Goldfish
is an ideal model for exploring fish morphology evolution. Although genes underlying several ornamental traits have been identified, little is known about the effects of artificial selection ...on embryo gene expression. In the present study, hybrid transcriptome sequencing was conducted to reveal gene expression profiles of Celestial-Eye (CE) and Ryukin (RK) goldfish embryos. Full-length transcriptome sequencing on the PacBio platform identified 54,218 and 54,106 transcript isoforms in CE and RK goldfish, respectively. Of particular note was that thousands of alternative splicing (AS) and alternative polyadenylation (APA) events were identified in both goldfish breeds, and most of them were inter-breed specific. RT-PCR and Sanger sequencing showed that most of the predicted AS and APA were correct. Moreover, abundant long non-coding RNA and fusion genes were detected, and again most of them were inter-breed specific. Through RNA-seq, we detected thousands of differentially expressed genes (DEGs) in each embryonic stage between the two goldfish breeds. KEGG enrichment analysis on DEGs showed extensive differences between CE and RK goldfish in gene expression. Taken together, our results demonstrated that artificial selection has led to far-reaching influences on goldfish gene expression, which probably laid the genetic basis for hundreds of goldfish variations.
The Pacific oyster Crassostrea gigas belongs to one of the most species-rich but genomically poorly explored phyla, the Mollusca. Here we report the sequencing and assembly of the oyster genome using ...short reads and a fosmid-pooling strategy, along with transcriptomes of development and stress response and the proteome of the shell. The oyster genome is highly polymorphic and rich in repetitive sequences, with some transposable elements still actively shaping variation. Transcriptome studies reveal an extensive set of genes responding to environmental stress. The expansion of genes coding for heat shock protein 70 and inhibitors of apoptosis is probably central to the oyster's adaptation to sessile life in the highly stressful intertidal zone. Our analyses also show that shell formation in molluscs is more complex than currently understood and involves extensive participation of cells and their exosomes. The oyster genome sequence fills a void in our understanding of the Lophotrochozoa.
Betaine, a methyl donor, plays a crucial role in lipid metabolism. Previous studies have shown that appropriate betaine supplementation in a high-fat diet reduces triglycerides (TG) of serum and ...hepatopancreas in fish. However, the underlying mechanism remains unclear. This study examined whether betaine can enhance the secretion of very low-density lipoprotein (VLDL) and sought to identify the specific mechanisms through which this enhancement occurs. A lipid accumulation model was established in gibel carp and L8824 cells using a high-fat diet and oleic acid, respectively. Different doses of betaine (1, 4, and 16 g/kg in the diet; 400 μmol in cell culture) were administered, and measurements were taken for lipid deposition, gene expression of HNF4α, MTTP, and ApoB, as well as the regulation of Mttp and Apob promoters by HNF4α. The results showed that betaine supplementation mitigated lipid droplet accumulation, TG levels, and VLDL production induced by the high-fat diet in gibel carp hepatopancreas and L8824 cells. Moreover, betaine not only increased VLDL content in the cell culture supernatant but also reversed the inhibitory effects of the high-fat diet on protein expression of MTTP, ApoB, and HNF4α in both gibel carp hepatopancreas and L8824 cells. Additionally, HNF4α exhibits transactivating activity on the promoter of Mttp in gibel carp. These findings suggest that betaine supplementation exerts its effects through the HNF4α/MTTP/ApoB pathway, promoting the assembly and secretion of VLDL and effectively reducing lipid accumulation in the hepatopancreas of farmed gibel carp fed a high-fat diet.
The northern bay scallop Argopecten irradians irradians (Lamarck) and the southern bay scallop Argopecten irradians concentricus (Say) were introduced into China in the 1980s and 1990s, and are now ...major aquaculture molluscs in China. Here, we report the transcriptome sequencing of the two subspecies and the subsequent association analysis on candidate gene on the trait of heat tolerance. In total, RNA from six tissues of 67 and 42 individuals of northern and southern bay scallops, respectively, were used and 55.5 and 34.9 million raw reads were generated, respectively. There were 82,267 unigenes produced in total, of which 32,595 were annotated. Altogether, 32,206 and 23,312 high-quality SNPs were identified for northern and southern bay scallops, respectively. For case-control analysis, two intercrossed populations were heat stress treated, and both heat-susceptible and heat-resistant individuals were collected. According to annotation and SNP allele frequency analysis, 476 unigenes were selected, and 399 pairs of primers were designed. Genotyping was conducted using the high-resolution melting method, and Fisher's exact test was performed for allele frequency comparison between the heat-susceptible and heat-resistant groups. SNP all-53308-760 T/C showed a significant difference in allele frequency between the heat-susceptible and heat-resistant groups. Notably, considerable difference in allele frequency at this locus was also observed between the sequenced natural populations. These results suggest that SNP all-53308-760 T/C may be related to the heat tolerance of the bay scallop. Moreover, quantitative expression analysis revealed that the expression level of all-53308 was negatively correlated with heat tolerance of the bay scallop.
