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Grouper (Epinephelus coioides) is an important commercial maricultural fish, which suffers from nervous necrosis virus (NNV) infection. The molecular mechanisms underlying the pathogenesis of the viral infection are not clear. In this study, we combined deep RNA sequencing and label-free mass spectrum for the first time to analyze the transcriptomic and proteomic profiles in infected/dead, infected/survival (persistent), and infection-free (control)orange-spotted groupers in the larval stage. Further analyses showed that the transcriptome and proteome changed dramatically among the three distinct groups, especially differentially-expressed genes in the infected/dead and infected/survival larvae enriched for pathways related to immune response. Notably, the overlapped genes between transcriptomes and proteomes identified that genes related to collagen synthesis and adhesion molecules were enhanced in the persistent (infected/survival) stage, which might contribute to suppressing the acute and lethal immune responses upon NNV infection. These transcriptomic and proteomic datasets enable the investigation of molecular mechanisms underlying NNV infection, thus may help further development of molecular breeding in marine fishery. • We performed coalition analysis of transcriptomes and proteomes of NNV-infected grouper larvae. • Differentially-expressed genes in the infected/dead and infected/survival larvae enriched for immune response pathways. • The overlapped genes were related to collagen synthesis and adhesion molecules in the infected/survival larvae. [ABSTRACT FROM AUTHOR]

The red‐spotted grouper Epinephelus akaara (E. akaara) is one of the most economically important marine fish in China, Japan and South‐East Asia and is a threatened species. The species is also considered a good model for studies of sex inversion, development, genetic diversity and immunity. Despite its importance, molecular resources for E. akaara remain limited and no reference genome has been published to date. In this study, we constructed a chromosome‐level reference genome of E. akaara by taking advantage of long‐read single‐molecule sequencing and de novo assembly by Oxford Nanopore Technology (ONT) and Hi‐C. A red‐spotted grouper genome of 1.135 Gb was assembled from a total of 106.29 Gb polished Nanopore sequence (GridION, ONT), equivalent to 96‐fold genome coverage. The assembled genome represents 96.8% completeness (BUSCO) with a contig N50 length of 5.25 Mb and a longest contig of 25.75 Mb. The contigs were clustered and ordered onto 24 pseudochromosomes covering approximately 95.55% of the genome assembly with Hi‐C data, with a scaffold N50 length of 46.03 Mb. The genome contained 43.02% repeat sequences and 5,480 noncoding RNAs. Furthermore, combined with several RNA‐seq data sets, 23,808 (99.5%) genes were functionally annotated from a total of 23,923 predicted protein‐coding sequences. The high‐quality chromosome‐level reference genome of E. akaara was assembled for the first time and will be a valuable resource for molecular breeding and functional genomics studies of red‐spotted grouper in the future. [ABSTRACT FROM AUTHOR]

The whiteleg shrimp (Litopenaeus vannamei) is one of the most economically important aquaculture species in China. Genetic diversity is crucial for maintaining the gene pool of farmed shrimp. In this study, the effects of artificial selection on the genetic structure of four whiteleg shrimp strains were evaluated using microsatellite sequences. The results showed that the observed heterozygosity (Ho), expected heterozygosity (He), and the polymorphism information content (PIC) of the four selected strains ranged from 0.446 to 0.574, 0.450 to 0.566, and 0.435 to 0.509, respectively. All the selected strains maintained a moderate level of genetic diversity. Most inbreeding coefficients (Fis) in the four strains were positive but not significantly different from zero, indicating a relatively low degree of inbreeding within each strain. However, He and PIC in line 5 showed a decreasing trend from the 2017 to the 2019 generations, and Fis in line 10 showed a significant increasing trend across generations, indicating that measures must be taken to maintain the level of genetic diversity for lines 5 and 10. UPGMA cluster trees showed that the four breeding lines had apparent genetic differences, which could provide a genetic basis for studying crossbreeding between selective lines and the utilization of heterosis. This study will be useful for population genetic research and the breeding strategies of whiteleg shrimp. [ABSTRACT FROM AUTHOR]

Nervous necrosis virus (NNV) is a kind of the betanodaviruses, which can cause viral nervous necrosis (VNN) and massive mortality in larval and juvenile stages of orange-spotted grouper ( Epinephelus coioides ). Due to the lack of viral genomes, virus-like particles (VLPs) are considered as one of the most promising candidates in vaccine study to control this disease. In this study, a type of VLPs, which was engineered on the basis of orange-spotted grouper nervous necrosis virus (OGNNV), was produced from prokaryotes. They possessed the similar structure and size to the native NNV. In addition, synthetic oligodeoxynucleotide (ODN) containing CpG motif was added in vaccines, and the expression patterns of several genes were analyzed after injecting with VLP and VLP with adjuvant (VA) to assess the regulation effect of vaccine for inducing immune responses. RT-PCR assays showed that six related genes in healthy tissues were ubiquitously expressed in all nine tested tissues. The vaccine alone was able to enhance the expression of genes, including MHCIa, MyD88, TLR3, TLR9 and TLR22 after vaccination, indicating that the vaccine was able to induce immune response in grouper. In liver, spleen and kidney, the gene expressions of VA group were all significantly higher than that of VLP group at 72 h post-stimulation, showing that the fish of VA challenge group obtained the longer-lasting protective immunity and resistance to pathogen challenge than that of VLP group. The data indicated that the efficacy of vaccine could be further enhanced by CpG ODN after vaccination and provided the reference for the development of future viral vaccine in grouper. [ABSTRACT FROM AUTHOR]

Abstract: Toll-like receptor 3 (TLR3) plays an important role in activating innate immune responses during viral infection. In this report, TLR3 (EcTLR3) was characterized and analyzed for the first time in Epinephelus coioides. The full-length EcTLR3 cDNA is predicted to encode a 909 amino acid polypeptide that contains a signal peptide sequence, 18 leucine-rich repeat (LRR) motifs, a transmembrane region and a Toll/interleukin-1 receptor (TIR) domain. Quantitative real-time PCR revealed that the EcTLR3 mRNA was much more abundant in the liver than in other immune organs, and that the expression levels were very low in hemocyte and muscle. During development of the grouper, the levels of EcTLR3 transcripts increased with age, with very low expression levels at the early stages of development. EcTLR3 mRNA levels were examined in the liver at different times after treatment with polyriboinosinic polyribocytidylic acid (Poly I:C), and in nervous necrosis virus (NNV)-infected larval groupers. The results suggested that EcTLR3 plays an important role in a fish's defense against viral infection. [Copyright &y& Elsevier]