A chromosome-level genome assembly of the miiuy croaker(Miichthys miiuy)using nanopore sequencing and Hi-C

Miiuy croaker,Miichthys miiuy is an ecologically important teleost species which is widely distributed in southeast coast of China.In this study,we present a chromosomal-scale genome assembly of the miiuy croaker which is an important Sciaenidae fish and economical species.We adopted Oxford Nanopore and Hi-C sequencing techniques to achieve an assembly with high accuracy and completeness.The investigation of genome characteristic and functional features may provide insights into the study of phylogenetic diversity of miiuy croaker.This study can also be beneficial to improve molecular assisted breeding techniques.Moreover,it can be a great resource to better conduct further study of other sciaenids.

Long noncoding RNA AANCR modulates innate antiviral responses by blocking miR-210-dependent MITA downregulation in teleost fish,Miichthys miiuy

Viral infection induces the initiation of antiviral effectors and cytokines which are critical mediators of innate antiviral responses.The critical molecular determinants are responsible for triggering an appropriate immune response.Long noncoding RNAs(lncRNAs)have emerged as new gene modulators involved in various biological processes,while how lncRNAs operate in lower vertebrates are still unknown.Here,we discover a long noncoding RNA,termed antiviral-associated long noncoding RNA(AANCR),as a novel regulator for innate antiviral responses in teleost fish.The results indicate that fish MITA plays an essential role in host antiviral responses and inhibition of Siniperca chuatsi rhabdovirus(SCRV)production.miR-210 reduces MITA expression and suppress MITA-mediated antiviral responses,which may help viruses evade host antiviral responses.Further,AANCR functions as a competing endogenous RNA(ceRNA)for miR-210 to control protein abundance of MITA,thereby inhibiting SCRV replication and promoting antiviral responses.Our data not only shed new light on understanding the function role of lncRNA in biological processes in teleost fish,but confirmed the hypothesis that ceRNA networks exist widely in vertebrates.

MicroRNA negatively regulates NF-κB-mediated immune responses by targeting NOD1 in the teleost fish Miichthys miiuy

Inflammation is a self-protection mechanism that can be triggered when innate immune cells detect infection.Eradication of pathogen infection requires appropriate immune and inflammatory responses,but excessive inflammatory responses can cause uncontrolled inflammation,autoimmune diseases,or pathogen dissemination.Mounting evidence has shown that microRNAs(miRNAs)in mammals act as important and versatile regulators of innate immunity and inflammation.However,miRNAmediated regulation networks are largely unknown in inflammatory responses in lower vertebrates.Here,miR-144 and miR-217 are identified as negative regulators in teleost inflammatory responses.We find that Vibrio harveyi and lipopolysaccharide(LPS)treatment significantly upregulate the expression of fish miR-144 and miR-217.Upregulated miR-144 and miR-217 suppress LPS-induced inflammatory cytokine expression by targeting nucleotide-binding oligomerization domain-containing protein 1(NOD1),thereby avoiding excessive inflammatory responses.In addition,miR-144 and miR-217 regulate inflammatory responses through NOD1-induced nuclear factor kappa(NF-κB)signaling pathways.These findings demonstrate that miR-144 and miR-217 play regulatory roles in inflammatory responses by modulating the NOD1-induced NF-κB signaling pathway.

A chromosome-level genome assembly of the blackspotted croaker(Protonibea diacanthus)

The blackspotted croaker(Protonibea diacanthus)is an endangered coastal marine fish.It is also a valuable species that is cultured on the southeast coast of China.While some genetic studies have been conducted to protect this species,genomic resources are lacking.Here,we report a chromosome-scale assembly of P.diacanthus genome by high-depth genome sequencing,assembly,and annotation.The genome scale was 635.69 Mb with contig and scaffold N50 length of 3.33 Mb and 25.60 Mb,respectively.Hi-C scaffolding of the genome resulted in 24 chromosomes of 94.15%total genome.We predicted 23,971 protein-coding genes.In addition,we constructed a phylogenetic tree using 2755 single-copy gene families and identified 462 unique gene families in P.diacanthus genome compared to three other sciaenids.What’s more,from the analysis of gene families,we found that several gene families related to innate immunity were significantly expanded in the blackspotted croaker genome compared to other teleost genomes.The high-quality genome can improve our understanding of the molecular mechanisms behind economically valuable traits and provide insights into characteristics of the immune system.

