Analyses of the molecular mechanisms associated with salinity adaption of Trachidermus fasciatus through combined iTRAQ-based proteomics and RNA sequencing-based transcriptomics

High-density lipoprotein remodeling affects the osmotic properties of plasma in goldfish under critical salinity

To investigate the stress response and physiological adaptations of goldfish (Carassius auratus) to critical salinity (CS) waters, we analyzed high-density lipoprotein (HDL) stoichiometry, stress markers (cortisol, glucose), and plasma osmotic properties (Na+ , osmolality, water content) using ichthyology, biochemistry, and proteomics approaches. After 21 days of exposure to CS, plasma concentrations of cortisol, glucose, and Na+ increased, indicating stress. Total plasma osmolality (Osmtotal ) and osmolality generated by inorganic (Osminorg ) and organic osmolytes (Osmorg ) also increased, the latter by ~2%. We associated the increase of Osmorg with (1) increased metabolite concentration (glucose), (2) dissociation of HDL particles resulting in increased HDL number per unit plasma volume (~1.5-2-fold) and (3) increased HDL osmotic activity. HDL remodeling may be the reason for the redistribution of bound and free water in plasma, which may contribute to water retention in plasma and, at the same time, to hemodynamic disturbances under CS conditions. The study's findings suggest that HDL remodeling is an important mechanism for maintaining osmotic homeostasis in fish, which is consistent with current capillary exchange models in vertebrates.

The Effect of Salinity Stress on Enzyme Activities, Histology, and Transcriptome of Silver Carp (Hypophthalmichthys molitrix)

A 56-day study was performed to examine the effect of freshwater (FW) and brackish water (BW 6‱ salinity) on the antioxidant ability, Na+/K+-ATPase (NKA) activities, histology, and transcriptome of the gill and kidney tissue in juvenile silver carp (Hypophthalmichthys molitrix). The results show that when juvenile silver carp were exposed to 6‱ salinity, the activities of superoxide dismutase (SOD) and catalase (CAT) were shown to be substantially increased (p < 0.05), while glutathione peroxidase (GSH-PX) activities in gill were not significantly affected (p < 0.05). In kidney tissue, SOD, CAT, and GSH-PX, enzyme activities peaked at 24, 8, and 4 h, respectively, but were not significantly different compared with the control group (p < 0.05). In addition, significant effects of salinity were observed for the NKA level in both the gills and kidney tissues (p < 0.05). The gill filaments of juvenile silver carp under the BW group all underwent adverse changes within 72 h, such as cracks and ruptures in the main part of the gill filaments, bending of the gill lamellae and enlargement of the gaps, and an increase in the number of mucus and chloride-secreting cells. Transcriptome sequencing showed 171 and 261 genes in the gill and kidney tissues of juvenile silver carp compared to the BW group, respectively. Based on their gene ontology annotations, transcripts were sorted into four functional gene groups, each of which may play a role in salt tolerance. Systems involved in these processes include metabolism, signal transduction, immunoinflammatory response, and ion transport. The above findings indicate that the regulation processes in juvenile silver carp under brackish water conditions are complex and multifaceted. These processes and mechanisms shed light on the regulatory mechanism of silver carp osmolarity and provide a theoretical foundation for future research into silver carp growth in brackish water aquaculture area.

Integrative analysis of transcriptomics and proteomics of longissimus thoracis of the Hu sheep compared with the Dorper sheep

Meat quality is becoming more important for sheep breeding programs. Meat quality is a complex trait affected by genetic and environmental factors. In the present study, an integrative analysis of the longissimus thoracis tissue transcriptome and proteome was conducted to identify genes, proteins, and pathways related to meat quality in sheep. The sheep breeds Hu and Dorper were considered. These breeds were compared for the differences in muscle fiber structure, chemical composition, and amino acid composition. In the Hu sheep vs. Dorper sheep comparison, 22 DEGs/DEPs showed the same mRNA and protein expression trends. These genes are associated with lipid transport, lipid metabolism, and muscular system development. Moreover, some pathways such as "lipid transport", "lipoprotein metabolic process", "Alanine, aspartate and glutamate metabolism", and "Arginine biosynthesis" were significantly enriched in this study. The reliability of the RNA-Seq results was verified by qRT-PCR. These findings provide new insights into the molecular mechanisms of meat quality in sheep.

