Comparative biochemistry and physiology. Part D, Genomics & proteomics最新文献

The oxygen content in the fish ponds is facing greater challenges than before in the aquaculture of mandarin fish (Siniperca chuatsi) due to the change of climate and eutrophication. Until now, little is known about the molecular mechanisms underlying the harmful effects of hypoxia on this species. In this work, we built transcriptomes for the mandarin fish that were exposed to decreased oxygen concentration at two times points (24 h and 96 h). The respiratory metabolism activities of pyruvate kinase (PK), hexokinase (HK), lactate dehydrogenase (LDH), succinate dehydrogenase (SDH) and malate dehydrogenase (MDH) had different significantly changes during hypoxic treatment. Histological observation of the gill and brain also revealed some damages by hypoxia. A total of 196,355 transcripts were involved in the Gene Ontology analysis, and the numbers of differentially expressed genes (DEGs) in the brain and the gill between the control and experiment groups are 141 and 552 respectively involved in the different hypoxic stress time. The DEGs were then analyzed using KEGG enrichment analysis. The results showed significant differences in the expression of some genes involved in ribosome pathways,biosynthesis of amino acids, hippo signaling pathway, and pentose phosphate pathway,glycolysis/gluconeogenesis pathway and the TCA cycle. The huge number of transcriptome sequences collected in this study has enhanced the mandarin fish gene resources, and the identified DEGs and related pathway analysis give essential information for understanding biological responses to hypoxia.

Hypoxia disrupts multiple physiological processes, including metabolism, immunity, and reproduction in teleosts. The brain plays a critical role in adapting to environmental changes, regulating the endocrine system, and controlling reproduction. The present study investigated the sex-specific cerebral responses to chronic hypoxia through an integrated analysis of the transcriptome, proteome, and metabolome of yellow catfish. Common cerebral responses in both females and males included activation of the HIF signaling pathway, angiogenesis, and improved oxygen delivery by red blood cells. Reproductive defects were indicated by the downregulation of gh1, cga, and tshb in both sexes. Thyroid hormone homeostasis was more severely disrupted by hypoxia in females than in males, accompanied by a significant decrease in the level of VTG in the female brain. Damaged brain function was evidenced by the highly enriched pathways of "cytokine-cytokine receptor interaction" and "ECM-receptor interaction," and the blood-brain barrier (BBB) also appeared to be disrupted in female fish. In the male brain, reproductive-related genes or proteins, including prl, lepr, and AVP, were specifically decreased. Dysfunction in the male brain was also indicated by the enrichment of pathways such as "cytokine-cytokine receptor interaction" and "neuroactive ligand-receptor interaction," based on differentially expressed genes (DEGs) and proteins (DEPs). Additionally, chronic hypoxia appeared to inhibit cerebral amino acid metabolism in males. In summary, our results offer insight into understanding the sex-specific cerebral responses induced by chronic hypoxia in teleosts.

Spodoptera frugiperda is a major invasive pest that poses a serious threat to crops worldwide. Low temperature is a key factor limiting the survival and reproduction for this pest. To study the responses of S. frugiperda to low-temperature stress, high-throughput sequencing was used to perform transcriptomic analysis on the 6^th instar larvae under low-temperature stress at 5 °C and 10 °C, along with 25 °C as a control. As a result, 215 differentially expressed genes (DEGs) were identified under different low-temperature stresses. Upon functional annotation of the DEGs in KEGG and GO databases, the number of DEGs annotated in control vs. LT10 comparison was the largest (n = 150), whereas fewer DEGs (n = 89) were annotated in control vs. LT5 comparison. This discrepancy suggested that S. frugiperda might adopt different strategies to cope with low-temperature stress. The DEGs in the GO database were particularly associated with cell catalytic activity, cell anatomical entity process, cell apoptosis, and cell binding channel. KEGG annotation analysis of the different low-temperature stresses showed that most of the enriched pathways were related to carbon metabolism, oxidative phosphorylation, and lipid metabolism. The results will be the basis for mastering the cold tolerant mechanism of S. frugiperda, and is of great significance for its prevention.

