Verify the Function of a Potential Growth-Regulating Gene in Marine Bivalve Using a Candidate Model Organism Mulinia lateralis

A better understanding of genetic bases of growth regulation is essential for bivalve breeding,which is helpful to improve the yield of the commercially important bivalves.While previous studies have identified some candidate genes accounting for variation in growth-related traits through genotype-phenotype association analyses,seldom of them have verified the functions of these putative,growth-related genes beyond the genomic level due to the difficulty of culturing commercial bivalves under laboratory conditions.Fortunately,dwarf surf clam Mulinia lateralis can serve as a model organism for studying marine bivalves given its short generation time,the feasibility of being grown under experimental conditions and the availability of genetic and biological information.Using dwarf surf clam as a model bivalve,we characterize E2F3,a gene that has been found to account for variation in growth in scallops by a previous genome-wide association study,and verify its function in growth regulation through RNA interference(RNAi)experiments.For the first time,E2F3 in dwarf surf clam,which is termed as MulE2F3,is characterized.The results reveal that dwarf surf clams with MulE2F3 knocked down exhibit a reduction in both shell size and soft-tissue weight,indicating the functions of MulE2F3 in positively regulating bivalve growth.More importantly,we demonstrate how dwarf surf clam can be used as a model organism to investigate gene functions in commercial bivalves,shedding light on genetic causes for variation in growth to enhance the efficiency of bivalve farming.

Did Species and Functional Diversities of Sandy Intertidal Marine Nematodes Reveal Similar Response to Environmental Changes?

Free living marine nematodes were sampled from two sandy beaches in Dalian City,in December of 2015,and April,July,and October of 2016.The spatial and seasonal variations of marine nematode species diversity(based on species abundance dataset)and functional diversity(based on functional traits dataset:feeding types and life history strategies)were investigated to understand the environmental drivers and how they respond to specific environmental variations.Sediment granularity was revealed to be the main environmental factor causing spatial differences in nematode diversity indices between the two beaches.Species diversity indices,namely species number,Margalef index,Shannon-Wiener diversity index(H’),were higher in fine-grained sediments,while the functional diversity indices,including functional evenness,functional dispersion,and Rao’s quadratic entropy index(RaoQ),were higher in coarse-grained sediments.Nematode species diversity indices also fluctuated with seasonal variations of temperature,dissolved oxygen,pH,salinity,and sediment chlorophyll-a within the study beaches.However,functional diversity indices did not show significant seasonal variations and exhibited weak correlation with the studied environmental variables.Overall,the functional diversity indices were negatively correlated with the species diversity indices,suggesting an inconsistent response to environmental changes.A decrease in nematode species diversity in coarse sands,accompanied by an increase in functional diversity,can be regarded as an early warning signal of environment disturbance.If more biological traits are involved in calculating functional diversity indices,it will be helpful for the future study of the internal connections of species diversity and functional diversity.

Effect of Skeleton Grain Size on the Saturation of Gas Hydrate in Natural Sediments

Natural gas hydrate is prospected as a new and promising,highly clean energy resource that mainly occurs in perma-frost or at continental margins.Its formation is subject to many soil conditions,such as grain size,matrix materials,pore morphology,and permeability.In this study,we propose that grain size is the most decisive parameter that affects the saturation of gas hydrate in sediments based on data from Ocean Drilling Program Leg 164 and Mallik 5L-38,which represent marine sediments and terrestrial sediments,respectively.Our study reveals that high gas hydrate saturation generally occurs in coarse-grained sand,regardless of whether sediment formation is homogeneous or inhomogeneous,and the sorting of sediments may affect the hydrate saturation to a certain degree.Using grain size and sorting of sediments may be the most intuitive proxy method for a rough estimation of hydrate saturation.Further study is necessary to fully understand the relationship between hydrate morphology and sediment grain size,even though massive hydrates are typically found in fine clayey-rich sediments.

