- Transcriptome analysis of the brain provides insights into the regulatory mechanism for Coilia nasus migration. - nasus) is an important anadromous fish species that resides in the Yangtze River of China, and has high ecological and economical value. - The Ministry of Agriculture and Rural Affairs of the People ’ s Republic of China has issued a notice banning the commercial fishing of wild C. - nasus in the Yangtze River. - The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. - If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. - 2 Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China Full list of author information is available at the end of the article. - The Coilia fish belongs to the family of Engraulidae and the order of Clupeiforme, and is distributed in the mid- west Pacific and Indian oceans. - nasus) is a precious fish species in the Yangtze River. - It is one of the “Three Delicious Species in the Yangze River”, with Reeve’s shad (Tenualosa reevesii) and obscure puf- ferfish (Takifugu fasciatus) being the other two species [1, 2]. - However, it has suffered from a serious population reduction in recent years as a result of the over- construction of water conservancy projects, overfishing, and environmental pollution [3–5]. - The Ministry of Agri- culture and Rural Affairs of the People’s Republic of China has issued a notice banning the fishing of wild C.. - nasus in the Yangtze River for production. - The brain serves as the center of the nervous system in vertebrates and exerts a more com- prehensive regulatory function than other tissues of per- ception system regulation, learning, and memory muscle activity, through which the organism responds to the changing environment [11, 12]. - Traditionally, research on the effects of temperature and salinity as environmental stressors in fish has been carried out in the liver and gills due to the pivotal roles of these organs in energy supply and osmoregulation.. - Recent studies that investigated the strengthening of the brain regulatory function in response to salinity and cold stress have indicated that the expression of hormones, neurotransmitters, receptors, and key regulatory proteins was upregulated [13–18]. - Xu et al. - In order to explore their regu- latory mechanisms during smoltification, some research has been carried on trout, and resident and migratory salmonids, including comparative transcriptome analyses of the brain, liver, gill, kidney, and olfactory rosettes [20–24]. - Relevant re- search on Atlantic salmon indicated that DEGs were in- volved in electron transport, oxygen transport and endocrinology, there was no change in the expression of thyroid-stimulating hormone (TSH), which is different from the results of similar research on steelhead trout and coho salmon . - Additionally, a compara- tive transcriptome analysis on coho salmon in freshwater and early marine environments showed that differential regulatory pathways in the brain were mainly involved in protein synthesis and MHC1-mediated antigen presenta- tion [24]. - nasus seaward migration is an important part of the species’. - nasus experiences during seaward migration, we performed a comparative transcriptome analysis of the brain under saline and cold stress, to in- vestigate the regulatory role that the brain of juvenile C.. - Correlation analysis on intraclass difference in the control and stressed group was made, validation of RNA-Seq data was carried out with quanti- tative real-time polymerase chain reaction (qPCR).. - The Q30 values of the samples reached up to 93.03%, and the GC-content of each sample reached around 48.5% (Table 1). - Correlation analysis on intraclass differences in the control and stressed group. - The results indicated that replicated groups in the control group had strong correlation, as well as in the stressed group, intraclass difference were both small in these two groups. - Then, we conducted a further GO enrich- ment analysis on DEGs and obtained the top 10 GO terms from each of the three categories (Fig. - Most BP terms, with the exception of some involved in the gen- eral function (Nos. - a C1-C3 refers to three replicated groups of the control group, S1-S3 refers to three replicated groups of the stressed group. - Top 10 GO terms were enriched from DEGs of the C. - Number of DEGs enriched in each term is shown at the right side of the bar. - Top 10 KEGG pathways were enriched from DEGs of the C. - NCKX1 solute carrier family 24 (sodium/potassium/calcium exchanger), member E-05 – PDE1 calcium/calmodulin-dependent 3 ’ ,5 ’ -cyclic nucleotide phosphodiesterase E-05 + PDE6A/6B rod cGMP-specific 3 ’ ,5 ’ -cyclic phosphodiesterase subunit alpha/beta E-06. - 3, expression of the genes were normalized