of all five populations aligned with the FAO/WHO ideal protein evaluation standards. Despite the same aquaculture environment, however, the nutrient composition of C. sinensis sampled from different populations varied significantly (P<0.05).Therefore, ex situ conservation did not eliminate nutritional differences between the different populations of C. sinensis. These findings highlight the importance of considering environmental and ecological factors in the nutritional assessment and cultivation of shellfish. In addition, C. sinensis from sampling sites closer to the transplantation sites had higher survival rates and growth rates, and the gonadal development of all populations showed adaption to the local environment, resulting in synchronization of the reproductive period.

High temperatures alter the patterns of growth and development and cause physiological and biochemical stresses in Chinese cyclina Cyclina sinensis

Prolonged high temperature is a critical environmental factor contributing to the mass mortality of clams in summer. We investigated the growth and development of Cyclina sinensis cultured at different temperatures (25, 28, 31, and 34 °C) and their physiological and biochemical responses following a long period of exposure. The mortality rates at 31 °C and 34 °C were significantly higher than at 25 °C and 28 °C after 48 d (P < 0.05). The overall survival rates at 25 °C and 28 °C did not differ significantly from the control group (at natural seawater temperature), but were significantly lower at 31 °C and 34 °C (P < 0.05). The growth parameters of C. sinensis in all of the experimental groups were significantly higher than in the control group (P < 0.05), with the highest specific growth rate at 28 °C. The shell to soft tissue ratio was greatly increased in the 31 °C and 34 °C groups and was significantly higher than in the other groups after 32 d (P < 0.05). The condition factor at 28 °C was significantly higher than in the other groups (P < 0.05), and started to decline after 32 days at 31 °C and 34 °C. The hepatopancreatic and gonadotropic indexes were significantly lower at 31 °C and 34 °C than in the control group (P < 0.05). Appropriate temperature rises increased the filtration rate and ingestion rate but these were clearly inhibited at 31 °C and 34 °C. The activities of superoxide dismutase, catalase, acid phosphatase (ACP), and lysozyme (LZM) were significantly reduced at 31 °C and 34 °C (P < 0.05). The activities of ACP, LZM, amylase, and the proteases were significantly increased at 28 °C (P < 0.05). Our study showed that high temperatures accelerate the growth of shells but inhibit the growth of soft tissues, negatively affecting the development, physiology, and biochemistry of C. sinensis. Cyclina sinensis demonstrates better overall performance at 28 °C, but aquaculture production would be severely affected if the temperature reaches, or exceeds 31 °C.

Comprehensive investigation of differentially expressed ncRNAs, mRNAs, and their ceRNA networks in the regulation of shell color formation in clam, Cyclina sinensis

Noncoding RNAs (ncRNAs) have gained significant attention in recent years due to their crucial roles in various biological processes. However, our understanding of the expression and functions of ncRNAs in Cyclina sinensis, an economically important marine bivalve, remains limited. This study aimed to address this knowledge gap by systematically identifying ncRNAs in the mantles of C. sinensis with purple and white shells. Through our analysis, we identified a differential expression of 1244 mRNAs, 196 lncRNAs, 49 circRNAs, and 23 miRNAs between purple- and white-shell clams. Functional enrichment analysis revealed the involvement of these differentially expressed ncRNAs in biomineralization and pigmentation processes. To gain further insights into the regulatory mechanisms underlying shell color formation, we established competitive endogenous RNA (ceRNA) networks. These networks allowed us to identify targeted differentially expressed miRNAs (DEMis) and genes associated with shell color formation. Based on the ceRNA networks, we obtained an up-down-up lncRNA-miRNA-mRNA network consisting of 13 upregulated lncRNAs and a circRNA-miRNA-mRNA network comprising three upregulated circRNAs (novel_circ_0004787, novel_circ_0001165, novel_circ_0000245). Through these networks, we identified and selected an upregulated novel gene (evm.TU.Hic_asm_7.988) and a downregulated sponge miRNA (hru-miR-1985) as potential contributors to shell color regulation. In summary, the present investigation offers a comprehensive analysis of ncRNA catalogs expressed in the clam mantle of C. sinensis. The findings enhance our comprehension of the molecular mechanisms governing shell coloration and offer new perspectives for selective breeding of C. sinensis in the future.