The Variation of Plankton Community Structure in Artificial Reef Area and Adjacent Waters in Haizhou Bay

Plankton are an important component of marine protected areas(MPAs),and its communities would require much smaller interpatch distances to ensure connection among MPAs.According to the survey from MPAs dominated by artificial reefs and adjacent waters(estuary area(EA),aquaculture area(AA),artificial reef area(ARA),natural area(NA)and comprehensive effect area(CEA))in Haizhou Bay in spring and autumn,we analyzed phyto-zooplankton composition,abundance and biomass,and correlation with hydrologic variables to gain information about the forces that structure the plankton.The results showed that the dominant zooplankton were copepods(spring,98.9%;autumn,94.2%),while the phytoplankton were mainly composed of Bacillariophyta(spring,61.8%;autumn,95.6%).The RDA results showed that temperature,salinity and depth highly associated with the distribution and composition of plankton species among the habitats than other factors in spring;temperature,Chla and DO had the strongest influence in autumn.The zooplankton in the ARA and AA ecosystems basically contained the same species as those in other habitats,and each habitat also exhibited a relatively unique combination of plankton species.The structures of the EA zooplankton in spring and the EA phytoplankton in both seasons were much different than other habitats,which may have been caused by factors such as currents and tides.We concluded that there exists similarity of the plankton community between artificial reef area and adjacent waters,whereas the EAs may be relatively independent systems.Therefore,these interaction between plankton community should be considered when designing MPA networks,and ocean circulations should be considered more than the environmental factors.

Effects of Biostimulation-Bioaugmentation on Coastal Microbial Community in an in situ Mesocosm System

Globally,various types of pollution affect coastal waters as a result of human activities.Bioaugmentation and biostimulation are effective methods for treating water pollution.However,few studies have explored the response of coastal prokaryotic and eukaryotic communities to bioaugmentation and biostimulation.Here,a 28-day outdoor mesocosm experiment with two treatments(bioaugmentation-A and combined treatment of bioaugmentation and biostimulation-AS)and a control(untreated-C)were carried out.The experiment was conducted in Meishan Bay to explore the composition,dynamics,and co-occurrence patterns of prokaryotic and eukaryotic communities in response to the A and AS using 16S rRNA and 18S rRNA gene amplicon sequencing.After treatment,Gammaproteobacteria and Epsilonproteobacteria were significantly increased in group AS compared to group C,while Flavobacteriia and Saprospirae were significantly reduced.Dinoflagellata was significantly reduced in AS compared to C,while Chrysophyta was significantly reduced in both AS and A.Compared to C,the principal response curve analyses of the prokaryotic and eukaryotic communities both showed an increasing trend followed by a decreasing trend for AS.Furthermore,the trends of prokaryotic and eukaryotic communities in group A were similar to those in group AS compared with group C,but AS changed them more than A did.According to the species weight table on principal response curves,a significant increase was observed in beneficial bacteria in prokaryotic communities,such as Rhodobacterales and Oceanospirillales,along with a decrease in autotrophs in eukaryotic communities,such as Chrysophyta and Diatom.Topological properties of network analysis reveal that A and AS complicate the interactions between the prokaryotic and eukaryotic communities.Overall,these findings expand our understanding of the response pattern of the bioaugmentation and biostimulation on coastal prokaryotic and eukaryotic communities.

Transcriptome profiling and RXR gene family identification reveals the molecular mechanism of rapid aging after spawning of cuttlefish Sepiella japonica

Sepiella japonica is a worldwide marine cuttlefish species of high economic value.S.japonica routinely modifying behaviors in reproductive life,such as rapid aging until death after spawning,has been recognized in artificial breeding.However,reproductive behavior at the level of genes is rarely reported,thus,the research on the genetic basis of behavior,reproduction,and artificial breeding was limited.We applied RNA-seq in different stages of reproduction to investigate the reason of rapid aging after spawning,pre-maturity,pre-spawning after maturity,and post-spawning.The retinoid X receptor(RXR)gene family in S.japonica was identified,and 1343–1452 differentially expressed genes(DEGs)in all 3 stages of reproductive life were identified from pairwise m RNA comparisons.Furthermore,through the GO term and KEGG analysis,S.japonica could handle neuronal development and network formation before maturity and have a functional degradation of neural communication,signal transduction,vision,and gene expression after spawning.Eight Sj RXRαs have been identified and they played different roles in growth development or reproduction.Therefore,the regulation of several channels and receptors is the intrinsic molecular mechanism of rapid aging after spawning in S.japonica.This study revealed the survival strategy and provided fundamental data on the level of genes for understanding the reproductive behavior and the reproduction of S.japonica.