Global warming linked to climate change poses a significant risk to aquatic animals. Invertebrates, such as Cipangopaludina cathayensis are especially susceptible to elevated temperature. Understanding how C. cathayensis responds to high-temperature stress is crucial for predicting the putative effects of climate change on its cultivation. In this study, we exposed C. cathayensis to various temperature conditions (26 °C, 28 °C, 30 °C, and 32 °C) for 3 h, revealing that both oxygen consumption and ammonia excretion rates increased gradually with increasing temperature, reaching maximum values of 77.711 ± 2.364 μg·(g·h)^-1 and 4.701 ± 0.036 μg·(g·h)^-1 at 30 °C and 28 °C, respectively. However, values of these parameters decreased when the culture temperature increased to 32 °C. High-temperature stress also resulted in a reduced O:N ratio and decreased energy metabolism rate. To investigate how high temperature impacts antioxidant activities, immune function, and transcriptional regulation in the hepatopancreas, C. cathayensis were exposed to temperatures of 26 °C or 32 °C for 3 and 7 days, respectively. Our results indicated that high temperature disrupted the antioxidant defense system and led to immunosuppression in the hepatopancreas. Comparative transcriptome analysis identified 6638 genes with significantly altered expression between these two temperature groups. Functional enrichment analysis of differentially expressed genes demonstrated that high temperature affected protein homeostasis, energy metabolism, and immune function of C. cathayensis. Together, these findings offer valuable information for evaluating the impacts of global warming on the culture of mud snail.

The sea cucumber Apostichopus japonicus is an economically significant marine species in China, with numerous studies focusing on its diverse physiological processes, including seasonal reproduction and aestivation. The neuroendocrine system plays a critical role in regulating these physiological transitions. In this study, we utilized transcriptomic techniques and bioinformatics tools to identify key functional genes in the nerve ring of A. japonicus during four distinct physiological phases: pre-reproduction, post-reproduction, aestivation, and recovery from aestivation. Totally 33 neuropeptide precursors and 521 G protein-coupled receptors (GPCRs) were identified. Highlighted key genes, such as AjCRZP, AjPDFP1b, AjSSP1, AjSSP2, and AjSSTR4, were proposed to contribute to transitions of reproduction to aestivation. The temporal trends and functions of differentially expressed genes (DEGs) were validated through qRT-PCR assays. Additionally, we constructed a preliminary neuroendocrine regulatory network, with AjGALR2 and AjCHRM5 identified as central hub genes. These findings offer valuable insights into the neuroendocrine regulation of reproduction and aestivation in A. japonicus, providing a foundation for further mechanistic studies and enhancing our understanding of sea cucumber biology.

Yak meat plays a significant economic role for yaks. The unique environment of the Qinghai-Tibet plateau profoundly impacts the meat production performance of yaks. Yet, the regulatory mechanisms influencing muscle growth and development in yaks within this plateau environment remain poorly understood. The study investigated the transcriptome gene expression in the buttock muscle tissue of yaks residing at varying altitudes. It revealed 516 differentially expressed genes in the buttock muscle tissue of yaks at high altitude (4500 m) and low altitude (3000 m). The Gene Ontology (GO) annotation indicated that these differentially expressed genes primarily function in RNA binding, identical protein binding, nucleotide binding, pre-mRNA branch point binding, unfolded protein binding, insulin receptor binding, fructose 1,6-bisphosphate 1-phosphatase activity, collagen binding, platelet-derived growth factor receptor binding, and sodium channel inhibitor activity. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis revealed that the differentially expressed genes predominantly participated in pathways such as the spliceosome, aminoacyl tRNA biosynthesis, RNA polymerase, cutin, suberin, and wax biosynthesis, ribosome biogenesis in eukaryotes, plant hormone signal transduction, axon guidance, fructose and mannose metabolism, pentose phosphate pathway, and gastric acid secretion. This study unveiled the impact of the plateau environment on transcriptome gene expression in yak buttock muscle tissue, mapping out the gene expression profiles specific to yaks living at varying altitudes (3000 m and 4500 m). The findings offer crucial genomic insights into the mechanisms behind yak muscle adaptation to plateau environments.