The effects of Cyclina sinensis bioturbation on alkaline phosphatase (APA) and total microbial hydrolytic activities (MBA) in marine clam-shrimp integrated ponds.

This study investigated the influence of Venus clam Cyclina sinensis bioturbation activities on the total benthic microbial and phosphatase activities and selected sediment properties: total phosphorous TP, total organic nitrogen-TON and total organic carbon-TOC. Sediments samples from clam-shrimp integrated-pond and non-clam integrated-pond were sampled for the study in which microbial activity (MBA) and alkaline phosphatase activity (APA), sediment organic contents: TP, TON, TOC, TOM and water quality parameter (dissolved oxygen, temperature, pH and moisture content were analyzed. The p-nitrophenyl phosphate disodium (p-NPP) and Fluorescein diacetate-(FDA) were adopted to measure APA and MBA respectively. Results indicated that microbial activity-MBA and alkaline-phosphatase activity-APA in sediments significantly increased in the pond cultured with clam/shrimp compared to non-clam cultured pond. Phosphate concentration increased significantly and varied among months (p<0.05) implying increased nitrogen concentration in the sediments. The concentrations of total organic nitrogen and total organic carbon didn't differ significantly among months and with the treatments (p>0.05), implying increased TON mineralization. Correlation analyses showed that there was positive correlation with the total microbial activity, alkaline-phosphatase activity, phosphorous concentration and organic matter content within the sediments bioturbated by the Venus clam. The results suggest that, the Venus clam sediment reworking mechanisms in sediment influenced the sediment microbial and APA activities and mineralization thereby affecting the pond alkaline phosphatase enzyme related activities.

Colorimetric and antioxidant films based on biodegradable polymers and black nightshade (Solanum nigrum L.) extract for visually monitoring Cyclina sinensis freshness.

In this study, colorimetric and antioxidant films were developed by using cassava starch (CS), κ-carrageenan (KC) and black nightshade fruit anthocyanins (BNA), and their physical and functional properties were investigated. We found BNA presented significant color changes in different pH solutions. And incorporation of BNA significantly increased the tensile strength, water vapor permeability, UV-vis light barrier property, pH-sensitivity and antioxidant activity of CS-KC film. Results of structural characterization indicated that H-bonds were formed between CS, KC and BNA in films and the film compactness was significantly improved by BNA incorporation. Results of the rheological property assay showed the films had high apparent viscosity with an obvious shear-thinning behavior. When applied to monitoring the quality change of Cyclina sinensis, CS-KC-BNA films exhibited significant color changes with the degradation process of C. sinensis qualities. Our results suggested CS-KC-BNA films could be utilized in smart packaging in food industry.

Clam challenges high concentrations of algae diet environment: Growth performance, metabolism physiology, and related gene expression characteristics

Increasing coastal pollution leads to frequent algal blooms, but little is known on the effect of growth and development in organisms with increasing algal concentration. In recent years, the clam Cyclina sinensis has been an important marine economic shellfish that is widely cultivated. This study investigated the effects of different Chlorella concentrations (5 × 105 cell/L (Diet T1), 1.25 × 106 cell/L (Diet T2), 1.3 × 107 cell/L (Diet T3), 1.25 × 108 cell/L (Diet T4), and 1.5 × 109 cell/L (Diet T5)) on the growth, enzyme activities of digestive, immune, and respiratory metabolism, and hepatopancreatic transcriptome gene expression characteristic response of C. sinensis. Results showed that the shell length growth rate, shell height growth rate, and survival rate of C. sinensis significantly decreased as the Chlorella concentration reached 5 × 105 cell/L. The condition factor of C. sinensis in Diet T1 and the hepatopancreas index of C. sinensis in Diet T4 were significantly higher than those in the other groups (P < 0.05). The enzyme activities of superoxide dismutase increased significantly with the rise in concentration of Chlorella, but the highest lysozyme in the hepatopancreas of C. sinensis was observed in the Diet T1 group. The enzyme activities of acid phosphatase and amylase in Diet T3, trypsin in Diet T5, lipase and succinate dehydrogenase in Diet T4, and lactate dehydrogenase in Diet T1 of C. sinensis were significantly higher than those in the other groups (P < 0.05). These results suggest that some enzyme activities related to digestion, metabolism, and respiration are inhibited with the Chlorella concentration increased. Furthermore, transcriptome results showed that the expression levels of G6P, IGFBP, CHI3L1, FAS, MyHC, and other genes related to glucose, protein, and fatty acid metabolism of C. sinensis were significantly downregulated in the Diet T3 and Diet T5 groups. All these results suggest that Chlorella concentrations above 5 × 105 cell/L should be avoided in practice. This study provides a scientific basis for C. sinensis culture and further extends the understanding of the metabolism of bivalves with diet concentration.