It is of great significance for the aquaculture industry to determine how rearing salinity impacts fish flesh quality. In the present study, largemouth bass was cultured in different salinities (0%, ...0.3%, 0.9%) for 10 weeks, and the effect on flesh texture, flavor compounds, taste, and fatty acid composition was evaluated. We show that rearing salinity not only increased flesh water-holding capacity, but also enhanced muscle hardness, chewiness, gumminess, and adhesiveness, which was consistent with the finding in the shear value test. Morphology analysis further revealed that the effect of salinity on flesh texture was probably related to changes in myofibril diameter and density. As for the taste of the flesh, water salinity improved the contents of both sweet and umami amino acids, and reduced the contents of bitter amino acid. Meanwhile, the content of IMP, the dominant flavor nucleotide in largemouth bass muscle, was significantly higher in the 0.9% group. Interestingly, electronic-tongue analysis demonstrated that the positive effect of salinity on flavor compounds enhanced the umami taste and taste richness of flesh. Moreover, rearing salinity improved the contents of C20: 5n-3 (EPA) and C22: 6n-3 (DHA) in back muscle. Therefore, rearing largemouth bass in adequate salinity may be a practical approach to improving flesh quality.
Vibrio spp. are major causes of mortality in white shrimp (Litopenaeus vannamei) which is lacking adaptive immunity. Passive immunization with a specific egg yolk antibody (IgY) is a potential method ...for the protection of shrimp against vibriosis. In this study, immune effects of the specific egg yolk powders (IgY) against both V. harveyi and V. parahaemolyticus on white shrimp were evaluated. The egg yolk powders against V. harveyi and V. parahaemolyticus for passive immunization of white shrimp were prepared, while a tube agglutination assay and an indirect enzyme-linked immunosorbent assay (ELISA) were used for detection of IgY titer. Anti-Vibrio egg yolk was encapsulated by β-cyclodextrin, which could keep the activity of the antibody in the gastrointestinal tract of shrimp. The results showed that the anti-Vibrio egg powders had an inhibiting effect on V. harveyi and V. parahaemolyticus in vitro. Lower mortality of infected zoeae, mysis, and postlarva was observed in groups fed with anti-Vibrio egg powders, compared with those fed with normal egg powders. The bacterial load in postlarva fed with specific egg powders in seeding ponds was significantly lower than those fed with normal egg powders in seeding ponds. These results show that passive immunization by oral administration with specific egg yolk powders (IgY) may provide a valuable protection of vibrio infections in white shrimp.
The fatty acid compositions of the fish muscle and liver are substantially affected by rearing environment. However, the mechanisms underlying this effect have not been thoroughly described. In this ...study, we investigated the effects of different culture patterns, i.e., marine cage culture and freshwater pond culture, on long-chain polyunsaturated fatty acids (LC-PUFA) biosynthesis in an aquaculturally important fish, the Japanese sea bass (Lateolabrax japonicus). Fish were obtained from two commercial farms in the Guangdong province, one of which raises Japanese sea bass in freshwater, while the other cultures sea bass in marine cages. Fish were fed the same commercial diet. We found that omega-3 long-chain polyunsaturated fatty acids (n-3 LC-PUFA) levels in the livers and muscles of the marine cage cultured fish were significantly higher than those in the livers and muscles of the freshwater pond cultured fish. Quantitative real-time PCRs indicated that fatty acid desaturase 2 (FADS2) transcript abundance was significantly lower in the livers of the marine cage reared fish as compared to the freshwater pond reared fish, but that fatty acid elongase 5 (Elovl5) transcript abundance was significantly higher. Consistent with this, two of the 28 CpG loci in the FADS2 promoter region were heavily methylated in the marine cage cultured fish, but were only slightly methylated in freshwater pond cultured fish (n = 5 per group). Although the Elovl5 promoter was less methylated in the marine cage reared fish as compared to the freshwater pond reared fish, this difference was not significant. Thus, our results might indicate that Elovl5, not FADS2, plays an important role in the enhancing LC-PUFA synthesis in marine cage cultures.
