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During the cultivation of Marsupenaeus japonicus, there are often obvious differences in the growth within the same family under the same food, water quality, and environment, which greatly affects cultivation efficiency. To explore the molecular mechanism of this growth difference, this study used RNA-seq technology to compare the transcriptomes of M. japonicus individuals with significant growth differences from the same family. A total of 1375 differentially expressed genes were identified, of which 1109 were upregulated and 266 were downregulated. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed on the differentially expressed genes, and the results showed that growth-related processes, including chitin metabolism, chitin-binding amino sugar metabolism, and antioxidant processes, including response to oxidative stress, peroxidase activity, antioxidant activity, and peroxidase activity, showed significant differences between the large-size and small-size groups. The expression levels of some differentially expressed genes, such as cuticular protein, low-density lipoprotein receptor, ecdysteroid kinase, myosin heavy chain, and apoptosis inhibitor, were verified by quantitative PCR experiments. One cuticle gene was annotated, and phylogenetic analysis showed that this sequence clustered with the penaeid cuticle genes. This study provides valuable data and a scientific basis for understanding the mechanism of growth differences in M. japonicus at the molecular-genetic level. [ABSTRACT FROM AUTHOR]

An 8-week feeding trial was performed to evaluate the effects of dietary β-hydroxy-β-methylbutyrate (HMB) supplementation on growth performance and muscle quality of kuruma shrimp (Marsupenaeus japonicas) (initial weight: 2.00 ± 0.01 g) fed a low protein diet. The positive control diet (HP) with 490 g/kg protein and negative control diet (LP) with 440 g/kg protein were formulated. Based on the LP, 0.25, 0.5, 1, 2 and 4 g/kg β-hydroxy-β-methylbutyrate calcium were supplemented to design the other five diets named as HMB0.25, HMB0.5, HMB1, HMB2 and HMB4, respectively. Results showed that compared with the shrimp fed LP, the HP, HMB1 and HMB2 groups had significantly higher weight gain and specific growth rate, while significantly lower feed conversion ratio (p < 0.05). Meanwhile, intestinal trypsin activity was significantly elevated in the above three groups than that of the LP group. Higher dietary protein level and HMB inclusion upregulated the expressions of target of rapamycin, ribosomal protein S6 kinase, phosphatidylinositol 3-kinase, and serine/threonine-protein kinase in shrimp muscle, accompanied by the increases in most muscle free amino acids contents. Supplementation of 2 g/kg HMB in a low protein diet improved muscle hardness and water holding capacity of shrimp. Total collagen content in shrimp muscle increased with increasing dietary HMB inclusion. Additionally, dietary inclusion of 2 g/kg HMB significantly elevated myofiber density and sarcomere length, while reduced myofiber diameter. In conclusion, supplementation of 1-2 g/kg HMB in a low protein diet improved the growth performance and muscle quality of kuruma shrimp, which may be ascribed to the increased trypsin activity and activated TOR pathway, as well as elevated muscle collagen content and changed myofiber morphology caused by dietary HMB. [ABSTRACT FROM AUTHOR]

Simple Summary: To inform the management of shrimp culture strategies, it is important to uncover the interaction of complex factors with shrimp behaviors in the culture environment. This study was carried out with the objective to investigate the behavioral patterns of Penaeus japonicus and the effects of the natural farming environment on its behavior. The results revealed the preference for maintaining silence for P. japonicus in their breeding environment, of which the behavior patterns were prominently influenced by the sex ratio. Light intensity is demonstrated as the most influential factor in the behavior of P. japonicus, followed by population density. In conclusion, this study provides scientific evidence for shrimp farming of significant practical value. Recent years have witnessed a tremendous development in shrimp farming around the world, which, however, has raised a variety of issues, possibly due to a lack of knowledge of shrimp behavior in farms. This study focused on the relationship between shrimp behavior and the various factors of natural farming environment through situ surveys, as distinguished from the majority of laboratory studies on shrimp behavior. In the survey, the behaviors of kuruma prawn (Penaeus japonicus) were investigated in the groups of swimming in the water, crawling on the sand, resting on the sand, and hiding in the sand, followed by the quantification of the sex ratio, water quality, density, and light intensity. The results showed the average proportions of resting, hiding, crawling, and swimming activities of 69.87%, 20.85%, 8.24%, and 1.04%, respectively, of P. japonicus. The behavior of hiding, resting, and crawling is significantly affected by the sex ratio of the shrimp (p < 0.05). The proportions of hiding behavior exhibited a negative connection with density and a positive connection with light intensity, while the proportions of resting behavior showed the opposite according to both Pearson correlation analysis and multiple linear regression analysis. The light intensity was the only factor that significantly influenced the swimming behavior, in which the probability of the swimming behavior was reduced from 48% to 5% when light intensity varied from 0 to 10 lx, as determined by the generalized linear model. It could be speculated that P. japonicus prefers a tranquil environment. Female shrimp might exhibit less aggression and more adventure compared to male shrimp. The findings suggested light intensity, followed by density, as the most crucial element influencing the behavior of P. japonicus in the culture environment. These findings will contribute to the comprehension of the behavior of P. japonicus and provide a novel perspective for the formulation of its culture management strategy. [ABSTRACT FROM AUTHOR]