Effects of chronic ammonia nitrogen stress on hydrolases and interleukin 17–3 (IL-17–3) in clam Cyclina sinensis

Effects of chronic ammonia nitrogen stress on hydrolases and interleukin 17–3 (IL-17–3) in clam Cyclina sinensis

Genome-wide identification, structural and evolutionary characteristics, and expression analysis of aquaporin gene family members in Mercenaria mercenaria

Aquaporins (AQPs) are highly-selective transmembrane water transporters that are involved in the adaptation to environmental challenges. However, the structure, function, and evolution of AQPs in bivalves remain largely unknown. In this study, AQP gene family members were identified in nine bivalve species, and their abundance rangs from 7 to 15. Nine AQPs (MmAQPs) were identified in the genome of hard clam (Mercenaria mercenaria), which is a euryhaline bivalve that has evolved sophisticated osmoregulatory mechanisms and salinity adaptation. Structurally, all MmAQPs contain 6 or 12 transmembrane α-helices, a major intrinsic protein (MIP) domain, and 2 asparagine-proline-alanine (NPA) motifs. MmAQPs were classified into three subfamilies based on phylogenetic analysis: AQP1-like, AQP3-like, and AQP8-like. No AQP11-like subfamily member was identified in the genome of hard clam. Tandem duplication resulted in a lineage-specific expansion in AQP8-like subfamily in hard clams. MmAQP8 genes showed different expression sensitivity to different environmental stressors. The gene expression patterns of three MmAQP8 were similar under heat, hypoxia, and air exposure stress, but differed greatly under salinity stress, indicating that tandem duplication events may accelerate the functional divergence of AQP8 genes in hard clams. AQP3-like members may have undergone gene loss during evolution, resulting in weakened glycerol and urea penetration in hard clams. Three orthologs of MmAQPs were detected in the genomes of Cyclina sinensis and Archivesica marissinica through synteny analyses. Tissue expression profiles showed that MmAQP genes were highly expressed in the foot and hepatopancreas. Under environmental stress, the expression levels of most of the MmAQP genes changed significantly to maintain metabolic homeostasis. Several MmAQP genes were downregulated to reduce water permeability under salinity and air exposure stress. Several MmAQP genes were significantly upregulated to promote the transmembrane transport of ammonia and reactive oxygen species and activate anti-apoptotic responses to resist stress. This study provides a comprehensive understanding of the AQP gene family in hard clams, and lays a foundation for further studies to explore the functions of AQPs in bivalves.

Effects of morphological traits on living body weight of wild Cyclina sinensis in different geographical populations

Eleven coastal geographical populations of wild Cyclina sinensis in China were collected in February 2020, and the effects of four morphological traits (shell length; shell height; shell width; external ligament length) on one weight trait (living body weight) were studied by correlation analysis, path analysis, determination coefficient analysis, and regression analyses. The statistical results showed that the coefficient of body weight variation was generally greater than morphological traits(P＜0.05). The correlation analysis results showed that the coefficient of correlation between morphological traits (except for external ligament length) and body weight are significantly positive (P＜0.05) in all populations. Based on the results of path analysis and determination coefficient analysis, shell length has the greatest direct effect on body weight in the Yancheng population; shell height has the greatest direct effect on body weight in Dandong, Fuzhou and Tangshan populations; shell width has the greatest direct effect on body weight in Zhanjiang, Wenzhou, Dongtai, Ningbo, Tianjin, Dongying, and Wanning populations. Multiple regression equations were obtained with body weight as the dependent variable, shell length, height, and width and external ligament length as independent variables. The results of systematic clustering showed that there are no apparent geographical differentiation characteristics among eleven geographical populations in morphology. This study provided a scientific basis for selective and genetic breeding and can guide the development and utilization of wild C. sinensis seed resources.