Combined proteomic and metabolomic studies on the liver of Amur sturgeon Acipenser schrenckii under titanium dioxide nanoparticle exposure

Nanomaterials,particularly titanium dioxide nanoparticles(TiO_(2)-NPs),are extensively utilized across various industries.However,their environmental release has raised concerns regarding their potential ecological and environmental impacts.The reproductive toxicity of TiO_(2)-NPs in fish species has attracted considerable attention,yet conflicting research outcomes have been reported.We investigated the effects of TiO_(2)-NPs exposure on the liver of juvenile Amur sturgeon Acipenser schrenckii using label-free proteomic and untargeted metabolomic analyses.The experiment included a control group and three groups exposed to different concentrations of TiO_(2)-NPs(low,TL;medium,TM;high,TH).Compared to the control group,9,19,and 25 proteins and 35,73,and 158 metabolites were differentially expressed in the TH,TM,and TL TiO_(2)-NP-exposed groups,respectively.The differentially expressed genes(DEGs)were enriched in the Kyoto Encyclopedia for Genes and Genomes(KEGG)pathways related to glycolysis and gluconeogenesis.Moreover,among the 126 correlated proteins,the most enriched pathways were associated with endocytosis and protein processing in the endoplasmic reticulum.Notably,syringic acid was significantly downregulated across all three TiO_(2)-NP-exposed groups.To obtain a comprehensive overview of the TiO_(2)-NP-induced expression changes,a co-regulated network of proteins and metabolites associated with TiO_(2)-NPs exposure was constructed.Exposure to TiO_(2)-NPs led to enrichment and alteration of pathways related to immune responses,including endocytosis,protein processing in the endoplasmic reticulum,and peroxisome proliferator-activated receptor(PPAR)signaling.In conclusion,our findings indicate that exposure to TiO_(2)-NPs might disrupt glucose metabolism and induce immune responses,thus contributing to our understanding of the environmental impacts of nanomaterials and highlighting the need for further research and development of potential mitigation strategies.

Integrated multi-omics analysis reveals liver metabolic reprogramming by fish iridovirus and antiviral function of alpha-linolenic acid

Iridovirus poses a substantial threat to global aquaculture due to its high mortality rate;however,the molecular mechanisms underpinning its pathogenesis are not well elucidated.Here,a multi-omics approach was applied to groupers infected with Singapore grouper iridovirus(SGIV),focusing on the roles of key metabolites.Results showed that SGIV induced obvious histopathological damage and changes in metabolic enzymes within the liver.Furthermore,SGIV significantly reduced the contents of lipid droplets,triglycerides,cholesterol,and lipoproteins.Metabolomic analysis indicated that the altered metabolites were enriched in 19 pathways,with a notable down-regulation of lipid metabolites such as glycerophosphates and alpha-linolenic acid(ALA),consistent with disturbed lipid homeostasis in the liver.Integration of transcriptomic and metabolomic data revealed that the top enriched pathways were related to cell growth and death and nucleotide,carbohydrate,amino acid,and lipid metabolism,supporting the conclusion that SGIV infection induced liver metabolic reprogramming.Further integrative transcriptomic and proteomic analysis indicated that SGIV infection activated crucial molecular events in a phagosome-immune depression-metabolism dysregulation-necrosis signaling cascade.Of note,integrative multi-omics analysis demonstrated the consumption of ALA and linoleic acid(LA)metabolites,and the accumulation of L-glutamic acid(GA),accompanied by alterations in immune,inflammation,and cell death-related genes.Further experimental data showed that ALA,but not GA,suppressed SGIV replication by activating antioxidant and anti-inflammatory responses in the host.Collectively,these findings provide a comprehensive resource for understanding host response dynamics during fish iridovirus infection and highlight the antiviral potential of ALA in the prevention and treatment of iridoviral diseases.

Advances in Biomedical Applications of Hydrogels from Seaweed-Derived Sulfated Polysaccharides:Carrageenan,Fucoidan,and Ulvan

Sulfated polysaccharides extracted from seaweeds,including Carrageenan,Fucoidan and Ulvan,are crucial bioactive compounds known for their diverse beneficial properties,such as anti-inflammatory,antitumor,immunomodulatory,antiviral,and anticoagulant effects.These polysaccharides form hydrogels hold immense promise in biomedicine,particularly in tissue engineering,drug delivery systems and wound healing.This review comprehensively explores the sources and structural characteristics of the three important sulfated polysaccharides extracted from different algae species.It elucidates the gelation mechanisms of these polysaccharides into hydrogels.Furthermore,the biomedical applications of these three sulfated polysaccharide hydrogels in wound healing,drug delivery,and tissue engineering are discussed,highlighting their potential in the biomedicine.