to beta-actin. - The correlation analysis results for these detected DEGs in the brain are as fol- lows: y = 0.9717x + 0.3891, and R r = 0.904, p = 0) (Fig. - The results indicated that key pathways and DEGs were mainly involved in the neuronal signal transduction, Table 2 Differentially expressed genes in response to salinity and cold stress (Continued). - A comprehensive analysis of the top 10 GO and top 10 KEGG terms indicated that the most significantly enriched pathways were involved in three categories: neuronal signaling (neuroactive lig- and–receptor interaction, the calcium signaling pathway, the glutamatergic synapse, retrograde endocannabinoid signaling, and the serotonergic synapse), the sensory sys- tem (olfactory transduction and phototransduction), and environmental adaptation (ECM–receptor interaction and circadian entrainment). - Neurotransmitters, recep- tors, and key regulatory proteins were shown to be up- regulated, constructing a regulatory network in the C.. - Quality of the de-novo assembled transcriptome. - Glutamate is a major excitatory neurotransmitter of the central nervous system. - In this study, salinity triggered the upregulated expres- sion of glutamate dehydrogenase in the brain, which may be the reason for the upregulation of the glutamate recep- tor [13]. - Retrograde endocannabinoid signaling, which plays a homeostatic role in the balance of neuronal activity between the glutamate and inhibitory se- rotonergic neurotransmitters, is mediated by retrograde messengers, including anandamide and 2-arachidonoyl gly- cerol (2-AG). - Of these compounds, there is evidence that galanin is involved in the regulation of coping with stressful events [33]. - Neuro- tensin, a key neurotransmitter, plays a regulatory role in easing pain in the brain, for example, by regulating the aversive memory of temperature nociception. - LRRTM4, it plays a pivotal role in the development and maintenance of nervous system of vertebrate [36]. - SIPA1L1, it functions in promoting reorganization of the actin cytoskeleton and plays a regulatory role in dendritic spine morphogenesis [38].. - TENM1, as a signal transducer, it plays a regulatory role in the establishment of proper connectivity in the ner- vous system [40].. - Regulation of the sensory system of C. - Salinity is a significant environmental factor during fish migration that can affect the expression of the olfactory receptors, which could be involved in olfactory imprinting.. - In contrast, in the Xu et al. - [19] study on the Yellow drum (Nibea albiflora), the pathways involved in the sen- sory system were not upregulated, possibly because Yellow. - Rod cGMP- specific 3’,5’-cyclic phosphodiesterase, a protein involved in the transmission and amplification of visual signals, plays a vital role in the formation of a functional phosphodiesterase holoenzyme. - In this study, the somatostatin receptor was upregulated in the experimental group to perform an in- hibitory role in growth, which is consistent with reports showing that high salinity stress inhibits the growth of til- apia fish [47]. - Research on the regulation mechanism of the brain during salmonid and steelhead trout smoltification showed the differential expression of growth hormone and thyroid hormone receptors [20, 22]. - Haptoglobin, a stress-activated acid glycoprotein, can bind to free plasma hemoglobin and present itself to the mononuclear macrophage system for processing, in order to maintain homeostasis of the blood micro-environment under stressful conditions [51].. - A comparative transcriptome ana- lysis of the brain of Atlantic salmon during smoltification showed a significant upregulation of hemoglobin [21]. - nasus have a similar regulatory pattern in maintaining homeostasis of the blood micro-environment during seaward migration.. - SLC is a group of membrane transport proteins, predominantly located in the cell membrane, which play roles in osmoregulation. - In this study, the significant up-regulation of the prolactin receptor in C. - It is also one of the methyl donors and participates in the synthesis of adrenaline, creatine, choline, carnitine, and DNA methylation. - In this study, many genes in the methionine and cysteine receptor pathways were significantly elevated, which also indicated the im- portant role that the methionine metabolism of juvenile C. - According to the theory of the phase transition of membrane lipids, it is believed that the content of unsat- urated fatty acids in membrane lipids can affect. - Sterol, a cholesterol-like substance, is widely regarded as a key functional substance in the response to environmental stresses such as extreme temperature and high salinity stress [58, 59]. - Sterol 14-demethylase is a