Characterization, expression profiling, and estradiol response analysis of DMRT3 and FOXL2 in clam Cyclina sinensis

The clam Cyclina sinensis is one of the important economical aquaculture shellfish in China. However, the mechanisms of sex determination and differentiation in C. sinensis have not been fully studied. In this study, full-length cDNAs of DMRT3 and FOXL2 were cloned and functionally characterized. The ORF region of CsDMRT3 consists of 1137 nucleotides, which encode 378 amino acids contains a conserved DM domain of DMRT family. The ORF region of CsFOXL2 is 1245 bp, encodes 414 amino acids, and contains a conserved FH domain. Tissue-specific expression results showed that the higher expression level of CsDMRT3 and CsFOXL2 was found in the ovary and testis of C. sinensis. The expression levels of CsDMRT3 and CsFOXL2 also peaked at the maturation stage of male and female gonadal development, respectively. Moreover, the expression levels of CsDMRT3 and CsFOXL2 were significantly higher in the trochophore and D-larval stages than in other stages. The transcript levels of CsDMRT3 reached the highest level at 11 months of age, while the CsFOXL2 reached the highest level at 7 months of age. In estradiol-treated experiments, the expression levels of CsDMRT3 and CsFOXL2 in the gonads were highest at 5 µg/L estradiol treatment, and histologically, it was observed that the oocytes diameters became larger with increasing estradiol concentration. These results suggest that CsDMRT3 and CsFOXL2 play an important role in gonadal development and sex differentiation of C. sinensis.

Cloning, Characterization, and Expression Prolife Analysis of Tyrosinase Genes: Insights into Black Shell Formation in Cyclina sinensis

Shell colors that exhibit a positive relationship with excellent traits can be employed as marker colors for breeding new varieties of bivalves. The clam Cyclina sinensis is an economically important marine bivalve that has three main colors: black, white, and purple. In the present study, we cloned and analyzed the full-length cDNA of the tyrosinase gene (TYR), which is the key gene for melanin synthesis, to explore the formation mechanism of black shells. The full-length cDNA of TYR was cloned by RACE-PCR, and the results showed that the full-length cDNA of TYR was 2993 bp, including a 2262 bp open reading frame encoding 753 amino acids. The results of functional domain prediction showed that deduced TYR protein contains a typical functional domain of tyrosinase, the common central domain. Phylogenetic analysis was conducted using neighbor-joining and maximum likelihood methods, and the results indicated that the evolutionary positions of C. sinensis and Meretrix meretrix were closest. The qRT‒PCR results showed that TYR mRNA was highly expressed in the outer edge of the mantle, which suggested that TYR was involved in the synthesis of melanin in the mantle of C. sinensis and might play an important regulatory role in the formation of melanin in black clam shells.

Exposure to polychlorinated biphenyls (PCBs) affects the histology and antioxidant capability of the clam Cyclina sinensis

Polychlorinated biphenyls (PCBs) are environmentally persistent and highly toxic organochlorine compounds that may cause toxic effects on aquatic animals. In this study we assess the toxic effect of PCBs on a bivalve used in aquaculture, the clam Cyclina sinensis. To this end, individuals of C. sinensis were exposed for 72 h at two PCB concentrations (1 ng/L and 10 ng/L) and control (absence of PCBs). At the end of the exposure, the hemolymph, hepatopancreas, and gills samples of C. sinensis were harvested for analysis of the enzyme activity and histology. The results showed that acute PCBs exposure decreased the survival rate of C. sinensis compared to the control. Acute PCBs exposure up-regulated the enzymatic activity of superoxide dismutase (SOD), catalase (CAT) and glutathione peroxidase (GSH-Px) and the content of malondialdehyde (MDA) in the hemolymph of C. sinensis, while down-regulated the non-specific enzymatic activity of alkaline phosphatase (AKP). For the hepatopancreas, 1 ng/L PCBs exposure up-regulated the enzymatic activity of SOD while down-regulated the enzymatic activity of CAT of C. sinensis. In the gill, the enzymatic activity of CAT decreased significantly and the MDA content increased of C. sinensis after 10 ng/L PCBs exposure. Moreover, histological observations showed that acute exposure to PCBs caused loss of gill filaments and lateral cilia and shortening of their length, in the studied organism. The present study will provide valuable reference data for marine shellfish aquaculture and toxicology research.