Reduced-representation sequencing technology is widely used in genotyping for its economical and efficient features. A popular way to construct the reduced-representation sequencing libraries is to ...digest the genomic DNA with restriction enzymes. A key factor of this method is to determine the restriction enzyme(s). But there are few computer programs which can evaluate the usability of restriction enzymes in reduced-representation sequencing. SimRAD is an R package which can simulate the digestion of DNA sequence by restriction enzymes and return enzyme loci number as well as fragment number. But for linkage mapping analysis, enzyme loci distribution is also an important factor to evaluate the enzyme. For phylogenetic studies, comparison of the enzyme performance across multiple genomes is important. It is strongly needed to develop a simulation tool to implement these functions.
Here, we introduce a Perl module named RestrictionDigest with more functions and improved performance. It can analyze multiple genomes at one run and generate concise comparison of enzyme performance across the genomes. It can simulate single-enzyme digestion, double-enzyme digestion and size selection process and generate comprehensive information of the simulation including enzyme loci number, fragment number, sequences of the fragments, positions of restriction sites on the genome, the coverage of digested fragments on different genome regions and detailed fragment length distribution.
RestrictionDigest is an easy-to-use Perl module with flexible parameter settings. With the help of the information produced by the module, researchers can easily determine the most appropriate enzymes to construct the reduced-representation libraries to meet their experimental requirements.
This research aimed to investigate the role of dietary betaine in high‐fat diet in cholesterol metabolism in gibel carp. Fish were randomly allocated to five groups and fed with basic diet, high‐fat ...diet and high‐fat diet with 1 g/kg, 4 g/kg and 16 g/kg betaine, respectively. The feeding trial lasted 10 weeks. The results showed that though betaine addition decreased fish final body weight, it alleviated lipid metabolism disorder caused by high‐fat diet according to serum TC, TG, LDLC and HDLC levels. More importantly, betaine supplementation enhanced cholesterol synthesis as well as conversion of cholesterol to bile acid by promoting expression of HMGCR and CYP7A1 genes. Meanwhile, betaine supplementation not only promoted bile acid efflux and increased total bile acid level in the intestine but also improved intestinal lipase activity. Moreover, high‐fat diet with betaine addition improved the hepatopancreas’ antioxidant capacity, lessened hepatopancreas injury and increased fish survival during the feeding trial and under bacterial challenge. In summary, dietary betaine supplementation was beneficial to alleviate high‐fat feeding‐induced lipid metabolism disorder, promote cholesterol conversion to bile acid and enhance hepatopancreas function in gibel carp.
Macrobrachium rosenbergii, the giant freshwater prawn, is an important aquaculture species in China and other Southeast Asian countries. Here, we report the positive effect of dietary betaine ...supplementation on growth performance and the innate immune system in M. rosenbergii. Four diets were formulated containing graded levels of betaine, and a 10-week feeding trial was conducted. Prawns fed a diet containing 0.5% betaine (B0.5) showed significantly higher growth performance, while feed efficiency was not significantly influenced compared with the control group. Moreover, the survival rate under bacterial challenge in the B0.5 group was significantly higher than in the control group infected. Betaine supplementation also significantly reduced crude lipid content and significantly increased crude protein content in the B0.5 and B1 groups. Similarly, the contents of total (essential) amino acids and many flavorful amino acids such as Aspartic, Serine, Alanine and Glycine in the muscle were also significantly higher than in the control group. Most interestingly, the contents of n-3 PUFA and n-3 LC-PUFA in all betaine supplementation groups were significantly higher than in the control group. In addition, significantly higher activities were detected in the B0.5 group than in the control group for hepatopancreas digestive enzymes Pepsin, Trypsin and Lipase, and serum enzymes including CAT, SOD, and TNF-α. We also checked the expression levels of five immune-related genes and found that Relish, TLR-1, and TLR-2 were all significantly down regulated in all supplementation groups, while HSP70 was significantly upregulated only in the B0.5 group. Taken together, our results demonstrated that a moderate amount of dietary betaine supplementation not only promotes growth but also benefits the innate immune system of M. rosenbergii.
•Betaine supplementation significantly improved crude protein content and flavor amino acid content in the B0.5 group.•Dietary betaine significantly reduced crude lipid content but significantly increased n-3 PUFA content in the muscle.•Both innate immunity and survival rate under bacterial challenge were enhanced by betaine supplementation at 0.5% level.•Dietary betaine significantly improved the activity of most hepatopancreas digestive enzymes in the B0.5 group.
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