Presence of a long nuclear-localization signal sequence in homeodomain transcription factor Nkx 1.2

Homeodomains,a 60-amino acid sequence encoded by 180 nucleotides,are highly conserved DNA-binding motifs that are present in a variety of transcription factors in species ranging from yeast to humans.The NKX proteins belong to the homeodomain(HD)-containing transcription factor family.They play vital roles in the regulation of morphogenesis.NKX1-2 is one member of the NKX subfamily.At present,information about its nuclear localization signal(NLS)sequence is limited.We studied the NLS sequence of zebrafish Nkx1.2 by introducing sequence changes such as deletion,mutation,and truncation,and identified an NLS motif(QNRRTKWKKQ)that is localized at the C-terminus of the homeodomain.Moreover,the deletion of two amino acid residues(RR)in this NLS motif prevents Nkx1.2 from entering the nucleus,indicating that the two amino acids are essential for Nkx1.2 nuclear localization.However,the NLS motif alone is unable to target cytoplasmic protein glutathione S-transferase(GST)to the nucleus.An intact homeodomain is necessary for mediating the complete nuclear transport of cytoplasmic protein.Unlike most nuclear import proteins with short NLS sequences,a long NLS is present in zebrafish Nkx1.2.We also demonstrated that the sequences of homeodomain of NKX1.2 are well conserved among different species.This study is informative to verify the function of the NKX1.2 protein.

LncRNA pol-lnc78 as a ceRNA regulates antibacterial responses via suppression of pol-miR-n199-3p-mediated SARM down-regulation in Paralichthys olivaceus

Long non-coding RNAs(lncRNAs)function as key modulators in mammalian immunity,particularly due to their involvement in lncRNA-mediated competitive endogenous RNA(ceRNA)crosstalk.Despite their recognized significance in mammals,research on lncRNAs in lower vertebrates remains limited.In the present study,we characterized the first immune-related lncRNA(pol-lnc78)in the teleost Japanese flounder(Paralichthys olivaceus).Results indicated that pol-lnc78 acted as a ceRNA for pol-miR-n199-3p to target the sterile alpha and armadillo motif-containing protein(SARM),the fifth discovered member of the Toll/interleukin 1(IL-1)receptor(TIR)adaptor family.This ceRNA network regulated the antibacterial responses of flounder via the Toll-like receptor(TLR)signaling pathway.Specifically,SARM acted as a negative regulator and exacerbated bacterial infection by inhibiting the expression of inflammatory cytokines IL-1βand tumor necrosis factor-α(TNF-α).Pol-miR-n199-3p reduced SARM expression by specifically interacting with the 3’untranslated region(UTR),thereby promoting SARM-dependent inflammatory cytokine expression and protecting the host against bacterial dissemination.Furthermore,pol-lnc78 sponged pol-miR-n199-3p to ameliorate the inhibition of SARM expression.During infection,the negative regulators pol-lnc78 and SARM were significantly down-regulated,while pol-miR-n199-3p was significantly up-regulated,thus favoring host antibacterial defense.These findings provide novel insights into the mechanisms underlying fish immunity and open new horizons to better understand ceRNA crosstalk in lower vertebrates.

Structural characteristics of phenylboronic acid-modified astaxanthin ester and its effect on DSS-induced ulcerative colitis by blocking reactive oxygen species and maintaining intestinal homeostasis

A novel and reactive oxygen species(ROS)responsive astaxanthin phenylboronic acid derivative(AstaDPBA)was constructed by grafting phenylboronic acid(PBA)onto astaxanthin succinate diester(AstaD),and its chemical structure and physicochemical property were identified.AstaD-PBA could effectively improve the ROS quenching ability in the lipopolysaccharide(LPS)-induced RAW264.7 cell inflammation model.Then,the bioactivity of AstaD-PBA was studied by 4 zebrafish ROS-responsive infl ammatory models induced by LPS,copper(Cu^(2+)),high-fat diet,and dextran sodium sulfate(DSS).The results suggest that AstaD-PBA might have high biosafety and the best effect on ulcerative colitis(UC)induced by DSS.Furtherly,AstaDPBA significantly alleviated and treated weight loss and colonic shrinkage,inhibited infl ammatory cytokines,and maintained microbiota homeostasis to improve UC in C57BL/6J mice.Alistipes and Oscillibacter were expected to be considered UC marker fl ora according to the Metastats analysis and Pearson correlation Mantel test(P<0.01)of 16S rRNA gene sequencing data.In conclusion,AstaD-PBA has been promised to be a functional compound to improve UC and maintain intestinal microbiota homeostasis.