Transcriptome reveals the immune and antioxidant effects of residual chlorine stress on Cyclina sinensis

Residual chlorine is a common by-product of warm drainage in coastal nuclear power plants. when accumulating to some limit, it may threaten marine ecosystem especially for benthic clam. However, there are few studies on the molecular mechanisms related to immunity and antioxidant of residual chlorine stress on clams. In this study, the clam (Cyclina sinensis) was exposed for 96 h at different concentrations (0, 50, 100, 150, 200, 250, 300, 350, 400, 450 and 500 mg/L) of residual chlorine to observe its mortality, measure the activity of antioxidant and immune-related enzymes, and analyses the gene expression level in the hepatopancreas by using the transcriptome sequencing. The results showed that the mortality rate increased with the increase of stress time and concentration, and the mortality rate in the 400, 450 and 500 mg/L groups reached 100% at 96 h. The tolerance to residual chlorine of C. sinensis decreased with the increase of chlorine dioxide concentration, and the LC50 of 96 h was 217.6 mg/L by linear regression method. After residual chlorine stress, the activity of antioxidant-related enzymes (T-AOC and SOD) in the hepatopancreas showed a trend of first increase and then decrease with the extension of stress time. The immune-related enzyme activities of AKP and LZM showed a downward trend between 0 and 96 h, while the ACP enzyme activity showed a trend of first rising and then decreasing. Transcriptome analysis showed that residual chlorine stress significantly changed the expression levels of immune-related molecules associated with signal transduction, prophenoloxidase cascade, cell apoptosis and pattern recognition protein/receptor. Moreover, glutathione S-transferase (GST), heat shock protein (HSP) and other antioxidant-related genes were significantly affected under residual chlorine stress. This study provided valuable information for understanding the effects of residual chlorine stress on survival, physiological metabolism and molecular mechanisms of immune and antioxidant functions of C. sinensis.

Gonad transcriptome analysis reveals the differences in gene expression related to sex-biased and reproduction of clam Cyclina sinensis

Sexual differentiation and gonad development are important biological processes for bivalve species. The clam Cyclina sinensis is an important cultured marine bivalve widely distributed along with the coastal areas of China. However, the information related to sexual determination/differentiation and gonadal development of C. sinensis almost has no reported. To study the molecular mechanisms of its sexual determination/differentiation and gonadal development, transcriptome analysis was performed in the gonad of C. sinensis, and the potential biological functions of reproduction-related gene were also investigated in this study. The results showed that 1 013 and 427 genes were differentially expressed in the ovary and testis, respectively. KEGG enrichment analysis showed that the DEGs in the gonad were significantly clustered in progesterone-mediated oocyte maturation, cell cycle and oocyte meiosis. Further analysis showed that 23 genes were mainly involved in sex determination/differentiation, including Dmrt1, Sox2/4/9, Foxl2, β-catenin and GATA-type zinc finger protein 1-like. Twenty key genes were mainly involved in the process of spermatogenesis, and five genes encode steroid biosynthesis and metabolism. Fifteen genes related to ovarian development were also identified in this study, such as Vitellogenin, MAM and LDL-receptor class A domain-containing protein 1 and Cell division cycle protein 20 homolog. Moreover, 50µg/L estradiol treatment significantly up-regulated the expression levels of CsVg in the ovary and hepatopancreas. These results highlight the genes involved in sexual determination/differentiation and gonadal development, which enhance our understanding for further studies of reproduction and breeding of C. sinensis and other marine bivalves.

