Comparative Transcriptomic Analysis of Largemouth Bass (Micropterus salmoides) Livers Reveals Response Mechanisms to High Temperatures.

High temperatures are considered one of the most significant limitations to subtropical fishery production. Largemouth bass (Micropterus salmoides) is an economically important freshwater species grown in subtropical areas, which are extremely sensitive to heat stress (HS). However, comprehensive transcriptomic data for the livers of largemouth bass in response to HS are still lacking. In this study, a comparative transcriptomic analysis was performed to investigate the gene expression profiles of the livers of largemouth bass under HS treatment. As a result, 6114 significantly differentially expressed genes (DEGs), which included 2645 up-regulated and 3469 down-regulated genes, were identified in response to HS. Bioinformatics analyses demonstrated that the 'ECM-receptor interaction' pathway was one of the most dramatically changed pathways in response to HS, and eight DEGs assigned to this pathway were taken as hub genes. Furthermore, the expression of these eight hub genes was determined by quantitative reverse transcription PCR, and all of them showed a significant change at the transcriptional level, suggesting a crucial role of the 'ECM-receptor interaction' pathway in the response of largemouth bass to HS. These findings may improve our understanding of the molecular mechanisms underlying the response of largemouth bass to HS.

Effects of dietary chito-oligosaccharide and ß-glucan on the water quality and gut microbiota, intestinal morphology, immune response, and meat quality of Chinese soft-shell turtle (Pelodiscus sinensis).

Chito-oligosaccharides (COS) and ß-glucan are gradually being applied in aquaculture as antioxidants and immunomodulators. However, this study examined the effects of dietary supplementation of COS and ß-glucan on the water quality, gut microbiota, intestinal morphology, non-specific immunity, and meat quality of Chinese soft-shell turtle. To investigate the possible mechanisms, 3-year-old turtles were fed basal diet (CK group) and 0.1%, 0.5%, and 1% COS or ß-glucan supplemented diet for 4 weeks. Colon, liver, blood and muscle tissues, colon contents, water and sediment of paddy field samples were collected and analyzed after feeding 2 and 4 weeks. The results indicated that COS and ß-glucan altered microbial community composition and diversity in Chinese soft-shell turtles. The relative abundance of Cellulosilyticum, Helicobacter and Solibacillus were increased after feeding COS, while Romboutsia, Akkermansia and Paraclostridium were increased after feeding ß-glucan, whereas Cetobacterium, Vibrio and Edwardsiella were enriched in the control group. Furthermore, colon morphology analysis revealed that COS and ß-glucan improved the length and number of intestinal villi, and the effect of 0.5% ß-glucan was more obvious. Both ß-glucan and COS significantly improved liver and serum lysozyme activity and antibacterial capacity. COS significantly increased the total antioxidant capacity in the liver. Further, 0.1% ß-glucan significantly increased the activity of hepatic alkaline phosphatase, which closely related to the bacteria involved in lipid metabolism. Moreover, dietary supplementation with 1% COS and 1% ß-glucan significantly enhanced the content of total amino acids, especially umami amino acids, in muscle tissue, with ß-glucan exerting a stronger effect than COS. Additionally, these two prebiotics promoted the quality of culture water in paddy fields and reshaped the bacterial community composition of aquaculture environment. All these phenotypic changes were closely associated with the gut microbes regulated by these two prebiotics. In summary, the findings suggest that dietary supplementation with COS and ß-glucan in Pelodiscus sinensis could modulate the gut microbiota, improve intestinal morphology, enhance non-specific immunity and antioxidant capacity of liver and serum, increase meat quality, and improve the culture water environment. This study provides new insights and a comprehensive understanding of the positive effects of COS and ß-glucan on Pelodiscus sinensis.

Whole-genome resequencing reveals genetic diversity and selection signals in warm temperate and subtropical Sillago sinica populations.

BACKGROUND: Genetic diversity and heterogeneous genomic signatures in marine fish populations may result from selection pressures driven by the strong effects of environmental change. Nearshore fishes are often exposed to complex environments and human activities, especially those with small ranges. However, studies on genetic diversity and population selection signals in these species have mostly been based on a relatively small number of genetic markers. As a newly recorded species of Sillaginidae, the population genetics and genomic selection signals of Sillago sinica are fragmented or even absent. RESULTS: To address this theoretical gap, we performed whole-genome resequencing of 43 S. sinica individuals from Dongying (DY), Qingdao (QD) and Wenzhou (WZ) populations and obtained 4,878,771 high-quality SNPs. Population genetic analysis showed that the genetic diversity of S. sinica populations was low, but the genetic diversity of the WZ population was higher than that of the other two populations. Interestingly, the three populations were not strictly clustered within the group defined by their sampling location but showed an obvious geographic structure signal from the warm temperate to the subtropics. With further analysis, warm-temperate populations exhibited strong selection signals in genomic regions related to nervous system development, sensory function and immune function. However, subtropical populations showed more selective signalling for environmental tolerance and stress signal transduction. CONCLUSIONS: Genome-wide SNPs provide high-quality data to support genetic studies and localization of selection signals in S. sinica populations. The reduction in genetic diversity may be related to the bottleneck effect. Considering that low genetic diversity leads to reduced environmental adaptability, conservation efforts and genetic diversity monitoring of this species should be increased in the future. Differences in genomic selection signals between warm temperate and subtropical populations may be related to human activities and changes in environmental complexity. This study deepened the understanding of population genetics and genomic selection signatures in nearshore fishes and provided a theoretical basis for exploring the potential mechanisms of genomic variation in marine fishes driven by environmental selection pressures.