Production traits and fertility of reciprocal hybrids between Argopecten irradians irradians and A.i.concentricus

The two bay scallop subspecies,Argopecten irradians irradians(NN)and A.i.concentricus(SS),are fast growing and major cultured bivalves in China.However,their relatively small sizes and decreasing production traits caused by long-term inbreeding have been major concerns to the industry in the last two decades.Hybridization between the two bay scallop subspecies may provide a new approach to breed a new variety with superior production traits for the industry.For this end,in this study,we hybridized the two bay scallop subspecies in order to obtain a new strain that incorporates the genes of both subspecies.No significant difference was found in fertilization rate,hatching rate and metamorphosis rate between the purebred and crossbred cohorts(NN♀×SS♂,denoted as NS;SS♀×NN♂,denoted as SN).Both mating strategy(intra-vs.inter-population crosses)and egg origin had significant effects on growth and survival at the larval stage.Heterosis was observed in the crossbred and was more pronounced in older stages.Genetic diversity of the reciprocal hybrids,especially that of SN,was increased compared with the purebred cohorts.Almost all hybrids were completely fertile and able to reproduce by selffertilization or by backcrossing with either parent.Apparently,male sterile individuals whose gonads were fully occupied by the ovary part at mature stage were found in the hybrids for the first time.The hybrids,especially SN,may provide precious germplasm resources for the production of ternary hybrids with the Peruvian scallop,A.purpuratus.

Numerical simulation of inlet placement on sewage characteristics in the rounded square aquaculture tank with single inlet

To improve the self-cleaning ability of aquaculture tank and the efficiency of circulating water,physical and numerical experiments were conducted on the influence of inlet structure on sewage discharge in a rounded square aquaculture tank with a single inlet.Based on the physical model of the tank,analysis of how inlet structure adjustment affects sewage discharge efficiency and flow field characteristics was conducted to provide suitable flow field conditions for sinkable solid particle discharge.In addition,an internal flow field simulation was conducted using the RNG k-εturbulence model in hydraulic drive mode.Then a solid-fluid multiphase model was created to investigate how the inlet structure affects sewage collection in the rounded square aquaculture tank with single inlet and outlet.The finding revealed that the impact of inlet structure is considerably affecting sewage collection.The conditions of C/B=0.07-0.11(the ratio of horizontal distance between the center of the inlet pipe and the tank wall(C)to length of the tank(B))andα=25°(αis the angle between the direction of the jet and the tangential direction of the arc angle)resulted in optimal sewage collection,which is similar to the flow field experiment in the rounded square aquaculture tank with single inlet and outlet.An excellent correlation was revealed between sewage collection and fluid circulation stability in the aquaculture tank.The present study provided a reference for design and optimization of circulating aquaculture tanks in aquaculture industry.

Origin and evolution of a new tetraploid mangrove species in an intertidal zone

Polyploidy is a major factor in the evolution of plants,yet we know little about the origin and evolution of polyploidy in intertidal species.This study aimed to identify the evolutionary transitions in three truemangrove species of the genus Acanthus distributed in the Indo-West Pacific region.For this purpose,we took an integrative approach that combined data on morphology,cytology,climatic niche,phylogeny,and biogeography of 493 samples from 42 geographic sites.Our results show that the Acanthus ilicifolius lineage distributed east of the Thai-Malay Peninsula possesses a tetraploid karyotype,which is morphologically distinct from that of the lineage on the west side.The haplotype networks and phylogenetic trees for the chloroplast genome and eight nuclear genes reveal that the tetraploid species has two sub-genomes,one each from A.ilicifolius and A.ebracteatus,the paternal and maternal parents,respectively.Population structure analysis also supports the hybrid speciation history of the new tetraploid species.The two sub-genomes of the tetraploid species diverged from their diploid progenitors during the Pleistocene.Environmental niche models revealed that the tetraploid species not only occupied the near-entire niche space of the diploids,but also expanded into novel environments.Our findings suggest that A.ilicifolius species distributed on the east side of the Thai-Malay Peninsula should be regarded as a new species,A.tetraploideus,which originated from hybridization between A.ilicifolius and A.ebracteatus,followed by chromosome doubling.This is the first report of a true-mangrove allopolyploid species that can reproduce sexually and clonally reproduction,which explains the long-term adaptive potential of the species.