A chromosome-level genome assembly of the red drum, Sciaenops ocellatus

Sciaenops ocellatus,also known as red drum,is a valuable commercial fish that is widely cultured in China.In recent years,while the genetic research and molecular breeding on S.ocellatus has been widely performed,whole-genome resources are lacking.In our study,we assembled the S.ocellatus genome by high-quality genome sequencing,followed by complete annotation.The size of final genome was 686.62 Mb and N50 length of contig and scaffold is 99.71 Kb and 25.62 Mb,respectively.Using the Hi-C technology,we obtained 24 pseudochromosomes containing 87.82%of the total scaffolds.We annotated 20,053 protein-coding genes in S.ocellatus genome,of which 99.93%were homologous to proteins in different database.Totally,we detected 133.54 Mb repeat sequences,which accounts for 19.45%of the assembly.According to the phylogenetic analysis,S.ocellatus is most closed to L.croea with a divergence time about 30 million years ago.We assembled a high-quality genome that will be a valuable resource to further study the biology of S.ocellatus and will inform how to breed the red drum to enhance its economic traits.

Long noncoding RNA TARL promotes antibacterial activity and prevents bacterial escape in Miichthys miiuy through suppression of TAK1 downregulation

Noncoding RNA(ncRNA)is an important regulatory factor that plays a major role in innate immunity.However,most studies on ncRNA have focused on mammals,resulting in a knowledge gap on nc RNA in lower vertebrates such as teleost fish.In this study,we identified a new long noncoding RNA(lncRNA),termed TAK1-related lnc RNA(TARL),which can play a positive role in the antibacterial immunity of Miichthys miiuy to Vibrio anguillarum and V.harveyi.We also found a novel micro RNA miR-2188-3p that could target TAK1 and inhibit the host antibacterial response and promote bacterial escape.We further found that the antibacterial effect inhibited by miR-2188-3p could be reversed with TARL.Moreover,V.anguillarum and V.harveyi are the two most susceptible Gram-negative pathogens of aquaculture fish,and the economic losses caused by these two bacteria are immeasurable every year.This study is the first to report on the ability of lnc RNA to prevent the escape of V.anguillarum and V.harveyi in fish through the competing endogenous RNA(ceRNA)mechanism.Our results not only elucidate the ce RNA mechanism of the lncRNA in antibacterial immune responses but also provide new insights into the impact of lnc RNA on host immunity and bacterial escape.

LncRNA MIR144HG-derived miR-144 suppresses antibacterial signaling and facilitates bacteria escape in fish

Growing number studies show that lncRNA is an important regulatory factor and plays an irreplaceable role in innate immunity.However,most studies on lncRNA have focused on mammals and it is unknown in lower vertebrates.In this study,we identify a new lncRNA,named MIR144HG,which can have a negative role in antibacterial immunity of Miichthys miiuy caused by Vibrio anguillarum and V.harveyi.MyD88,TAK1 and p65 are very important pathway genes in antibacterial innate immune responses,whether in mammals or lower vertebrates.Here,we found that miR-144–3p could target MyD88,TAK1 and p65,inhibit host antibacterial response and promote bacterial escape.Further studies found that miR-144–3p can be derived by MIR144HG,and finally enhance the inhibitory effect of miR-144–3p on host antibacterial immunity.Moreover,V.anguillarum and V.harveyi are the two most susceptible Gram-negative pathogens in aquaculture,and the economic losses caused by these two bacteria are immeasurable every year.Our results not only elucidate the mechanism of the lncRNAmiRNA-mRNA axis in antibacterial immune responses,but also provide new insights for understanding the impact of lncRNA on host immunity and bacteria escape.