Integrated microRNA-mRNA analysis provides new insights into gonad coloration in the sea urchin Strongylocentrotus intermedius

Comparative microRNA (miRNA) and mRNA transcriptome analyses were performed on Strongylocentrotus intermedius of the same sex with significant gonadal color differences. The results indicated that 1) the color of female gonads was generally superior to that of males. 2) Comparative and integrated miRNA and mRNA transcriptome analyses identified differentially expressed genes (DEGs) and differentially expressed miRNAs (DEMs) in female and male individuals with significant gonadal color differences. Common and sex-specific DEGs and “DEM-DEG” pairs involved in carotenoid absorption, accumulation, and transformation were identified as candidates correlated with gonad coloration in S. intermedius. Collectively, the results from this study have enriched our knowledge of the process of sea urchin gonad coloration and should provide additional clues for increasing the gonad quality of commercial sea urchins from molecular and metabolic aspects

Role Analysis of the scarb1 Gene in the Pigmentation of Neocaridina denticulata sinensis

Body color is a key economic trait for Neocaridina denticulata sinensis, an important ornamental shrimp. Scarb1 may be an important mediator of astaxanthin uptake, changing the shrimp’s body color. To discover the relationship between scarb1 and the pigmentation of cherry shrimp, the expression profiles, RNAi, and SNP genotyping of scarb1 were studied. There were significant differences in four color populations and five development stages (p < 0.05). The highest expression level of scarb1 appeared in the red population and the pre-nauplius stage. Exposure to scarb1 dsRNA increased the number and development of chromatophores at the metanauplius stage, but almost no phenotypic changes were observed at the pre-zoea stage. There was a synonymous SNP (G1593A) with a significantly different genotype frequency between the red and yellow populations (p < 0.05). The above results suggested that scarb1 is involved in pigmentation by affecting the development of chromatophores

Functional Analysis of NdBCO-like4 Gene in Pigmentation of Neocaridina denticulata sinensis

Cherry shrimp (Neocaridina denticulata sinensis) is one of the main ornamental shrimp because of its bright body color. β, β-carotene 9′,10′-dioxygenase (BCO2) is closely related to the body color produced by carotenoids. In order to study the role of NdBCO-like4 (homologous gene of BCO2) in the pigmentation of cherry shrimp, the expression profiles, RNA interference, and SNP genotyping were applied in this study. The NdBCO-like4 expression varied significantly among four color strains and five development stages (p < 0.05). The results showed that the NdBCO-like4 expression was the highest in the red strain and the lowest in the wild strain. During the embryonic development, the expression in the metanauplius stage was significantly lower than other stages (p < 0.05), and the expression of NdBCO-like4 was the highest in the membrane-zoea stage. In the metanauplius stage, the RNAi knockdown of NdBCO-like4 mediated the red pigment brightness value, and the pigment cell index in the treatment group was significantly lower than the control group (p < 0.05). After the first round of screening, a total of 8424 high-quality SNPs were obtained. There was one candidate SNP located on the NdBCO-like4 target gene, named G.1719G>A. The synonymous SNP exhibited significantly different genotype frequencies between the yellow and wild strains compared to other strains (p < 0.05), suggesting an association with these phenotypes. These results suggest that NdBCO-like4 has a close relation with carotenoid accumulation in cherry shrimp, providing valuable insights into the molecular mechanisms underlying pigmentation in this species

Non-coding RNAs targeting NF-κB pathways in aquatic animals: A review

Nuclear factor-kappa B (NF-κB) pathways have a close relationship with many diseases, especially in terms of the regulation of inflammation and the immune response. Non-coding RNAs (ncRNAs) are a heterogeneous subset of endogenous RNAs that directly affect cellular function in the absence of proteins or peptide products; these include microRNAs (miRNAs), long noncoding RNAs (lncRNAs), circular RNAs (circRNAs), etc. Studies on the roles of ncRNAs in targeting the NF-κB pathways in aquatic animals are scarce. A few research studies have confirmed detailed regulatory mechanisms among ncRNAs and the NF-κB pathways in aquatic animals. This comprehensive review is presented concerning ncRNAs targeting the NF-κB pathway in aquatic animals and provides new insights into NF-κB pathways regulatory mechanisms of aquatic animals. The review discusses new possibilities for developing non-coding-RNA-based antiviral applications in fisheries.</jats:p

Characterization of a novel glutamate dehydrogenase gene and its response to heat stress in the sea urchin Strongylocentrotus intermedius

Glutamate dehydrogenase (GDH), a key metabolic enzyme that is ubiquitous across almost all living species, is essential for cell survival. To elucidate the characteristics and functions of the GDH gene in the sea urchin, we cloned and characterized the full-length cDNA of a novel GDH homolog from Strongylocentrotus intermedius, herein designated SiGDH. The full-length SiGDH gene was 2499 bp, with an open reading frame (ORF) of 1635 bp, encoding 544 amino acids. Bioinformatic analyses revealed that the predicted SiGDH protein contained the conserved ELFV_dehydrog_N and ELFV_dehydrog domains and that this protein had the highest sequence identity with the GDH protein from Strongylocentrotus purpuratus. Tissue-specific differences in SiGDH relative expression patterns and enzyme activity levels were observed, and the highest relative expression and total enzyme activity of SiGDH were determined to be in the gonad. Changes in SiGDH relative expression and enzyme activity in the gonad were observed after both gradual and acute heat stress. Together, our observations help to clarify the characteristics of this GDH homolog, as well as its associations with heat resistance in echinoderms