Analysis of environmental selection pressure of superoxide dismutase in deep-sea sea cucumber

Manganese superoxide dismutase(MnSOD)is an antioxidant that exists in mitochondria and can effectively remove superoxide anions in mitochondria.In a dark,high-pressure,and low-temperature deep-sea environment,MnSOD is essential for the survival of sea cucumbers.Six MnSODs were identified from the transcriptomes of deep and shallow-sea sea cucumbers.To explore their environmental adaptation mechanism,we conducted environmental selection pressure analysis through the branching site model of PAML software.We obtained night positive selection sites,and two of them were significant(97F→H,134K→V):97F→H located in a highly conservative characteristic sequence,and its polarity c hange might have a great impact on the function of MnSOD;134K→V had a change in piezophilic a bility,which might help MnSOD adapt to the environment of high hydrostatic pressure in the deepsea.To further study the effect of these two positive selection sites on MnSOD,we predicted the point mutations of F97H and K134V on shallow-sea sea cucumber by using MAESTROweb and PyMOL.Results show that 97F→H,134K→V might improve MnSOD’s efficiency of scavenging superoxide a nion and its ability to resist high hydrostatic pressure by moderately reducing its stability.The above results indicated that MnSODs of deep-sea sea cucumber adapted to deep-sea environments through their amino acid changes in polarity,piezophilic behavior,and local stability.This study revealed the correlation between MnSOD and extreme environment,and will help improve our understanding of the organism’s adaptation mechanisms in deep sea.

Analysis of Sea Surface Temperature Cooling in Typhoon Events Passing the Kuroshio Current

The aim of this study is to investigate the sea surface temperature(SST) cooling as typhoons pass the Kuroshio Current.A numerical circulation model,denoted as the Stony Brook Parallel Ocean Model(sbPOM),was used to simulate the SST,which includes four wave-induced effect terms(i.e.,radiation stress,nonbreaking waves,Stokes drift,and breaking waves) simulated using the third-generation wave model,called WAVEWATCH-Ⅲ(WW3).The significant wave height(SWH) measurements from the Jason-2 altimeter were used to validate the WW3-simulated results,yielding a root mean square error(RMSE) of less than 0.50 m and a correlation coefficient(COR) of approximately 0.93.The water temperature measured from the Advanced Research and Global Observation Satellite was applied to validate the model simulation.Accordingly,the RMSE of the SST is 0.92℃ with a COR of approximately 0.99.As revealed in the sbPOM-simulated SST fields,a reduction in the SST at the Kuroshio Current region was observed as a typhoon passed,although the water temperature of the Kuroshio Current is relatively high.The variation of the SST is consistent with that of the current,whereas the maximum SST lagged behind the occurrence of the peak SWH.Moreover,the Stokes drift plays an important role in the SST cooling after analyzing four wave-induced terms in the background of the Kuroshio Current.The sensitivity experiment also showed that the accuracy of the water temperature was significantly reduced when including breaking waves,which play a negative role in the inside part of the ocean.The variation in the mean mixing layer depth(MLD) showed that a typhoon could enhance the mean MLD in the Kuroshio Current area in September and October,whereas a typhoon has little influence on the mean MLD in the Kuroshio Current area in May.Moreover,the mean MLD rapidly decreased with the weakening of the strong wind force and wave-induced effects when a typhoon crossed the Kuroshio Current.