key synthetase in the synthesis of cholesterol and phy- tosterol [60]. - In the present study, its expression level was significantly elevated after stress, indicating that the cholesterol level was elevated to enhance the anti-cold resistance of juvenile C. - Additionally, the function of the olfactory system was strengthened and the visual sig- naling pathways were weakened during juvenile C. - The identified significant differential expression of the growth hormone and receptors. - the upregulation of the genes which function in maintaining homeostasis of the blood environment, such as hapto- globin and the prolactin receptors, are similar results to those obtained in research on salmonids and steelhead trout smoltification adaptation. - nasus early seaward migration, and provides a glimpse of the regulation mechanism during C. - The fish were collected from Yixing, an experi- mental base of the Freshwater Fisheries Research Center of the Chinese Academy of Fishery Sciences, in Novem- ber. - For homology annotation, the obtained non-redundant sequences were aligned in the following priority order: non-redundant protein (Nr), non-redundant nucleotides (Nt), Swiss-prot (http://www.. - 5 Diagram of the sampling method. - C1-C3 indicated three replicated groups in the control group, S1-S3 indicated three replicated groups in the stressed group. - GO annotation of the obtained unigenes was performed using Blast2GO software (Bio- bam, Valencia, Spain) [65].. - The assembled unigenes were placed in a constructed library, and the expression of the abundance of each uni- gene in each sample was measured by bowtie2 software (http://bowtie-bio.sourceforge.net/bowtie2/manual.. - Fold change was calculated as the ratio of the expression level of genes in the stressed group and control group sam- ples, and |log 2 foldchange. - Finally, we obtained the top 10 GO terms and top 10 KEGG pathways in the brain. - Every sample was an- alyzed in triplicate, and the permitted variation of the. - Additional file 5 Appendix file 5: Table S4: FPKM of DEGs in the control and stressed group.. - The funding bodies had no role in the experimental design, sample collection, data analysis and interpretation, and manuscript writing.. - The dataset supporting the conclusions of this article is available in the NCBI Sequence Read Archive (SRA) repository, accession number SRP078492.. - The study was approved by the Animal Care and Use Committee of the Freshwater Fisheries Research Center at the Chinese Academy of Fishery Sciences (BC . - The fish sampling was carried out under a fieldwork permit of the Freshwater Fisheries Research Center (No. - Studies on biological characteristics and change of resource of Coilia nasus Schlegel in the lower reaches of the Yangtze River (in Chinese). - Population structure of Coilia nasus in the Yangtze River revealed by insertion of short interspersed elements. - Studies on resource change and MSY of Coilia mystus in the Yangtze River estuary. - Gene cloning and mRNA expression of glutamate dehydrogenase in the liver, brain, and intestine of the swamp eel, Monopterus albus (Zuiew), exposed to freshwater, terrestrial conditions, environmental ammonia, or salinity stress. - Effects of acclimation salinity on the expression of selenoproteins in the tilapia, Oreochromis mossambicus. - Salinity increases total body prolactin and gill and skin prolactin receptor expression in the Chinese edible frog, Hoplobatrachus rugulosus, tadpole. - Transcriptional response to low temperature in the yellow drum (Nibea albiflora) and identification ofgenes related to cold stress. - RNA-seq reveals differential gene expression in the brains of juvenile resident and migratory smolt rainbow trout (Oncorhynchus mykiss). - Transcriptional profiling of the parr-smolt transformation in Atlantic salmon. - neurotransmission in the nervous system. - Differential role of galanin receptors in the regulation of depression-like behavior and monoamine/stress-related genes at the cell body level.. - Expression of the nociceptin receptor during zebrafish development: influence of morphine and nociceptin. - Cbln1 is essential for synaptic integrity and plasticity in the cerebellum. - Dynamic expression pattern of leucine-rich repeat neuronal protein 4 in the mouse dorsal root ganglia during development. - C-terminal processing of the teneurin proteins: independent actions of a teneurin C-terminal associated peptide in hippocampal cells. - Molecular characterization and gene evolution of the heat shock protein 70 gene in snakehead fish with different tolerances to temperature. - Prolactin and upstream migration of the amphidromous teleost, Ayu Plecoglossus altivelis
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