Habitual feeding patterns impact polystyrene microplastic abundance and potential toxicity in edible benthic mollusks

That increasing microplastics (MPs, <5 mm) eventually end up in the sediment which may become a growing menace to diverse benthic lives is worthy of attention. In this experiment, three edible mollusks including one deposit-feeding gastropod (Bullacta exarate) and two filter-feeding bivalves (Cyclina sinensis and Mactra veneriformis) were exposed to polystyrene microplastic (PS-MP) for 7 days and depurated for 3 days. PS-MP numbers in the digestive system and non-digestive system, digestive enzymes, oxidative stress indexes, and a neurotoxicity index of three mollusks were determined at day 0, 3, 7, 8 and 10. After seven-day exposure, the PS-MP were found in all three mollusks' digestive and non-digestive systems. And PS-MP in M. veneriformis (9.57 ± 2.19 items/individual) was significantly higher than those in C. sinensis (3.00 ± 2.16 items/individual) and B. exarate (0.83 ± 1.07 items/individual) at day 7. Three-day depuration could remove most of the PS-MP in the mollusks, and higher PS-MP clearance rates were found in filter-feeding C. sinensis (77.78 %) and M. veneriformis (82.59 %) compared to surface deposit-feeding B. exarate (50.00 %). The digestive enzymes of B. exarate significantly reacted to PS-MP exposure, while oxidative responses were found in C. sinensis. After three-day depuration, the changes of digestive enzymes and the oxidative states were fixed, but neurotoxicity induced by PS-MP was not recoverable. Besides, it is noteworthy that changes of digestive enzymes and acetylcholinesterase are related to feeding patterns.

Effect of chronic ammonia nitrogen stress on the SOD activity and interferon-induced transmembrane protein 1 expression in the clam Cyclina sinensis

Ammonia nitrogen plays a crucial part in oxidative stress in aquatic animals. To elucidate the effect of ammonia nitrogen stress on the superoxide dismutase (SOD) activity and interferon-induced transmembrane protein 1 (IFITM1) expression in the clam Cyclina sinensis, clams were exposed to ammonia nitrogen (8.07 mg/L) for 768 h (32 days) and then challenged with Vibrio parahaemolyticus. The results showed that the SOD activity in the hepatopancreas of C. sinensis exposed to ammonia nitrogen first increased and then decreased with time, returning to the control group’s normal level at 768 h. Following infection with V. parahaemolyticus, the SOD activity in the hepatopancreas fluctuated over time. The SOD activity in clams infected with V. parahaemolyticus at 144 h did not return to the control group’s normal level. The full-length cDNA of CsIFITM1 was 2,434 bases in length, including a 2,301-bp open reading frame (ORF) encoding 714 amino acids, with a putative molecular weight of 83.86 kDa. CsIFITM1 contains an RNA helicase domain (DEXHc_RLR, DR) and a Helicase_C (HC) domain. The transcriptional levels of CsIFITM1 were upregulated by exposure to ammonia nitrogen and were significantly higher from 6 to 768 h compared to the control (0 h) (p &amp;lt; 0.05). Following infection with V. parahaemolyticus, the transcript levels of CsIFITM1 in the hepatopancreas were upregulated and were significantly higher from 6 to 144 h, in contrast to those of the control (0 h) (p &amp;lt; 0.05). The present data provide the first evidence of the SOD activity and CsIFITM1 transcript levels being able to reflect the effect of ammonia on the clam C. sinensis.

Unravelling the characterization of hypoxia‐inducible factor‐1α ( HIF‐1α ) and antioxidant enzymes in clam Cyclina sinensis in response to hypoxia