Transcriptome analysis reveals immune-related genes in tissues of Vibrio anguillarum-infected turbot Scophthalmus maximus

Turbot Scophthalmus maximus is an important mariculture fish species with high economic value.However,the bacterial diseases caused by Vibrio anguillarum infection bring huge economic losses to the turbot aquaculture industry.To understand the immune response of the turbot against V.anguillarum infection and to explore novel immune-related genes,the transcriptome analysis of turbot spleen and gills were conducted after V.anguillarum infection.Differentially expressed genes(DEGs)were identified in spleen and gill of the turbot amounted to 17261 and 16436,respectively.A large number of immunerelated DEGs were enriched in cytokine-cytokine receptor interaction signaling pathway,and the others by the kyoto encyclopedia of genes and genomes(KEGG)enrichment.The gene ontology(GO)classification analysis revealed that V.anguillarum infection had the greatest effect on biological processes and cellular components.Twelve immune-related DEGs were identified in the spleen(cstl.1,egfl6,lamb21,v2rx4,calcr,and gpr78a)and gills(ghra,sh3gl2a,cst12,inhbaa,cxcl8,and il-1b)by heat map.The proteinprotein interaction(PPI)networks were constructed to analyze the immune mechanism.The results demonstrate that the maturation and antigen processing of major histocompatibility complex(MHC)class II molecule,and calcitonin-or adrenomedullin-regulated physiological activity were important events in the immunity of turbot against V.anguillarum infection.In the gills,the protein interactions in TGF-βsignaling pathway,production of inflammatory factors,and endocytosis regulation were most significant.Our research laid a foundation for discovering novel immune-related genes and enriching the knowledge of immune mechanisms of turbot against V.anguillarum infection.

Genome-Wide Characterization of the Hyaluronidase Gene Family and Their Potential Roles in Viviparous Black Rockfish(Sebastes schlegeli)

Black rockfish(Sebastes schlegelii)has evolved viviparous reproduction mode.Different from the oviparous fishes,the spermatozoa of black rockfish are stored on the surface of ovarian follicle for over four months until the egg mature in ovary,while the adaptive evolution of fertilization-related genes remains to be studied.In the present study,based on the genome and transcriptome information of black rockfish,a total of 10 hyaluronidase genes were identified by phylogenetic and sequence analyses,including hyal1,hyal2,hyal3,hyal4,hyal6 and spam1a,spam1b,spam1c and spam1d.The spam1 subfamilies,including spam1a,spam1b,spam1c and spam1d,were significantly expanded compared to other species.The adaptive evolution of hyaluronidase was further investigated by selection pressure analysis of branch model and branch site model.The results showed that only spam1 subfamily was positively selected with a large number of positive selection sites,and the evolution rate was significantly higher thanthose of other teleosts.Two positively selected sites,LYS-171 and GLY-164,were located in the neutral hyaluronidase activity domain,which was pivotal for SPAM1 to participate in enzymatic hydrolysis of the extracellular hyaluronic acid matrix and mediate acrosome reaction in mammals.Furthermore,spam1 was mainly expressed in spermatocytes,secondary spermatocytes,and spermatids of testis,whereas it was not found in metamorphic sperm and mature sperm based on the spatiotemporal expression analysis.All results indicated that spam1 might originate from the testis and might be an adaptation of viviparous trait in black rockfish.

Integrative analysis of transcriptomic profile reveals potential roles of miRNAs in regulating development of Marsupenaeus japonicas

Regulation of microRNAs(miRNAs)on various biological processes has been a surprising and exciting field.Identification of miRNAs is the first step to comprehensively understand their functions.However,attempts on global identification and functional verification of miRNAs are very limited in penaeid shrimp Marsupenaeus japonicus,an economically important aquatic species.By performing an integrated analysis of transcriptomic profile from gastrula embryos of M.japonicus,21conserved miRNAs in M.japonicas(mja-miRNAs),belonging to 19 miRNA families,were identified and characterized.Of the 21 mja-miRNAs,15 miRNAs were successfully verified to be predominantly expressed in gastrula stage,where they displayed dynamic expression patterns compared with those in naupliuin stage.Based on perfect or near-perfect match to target region,120 target genes were predicted at transcriptome-wide level.Noteworthy,gene ontology(GO)classification and metabolic pathway annotation revealed eight targets that were actively involved in developmental processes.Of the predicted miRNA-mRNA pairs,six targets were then randomly selected and experimentally validated by dual luciferase reporter assay,where three pairs were proved with potential targeting activity.Overall,to search for conserved miRNAs potentially involved in early development of M.japonicus,we combined in silico and experimental methods,which can be applied in other organisms as well.Our data implied important roles of miRNAs in the early embryonic development and also suggested the presence of complex miRNA-mRNA functional networks in M.japonicus.