Background: Kuruma shrimp, a major commercial shrimp species in the world, has two cryptic or sibling species, Marsupenaeus japonicus and Marsupenaeus pulchricaudatus. Codon usage analysis would contribute to our understanding of the genetic and evolutionary characteristics of the two Marsupenaeus species. In this study, we analyzed codon usage and related indices using coding sequences (CDSs) from RNA-seq data. Results: Using CodonW 1.4.2 software, we performed the codon bias analysis of transcriptomes obtained from hepatopancreas tissues, which indicated weak codon bias. Almost all parameters had similar correlations for both species. The gene expression level (FPKM) was negatively correlated with A/T3s. We determined 12 and 14 optimal codons for M. japonicus and M. pulchricaudatus, respectively, and all optimal codons have a C/G-ending. The two Marsupenaeus species had different usage frequencies of codon pairs, which contributed to further analysis of transcriptional differences between them. Orthologous genes that underwent positive selection (ω > 1) had a higher correlation coefficient than that of experienced purifying selection (ω < 1). Parity Rule 2 (PR2) and effective number of codons (ENc) plot analysis showed that the codon usage patterns of both species were influenced by both mutations and selection. Moreover, the average observed ENc value was lower than the expected value for both species, suggesting that factors other than GC may play roles in these phenomena. The results of multispecies clustering based on codon preference were consistent with traditional classification. Conclusions: This study provides a relatively comprehensive understanding of the correlations among codon usage bias, gene expression, and selection pressures of CDSs for M. japonicus and M. pulchricaudatus. The genetic evolution was driven by mutations and selection pressure. Moreover, the results point out new insights into the specificities and evolutionary characteristics of the two Marsupenaeus species. [ABSTRACT FROM AUTHOR]

The kuruma shrimp (Marsupenaeus japonicus) includes two cryptic species, which are distributed mostly allopatrically but co-occur in the northern South China Sea (from Huilai to Beihai). To obtain a better understanding of the fine-scale genetic structure and parapatric diversification of these two varieties in the northwestern Pacific region, we used a genotyping-by-sequencing (GBS) and comparative transcriptomics approach to establish their phylogenetic relationships. Using the GBS technique, we genotyped 28891 SNPs in 160 individuals in the Northwest Pacific. The results supported two highly diverged evolutionary lineages of kuruma shrimp (var. I and II). The ND and XM populations showed complex genetic patterns, which might be affected by the complex environment of the Taiwan Strait. In addition, the migration rates and inbreeding coefficients of XM and BH were much lower than those of the other populations, which might be related to the land-sea changes and complex ocean currents in the Taiwan Strait and Qiongzhou Strait. Based on the synonymous substitution rates (ds) of 2,491 candidate orthologs, we estimated that the divergence time between the two varieties was 0.26~0.69 Mya. Choice and no-choice interbreeding experiments provided support for the biological species concept, by showing the existence of reproductive isolation or incompatibility. In view of these differences between the two Marsupenaeus species, we believe that it is essential and urgent to establish a genetic database for each and reevaluate their ecological suitable conditions in order to improve species-specific culturing techniques. Moreover, this research can serve as a case study for future research on speciation and hybridization. [ABSTRACT FROM AUTHOR]

Kuruma prawn, Marsupenaeus japonicus, has the third largest annual yield among shrimp species with vital economic significance in China. White spot syndrome virus (WSSV) is a great threat to the global shrimp farming industry and results in high mortality. Pellino, a highly conserved E3 ubiquitin ligase, has been found to be an important modulator of the Toll-like receptor (TLR) signaling pathways that participate in the innate immune response and ubiquitination. In the present study, the Pellino gene from Marsupenaeus japonicus was identified. A qRT-PCR assay showed the presence of MjPellino in all the tested tissues and revealed that the transcript level of this gene was significantly upregulated in both the gills and hemocytes after challenge with WSSV and Vibrio parahaemolyticus. The function of MjPellino was further verified at the protein level. The results of the three-dimensional modeling and protein–protein docking analyses and a GST pull-down assay revealed that the MjPellino protein was able to bind to the WSSV envelope protein VP26. In addition, the knockdown of MjPellino in vivo significantly decreased the expression of MjAMPs. These results suggest that MjPellino might play an important role in the immune response of kuruma prawn. [ABSTRACT FROM AUTHOR]