Aquatic hypoxia has negative or detrimental effects on clams. To cope with hypoxia stress, a complex series of physiological and biochemical strategies can be employed in clams. Hypoxia-inducible factor-1α (HIF-1α) and antioxidant enzymes are commonly found in aquatic animals as an adaptation against hypoxia. In the present study, we cloned the HIF-1α sequence in clam Cyclina sinensis, and it consists of 2654 base pairs (bp) carrying a single open-reading frame that encompasses 2235 bp of the coding region. The predicted C. sinensis HIF-1α protein (744 amino acids) has the conserved HLH-PAS domain, which contained one N-terminal basic helix–loop–helix (bHLH) domain and two Per-ARNT-Sim A/B (PAS) domains, followed by PAS-associated C-terminal (PAC) domain. HIF-1α is expressed predominantly in gills. Exposed to hypoxia, the transcript level of HIF-1α was significantly up-regulated in response to hypoxia, and then, the transcript level declined continuously with the time elapsed. The antioxidant enzymes (SOD, CAT and GSH-PX) in gills were increased initially and then decreased after acute hypoxia exposure. Our study indicates that the HIF-1α gene and antioxidant enzymes may play an important role in cope with acute hypoxia exposure.

Identification of suitable reference genes for quantitative gene expression analysis in clam Cyclina sinensis under salinity stress and Vibrio infection

Identification of suitable reference genes for quantitative gene expression analysis in clam Cyclina sinensis under salinity stress and Vibrio infection

Chromosome-Level Genome Assembly of the Butter Clam Saxidomus purpuratus.

Herein, we provide the first whole-genome sequence of the purple butter clam (Saxidomus purpuratus), an economically important bivalve shellfish. Specifically, we sequenced and de novo assembled the genome of Sa. purpuratus based on PromethION long reads and Hi-C data. The 978-Mb genome of Sa. purpuratus comprises 19 chromosomes with 36,591 predicted protein-coding genes. The N50 length of Sa. purpuratus genome is 52 Mb, showing the highest continuous assembly among bivalve genomes. The Benchmarking by Universal Single-Copy Orthologs assessment indicated that 95.07% of complete metazoan universal single-copy orthologs (n = 954) were present in the assembly. Approximately 51% of Sa. purpuratus genome comprises repetitive sequences. Based on the high-quality Sa. purpuratus genome, we resolved half of the immune-associated genes, namely, scavenger receptor (SR) proteins, which are collinear to those in the closely related Cyclina sinensis genome. This finding suggested a high degree of conservation among immune-associated genes. Twenty-two (19%) SR proteins are tandemly duplicated in Sa. purpuratus genome, suggesting putative convergence evolution. Overall, Sa. purpuratus genome provides a new resource for the discovery of economically important traits and immune-response genes.

Description of Flavobacterium cyclinae sp. nov. and Flavobacterium channae sp. nov., isolated from the intestines of Cyclina sinensis (Corb shell) and Channa argus (Northern snakehead).

Two novel bacterial strains, KSM-R2A25T and KSM-R2A30T, were isolated from intestines of Cyclina sinensis (corb shell) and Channa argus (northern snakehead), respectively. Both specimens were collected in Korea. The strains were Gramstain-negative, non-motile, and strictly aerobic. According to phylogenetic analyses based on 16S rRNA gene sequences, strains belonged to the genus Flavobacterium within the family Flavobacteriaceae. 16S rRNA gene sequences of strains KSM-R2A25T and KSM-R2A30T were closely related to Flavobacterium cucumis DSM 18830T and Flavobacterium aquaticum JC164T with sequence similarities of 97.77% and 98.54%, respectively. Further genomic analyses including reconstruction of the UBCG tree and overall genome-related indices suggested them as novel species of the genus Flavobacterium. Both strains contained menaquinone with six isoprene units (MK-6) as a major isoprenoid quinone and iso-C15:1 G, iso-C15:0 and iso-C16:0 as major cellular fatty acids. The major polar lipid in both strains was phosphatidylethanolamine. The genomic G + C contents of strains KSM-R2A25T and KSM-R2A30T were 31.7 and 31.9%, respectively. Based on the polyphasic taxonomic study presented here, strains KSM-R2A25T and KSM-R2A30T represent novel species of the genus Flavobacterium, for which the names Flavobacterium cyclinae sp. nov and Flavobacterium channae sp. nov are proposed. The type strains of F. cyclinae sp. nov and F. channae sp. nov are KSM-R2A25T (= KCTC 82978T = JCM 34997T) and KSM-R2A30T (= KCTC 82979T = JCM 34998T), respectively.