Transcriptional response to cold and fasting acclimation in Onychostoma macrolepis during the overwintering stage

In this study, we investigated the transcriptome responses of the liver of Onychostoma macrolepis in by RNA sequencing. The sampling process involved three groups: 1G (0 week, 10 °C), 2G (12 weeks, 0 °C) and 3G (24 weeks, 10 °C). The body weight, viscera index, hepatopancreas index and intraperitoneal fat index of O. macrolepis showed a decreasing trend with the prolonging of overwintering time. The crude fat contents of whole fish, muscle and liver in O. macrolepis after overwintering were significantly lower than those of the fish before overwintering (p < 0.05). In 1G versus 2G group, 2G versus 3G group and 1G versus 3G group, the differently expressed genes (DEGs) were 4630, 3976 and 2311, respectively. These results indicated that different stages of overwintering period had significant effects on gene expression of O. macrolepis, and the influence degree gradually decreased with the extension of overwintering period. The results of Gene ontology (GO) enrichment showed that these DEGs were mainly related to metabolism and immunity, and most of them were down-regulated. In this study, the KEGG pathway classification results showed that signal transduction was the most representative. In addition, KOG enrichment results showed that many DEGs associated with lipid transport and metabolism were down-regulated during the overwintering period. These observations suggested that slowing metabolism and delaying immunity may be the strategies for overwintering adaptation of O. macrolepis.

Investigating Diadromy in Fishes and Its Loss in an -Omics Era

Diadromy, the predictable movements of individuals between marine and freshwater environments, is biogeographically and phylogenetically widespread across fishes. Thus, despite the high energetic and potential fitness costs involved in moving between distinct environments, diadromy appears to be an effective life history strategy. Yet, the origin and molecular mechanisms that underpin this migratory behavior are not fully understood. In this review, we aim first to summarize what is known about diadromy in fishes; this includes the phylogenetic relationship among diadromous species, a description of the main hypotheses regarding its origin, and a discussion of the presence of non-migratory populations within diadromous species. Second, we discuss how recent research based on -omics approaches (chiefly genomics, transcriptomics, and epigenomics) is beginning to provide answers to questions on the genetic bases and origin(s) of diadromy. Finally, we suggest future directions for -omics research that can help tackle questions on the evolution of diadromy.

Genomic basis of the loss of diadromy in Galaxias maculatus: Insights from reciprocal transplant experiments

Diadromy is known for having major effects on the distribution and richness of aquatic species, and so does its loss. The loss of diadromy has led to the diversification of many species, yet research focusing on understanding its molecular basis and consequences are limited. This is particularly true for amphidromous species despite being the most abundant group of diadromous species. Galaxias maculatus, an amphidromous species and one of the most widely distributed fishes in the Southern Hemisphere, exhibits many instances of nonmigratory or resident populations. The existence of naturally replicated resident populations in Patagonia can serve as an ideal system for the study of the mechanisms that lead to the loss of the diadromy and its ecological and evolutionary consequences. Here, we studied two adjacent river systems in which resident populations are genetically differentiated yet derived from the same diadromous population. By combining a reciprocal transplant experiment with genomic data, we showed that the two resident populations followed different evolutionary pathways by exhibiting a differential response in their capacity to survive in salt water. While one resident population was able to survive salt water, the other was not. Genomic analyses provided insights into the genes that distinguished (a) migratory from nonmigratory populations; (b) populations that can vs those that cannot survive a saltwater environment; and (c) between these resident populations. This study demonstrates that the loss of diadromy can be achieved by different pathways and that environmental (selection) and random (genetic drift) forces shape this dynamic evolutionary process.

Population Genomic Signatures of Genetic Structure and Environmental Selection in the Catadromous Roughskin Sculpin Trachidermus fasciatus