De novo transcriptome analysis reveals insights into different mechanisms of growth and immunity in a Chinese soft-shelled turtle hybrid and the parental varieties.

The Chinese soft-shelled turtle (Pelodiscus sinensis) is a highly important freshwater aquaculture species in China. The molecular mechanisms underlying changes in immunity and growth in hybrid vigor are not well understood. In the present study, the transcriptomes from significantly different P. sinensis strains (Qingxi black turtle, B and Japanese strain, J) and the resulting hybrid (Zajiao-1, F) were sequenced using an Illumina sequencing platform. Differentially expressed genes (DEGs) between Zajiao-1 and the Qingxi black turtle were enriched mainly in the HTLV-I infection and Hippo signaling pathways, while DEGs between the Zajiao-1 and Japanese strain were enriched mainly in tryptophan metabolism, caner-associated pathways, transcriptional dysregulation in cancer, amebiasis, Fcγ-mediated phagocytosis and the peroxisome pathway. Highly expressed genes involved in the regulation of disorders of the fatty acid biosynthesis, immune and cardiovascular systems in P. sinensis were found among the DEGs. Enrichment categories for gene ontology included cellular processes, metabolic pathways, and the actin cytoskeleton pathway. The reliability of the sequencing data was verified through quantitative real-time polymerase chain reaction analysis of 20 immunity or growth-related genes. These findings offer new insights into heterosis of growth traits and resistance to stresses and potential strategies for selective breeding.

Genetic organization of ascB-dapE internalin cluster serves as a potential marker for Listeria monocytogenes sublineages IIA, IIB, and IIC.

Listeria monocytogenes is an important foodborne pathogen that comprises four genetic lineages: I, II, III, and IV. Of these, lineage II is frequently recovered from foods and environments and responsible for the increasing incidence of human listeriosis. In this study, the phylogenetic structure of lineage II was determined through sequencing analysis of the ascB-dapE internalin cluster. Fifteen sequence types proposed by multilocus sequence typing based on nine housekeeping genes were grouped into three distinct sublineages, IIA, IIB, and IIC. Organization of the ascBdapE internalin cluster could serve as a molecular marker for these sublineages, with inlGHE, inlGC2DE, and inlC2DE for IIA, IIB, and IIC, respectively. These sublineages displayed specific genetic and phenotypic characteristics. IIA and IIC showed a higher frequency of recombination (rho/theta). However, recombination events had greater effect (r/m) on IIB, leading to its high nucleotide diversity. Moreover, IIA and IIB harbored a wider range of internalin and stress-response genes, and possessed higher nisin tolerance, whereas IIC contained the largest portion of low-virulent strains owing to premature stop codons in inlA. The results of this study indicate that IIA, IIB, and IIC might occupy different ecological niches, and IIB might have a better adaptation to a broad range of environmental niches.

Genomic presence of gadD1 glutamate decarboxylase correlates with the organization of ascB-dapE internalin cluster in Listeria monocytogenes.

The ability to survive and proliferate in acidic environments is a prerequisite for the infection of Listeria monocytogenes. The glutamate decarboxylase (GAD) system is responsible for acid resistance, and three GAD homologs have been identified in L. monocytogenes: gadD1, gadD2, and gadD3. To examine whether GAD genes are specific to lineage, serovar, or certain subpopulation, we performed a systematic investigation on the prevalence of GAD genes in 164 L. monocytogenes. In contrast to gadD2 and gadD3 conserved in all L. monocytogenes strains, gadD1 was identified in 36.6% (60/164) of L. monocytogenes strains, including all serovar 1/2c and 68.5% (37/54) of serovar 1/2a strains, as well as a small fraction of serovar 1/2b (3.4%, 1/29) and lineage III (13.8%, 4/29) strains. All serovar 4b and lineage IV strains lacked this gene. According to the ascB-dapE structure, L. monocytogenes strains were classified into four subpopulations, carrying inlC2DE, inlGC2DE, inlGHE, or no internalin cluster, respectively. All L. monocytogenes strains with inlGC2DE or inlGHE pattern harbored gadD1, whereas those bearing inlC2DE or no internalin cluster between ascB and dapE lacked gadD1. In addition, other five non-monocytogenes Listeria species lacking ascB-dapE internalin cluster were gadD1-negative. Overall, the presence of gadD1 is not fully dependent on lineages or serovars but correlates with ascB-dapE internalin profiles, suggesting gadD1 might have co-evolved with the ascB-dapE internalin cluster in the primitive L. monocytogenes before divergence of serovars.