Transcriptomic analysis of changes in gene expression of immune proteins of gill tissue in response to low environmental temperature in fathead minnows (Pimephales promelas)

Establishment and characterization of a gill cell line from Takifugu obscurus and transcriptome analysis of its gene expression profiles upon low temperature

Takifugu obscurus is a farmed fish of great economic importance in China. The rapid development of T. obscurus aquaculture industry has been accompanied by disease and low-temperature stress, resulting in huge economic losses. Cell lines are used extensively in teleost physiology and pathology as the most cost-effective platform for in vitro research. A novel gill cell line of T. obscurus (named TOG) was first successfully established, and passed through 52 generations. The optimal conditions for TOG growth were 20 % FBS concentration and 24 °C, TOG could be grown in both hypotonic (150 mOsmol-kg-1) and hypertonic (600 mOsmol-kg-1) environments. TOG was determined to be derived from T. obscurus by sequencing the mitochondrial COI gene. Karyotype analysis revealed that the chromosome number of TOG was 44 (2n = 44). Transfection experiment showed that TOG was able to express foreign genes. Furthermore, several immune-related genes were significantly up-regulated in TOG after LPS and poly (I:C) stimulation, including tlr3, isg15, il1β and il10. Additionally, transcriptome analysis of TOG under low-temperature stress (24 °C, 18 °C, 12 °C, 10 °C and 8 °C) found that differentially expressed genes (DEGs) were significantly clustered in several immunological and energy metabolic pathways, and cold stress could disrupt the immune barrier and reduce immunity by downregulating the immune-related pathways. Additionally, weighted gene co-expression network analysis (WGCNA) revealed that bule module and turquoise module, which were closely correlated with low temperature and the degree of fish damage, were both predominantly found in PPAR, NOD-like receptor and Toll-like receptor signaling pathway. Hub genes were identified in these two modules, including mre11, clpb, dhx15, ddx18 and utp15. TOG cell line will become an effective experimental platform for genetic and immunological research, and our results would help us gain a deeper insight into the molecular mechanism of cold tolerance in teleost.

The role of the microbiome on fish mucosal immunity under changing environments

The environment is crucial for fish as their mucosal surfaces face continuous challenges in the water. Fish mucosal surfaces harbor the microbiome and mucosal immunity. Changes in the environment could affect the microbiome, thus altering mucosal immunity. Homeostasis between the microbiome and mucosal immunity is crucial for the overall health of fish. To date, very few studies have investigated mucosal immunity and its interaction with the microbiome in response to environmental changes. Based on the existing studies, we can infer that environmental factors can modulate the microbiome and mucosal immunity. However, we need to retrospectively examine the existing literature to investigate the possible interaction between the microbiome and mucosal immunity under specific environmental conditions. In this review, we summarize the existing literature on the effects of environmental changes on the fish microbiome and mucosal immunity. This review mainly focuses on temperature, salinity, dissolved oxygen, pH, and photoperiod. We also point out a gap in the literature and provide directions to go further in this research field. In-depth knowledge about mucosal immunity-microbiome interaction will also improve aquaculture practices by reducing loss during environmental stressful conditions.

Gene Expression Profile and Co-Expression Network of Pearl Gentian Grouper under Cold Stress by Integrating Illumina and PacBio Sequences

Simple Summary

In this study, we investigated the liver transcriptomic responses of pearl gentian grouper towards cold stress. Some cold-related key genes and biological pathways were screened, of which energy-related metabolic pathways and genes had higher expression levels under cold stress. This suggested that energy homeostasis plays a crucial role in the physiological adjustments of pearl gentian grouper when exposed to the cold stress environment. Our results will expedite the understanding of different fishes adaptive mechanisms to profound environmental temperature changes and provide insights into the molecular breeding of cold-tolerant pearl gentian grouper varieties.

Abstract

Pearl gentian grouper (Epinephelus fuscoguttatus ♀ × Epinephelus lanceolatus ♂) is a fish of high commercial value in the aquaculture industry in Asia. However, this hybrid fish is not cold-tolerant, and its molecular regulation mechanism underlying cold stress remains largely elusive. This study thus investigated the liver transcriptomic responses of pearl gentian grouper by comparing the gene expression of cold stress groups (20, 15, 12, and 12 °C for 6 h) with that of control group (25 °C) using PacBio SMRT-Seq and Illumina RNA-Seq technologies. In SMRT-Seq analysis, a total of 11,033 full-length transcripts were generated and used as reference sequences for further RNA-Seq analysis. In RNA-Seq analysis, 3271 differentially expressed genes (DEGs), two low-temperature specific modules (tan and blue modules), and two significantly expressed gene sets (profiles 0 and 19) were screened by differential expression analysis, weighted gene co-expression networks analysis (WGCNA), and short time-series expression miner (STEM), respectively. The intersection of the above analyses further revealed some key genes, such as PCK, ALDOB, FBP, G6pC, CPT1A, PPARα, SOCS3, PPP1CC, CYP2J, HMGCR, CDKN1B, and GADD45Bc. These genes were significantly enriched in carbohydrate metabolism, lipid metabolism, signal transduction, and endocrine system pathways. All these pathways were linked to biological functions relevant to cold adaptation, such as energy metabolism, stress-induced cell membrane changes, and transduction of stress signals. Taken together, our study explores an overall and complex regulation network of the functional genes in the liver of pearl gentian grouper, which could benefit the species in preventing damage caused by cold stress.

Expression analyses of C-type lectins (CTLs) in Manila clam under cold stress provide insights for its potential function in cold resistance of Ruditapes philippinarum

Manila clam Ruditapes philippinarum is an economically and scientifically important marine bivalve species. C-type lectin acts as a pattern-recognition receptor (PPR), plays a crucial role in the innate immunity of invertebrates, and involves in pathogen recognition, and cell-cell interaction. In this study, six different types of C-type lectin genes, CTL-1, CTL-2, CTL-3, CTL-4, CTL-5, and CTL-6, were identified from the R. philippinarum. CTL amino acid sequence was highly conserved compare to other invertebrate CTL sequences. Also, the temporal expressions of CTLs mRNA were detected in R. philippinarum with higher expression level in hepatopancreas and gill, and with lower expression levels in other tissues. The expression pattern of CTL genes in hepatopancreas were investigated under low-temperature stress using real-time quantitative fluorescence PCR (RT-qPCR) and the results showed that the transcription of CTL mRNAs were induced after low-temperature challenge. Overall, the sequence analysis and the expression patterns of CTLs provide clues for understanding the response of the Manila clam to low-temperature stress.

Mucosal Barrier Functions of Fish under Changing Environmental Conditions

The skin, gills, and gut are the most extensively studied mucosal organs in fish. These mucosal structures provide the intimate interface between the internal and external milieus and serve as the indispensable first line of defense. They have highly diverse physiological functions. Their role in defense can be highlighted in three shared similarities: their microanatomical structures that serve as the physical barrier and hold the immune cells and the effector molecules; the mucus layer, also a physical barrier, contains an array of potent bioactive molecules; and the resident microbiota. Mucosal surfaces are responsive and plastic to the different changes in the aquatic environment. The direct interaction of the mucosa with the environment offers some important information on both the physiological status of the host and the conditions of the aquatic environment. Increasing attention has been directed to these features in the last year, particularly on how to improve the overall health of the fish through manipulation of mucosal functions and on how the changes in the mucosa, in response to varying environmental factors, can be harnessed to improve husbandry. In this short review, we highlight the current knowledge on how mucosal surfaces respond to various environmental factors relevant to aquaculture and how they may be exploited in fostering sustainable fish farming practices, especially in controlled aquaculture environments.