Understanding the patterns of genetic diversity and adaptation across species' range is crucial to assess its long-term persistence and determine appropriate conservation measures. The impacts of human activities on the genetic diversity and genetic adaptation to heterogeneous environments remain poorly understood in the marine realm. The roughskin sculpin (Trachidermus fasciatus) is a small catadromous fish, and has been listed as a second-class state protected aquatic animal since 1988 in China. To elucidate the underlying mechanism of population genetic structuring and genetic adaptations to local environments, RAD tags were sequenced for 202 individuals in nine populations across the range of T. fasciatus in China. The pairwise FST values over 9,271 filtered SNPs were significant except that between Dongying and Weifang. All the genetic clustering analysis revealed significant population structure with high support for eight distinct genetic clusters. Both the minor allele frequency spectra and Ne estimations suggested extremely small Ne in some populations (e.g., Qinhuangdao, Rongcheng, Wendeng, and Qingdao), which might result from recent population bottleneck. The strong genetic structure can be partly attributed to genetic drift and habitat fragmentation, likely due to the anthropogenic activities. Annotations of candidate adaptive loci suggested that genes involved in metabolism, development, and osmoregulation were critical for adaptation to spatially heterogenous environment of local populations. In the context of anthropogenic activities and environmental change, results of the present population genomic work provided important contributions to the understanding of genetic differentiation and adaptation to changing environments.

Comparative analysis of growth performance and liver transcriptome response of juvenile Ancherythroculter nigrocauda fed diets with different protein levels

This study aimed at investigating the effects of dietary protein levels on the growth and liver transcriptome in juvenile Ancherythroculter nigrocauda. Six semi-purified diets were formulated containing 25 (control), 30, 35, 40, 45, and 50% protein. Each diet was fed to three groups of 35 fish (mean initial weight: 5.86 ± 0.10 g) for 56 days. The rate of weight gain and specific growth rate increased with dietary protein levels from 25% to 40%, but remained unchanged when fed with 45 or 50% dietary protein. The feed conversion ratio was significantly influenced by the dietary protein levels, being the lowest in fish fed 40% protein. Illumina RNA-seq analysis was performed to investigate liver gene expression changes under different dietary protein treatments. A total of 367.78 million clean reads were obtained from the six libraries. Compared with 25% protein treatment library, there were 734, 1946, 1755, 2726, and 1523 upregulated genes, and 407, 1882, 1865, 2216 and 1624 downregulated genes in the 30, 35, 40, 45, and 50% protein treatment libraries, respectively. Trend analysis of these differentially expressed genes (DEGs) identified six statistically significant trends. A series of DEGs that related to protein metabolism, growth and development, lipid metabolism and immune and stress response were identified. Moreover, gene ontology enrichment analysis of the DEGs demonstrated that cellular process, single-organism process, metabolic process and biological regulation were the most highly overrepresented biological processes. Kyoto Encyclopedia of Genes and Genomes enrichment analysis revealed that protein processing in endoplasmic reticulum, PPAR signaling pathway, complement and coagulation cascades, and cytochrome P450 (CYP450s) were significantly enriched in the dietary protein treatment groups. Furthermore, qPCR results showed excellent agreement on those of RNA-seq for both up- and down-regulated genes (including fasn, accα, SCD, CPT-I, igf1, ST, AST, trdmt1, hsp70, cyp450, MHC-II, C4, tgfβ, ube4b, apoE and abcb7). Thus, our results provide the baseline information for the feed formulation and nutritional research for A. nigrocauda.

iTRAQ-Based Analysis of Proteins Co-Regulated by Brassinosteroids and Gibberellins in Rice Embryos during Seed Germination

Seed germination, a pivotal process in higher plants, is precisely regulated by various external and internal stimuli, including brassinosteroid (BR) and gibberellin (GA) phytohormones. The molecular mechanisms of crosstalk between BRs and GAs in regulating plant growth are well established. However, whether BRs interact with GAs to coordinate seed germination remains unknown, as do their common downstream targets. In the present study, 45 differentially expressed proteins responding to both BR and GA deficiency were identified using isobaric tags for relative and absolute quantification (iTRAQ) proteomic analysis during seed germination. The results indicate that crosstalk between BRs and GAs participates in seed germination, at least in part, by modulating the same set of responsive proteins. Moreover, most targets exhibited concordant changes in response to BR and GA deficiency, and gene ontology (GO) indicated that most possess catalytic activity and are involved in various metabolic processes. Search Tool for the Retrieval of Interacting Genes/Proteins (STRING) analysis was used to construct a regulatory network of downstream proteins mediating BR- and GA-regulated seed germination. The mutation of GRP, one representative target, notably suppressed seed germination. Our findings not only provide critical clues for validating BR–GA crosstalk during rice seed germination, but also help to optimise molecular regulatory networks.