Apostichopus japonicus is a representative temperate sea cucumber species, that mainly inhabits in coastal zone of the continental shelf. With high nutritional value and important medical value, A. japonicus become an important commercial aquaculture species and produce significant economic value in recent years. A. japonicus has no sexual dimorphism that can be used to distinguish female and male individuals by external appearance and morphology. The phenotype sex can be only detected by dissecting and observing gonad tissue, thus the breeding efficiency could be greatly reduced. This limitation has hindered the advancement of selective breeding programs and sea cucumber industry. To investigate the genetic basis of reproductive biology in A. japonicus, advanced sequencing techniques, such as next- and third-generation sequencing, have been employed to explore the roles of non-coding RNAs and other genetic factors, offering new insights into sex determination mechanisms. To further gain a deeper understanding of the knowledge underlying lncRNAs in gonadal differentiation, we conducted a comparative transcriptome sequencing analysis of gonadal tissues from both sexes. In our research, a total of 3990 novel lncRNAs and 1441 differentially expressed lncRNAs were identified between female and male gonads. Additionally, a molecular regulatory network indicating lncRNA-mRNA interactions was constructed based on transcriptional profiles, which provide insights into the potential cis- and trans- target genes of lncRNAs. The gonadal transcriptome analysis identified a number of novel long non-coding RNAs involved in female and male reproduction process. Both cis- and trans-acting regulatory networks indicating lncRNA-mRNA interaction were constructed based on transcriptional profiles. These findings provide new insights into the lncRNA-mediated regulation of reproductive biology in marine invertebrates, indicating the crucial roles of long non-coding sequences in regulating expression profiles. Further, the GO and KEGG enrichment analyses of cis- and trans- targeted mRNA for differentially expressed lncRNA indicated that sexual reproduction (GO:0019953), germ cell development (GO:0007281), and negative regulation of hormone secretion (GO:0046888) are potentially involved in gonadal differentiation through the regulation of long non-coding sequences. Notably, besides the classical reproduction related signaling pathway like Gonadotropin-releasing hormone (GnRH) secretion (ko04929), several regulatory pathways, such as Epidermal growth factor receptor (ErbB) signaling pathway (ko04012), TGF-beta signaling pathway (ko04350), and neurotrophin signaling pathway (ko04722) were also enriched and potentially involved in sex differentiation and gonadal development.

Aeromonas salmonicida belongs to the Aeromonas family, which could widely infect economic fish, causing diseases and huge economic losses. Recently, A. salmonicida was also detected in diseased Odontobutis potamophila. Transcriptomic model of A. salmonicida-infected O. potamophila was analyzed to reveal immune response. A total of 113,282 unigenes were obtained and annotated in six databases. After 12 h of infection with A. salmonicides, a total of 614 differentially expressed genes (DEGs) (355 up-regulated genes and 259 down-regulated genes) were identified in the head kidney tissues. Following 24 h of infection, a total of 1689 DEGs were detected in the head kidney tissues, including 313 up-regulated genes and 1376 down-regulated genes. GO and KEGG pathway analyses were conducted to provide functional insights and a clearer understanding of the signal transduction pathways associated with the DEGs. Further analysis of the complement and coagulation cascades pathway and PPAR signaling pathway exhibited that the expression of immune genes was widely activated at the beginning of A. salmonicides infection. Additionally, six DEGs were randomly selected and validated using quantitative real-time PCR, showing expression patterns consistent with the high-throughput sequencing data. These results offer important insights that enhance the understanding of immune response in O. potamophila against A. salmonicida infection.

Opsariichthys bidens is a unique economically important freshwater fish in China. Male O. bidens grow faster than females, and male fish have attractive blue-green stripes on the body surface during the breeding period. The breeding of all-male stocks can significantly improve the efficiency of breeding. To accelerate the breeding of all-male stocks, additional studies of the mechanism regulating sex differentiation and gonad development are needed. In this study, transcriptome sequencing of the ovaries and testes of O. bidens was performed using Illumina high-throughput sequencing. The results revealed a total of 21,703 differentially expressed genes, including 8645 up-regulated genes and 5880 down-regulated genes expressed in the ovary compared with the testis. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses revealed multiple differentially expressed genes involved in sex differentiation and gonad development. Eight differentially expressed genes (zp3, cyp19a, hsd17b1, msh4, dmrt1, rspo2, kif23, and gdf9) that play a key role in sex differentiation and gonadal development were selected for RT-qPCR validation. The expression levels of selected genes in the testes and ovaries were significantly different (P < 0.05). zp3, cyp19a, hsd17b1, and gdf9 were female-biased genes, and msh4, dmrt1, rspo2, and kif23 were male-biased genes. zp3, cyp19a, hsd17b, and msh4 were only slightly expressed in the kidney and liver, and dmrt1, rspo2, kif23, and gdf9 were all expressed in gill, kidney, and liver tissue. None of the genes were expressed in the heart or muscle. In this study, differentially expressed genes related to the sex determination and differentiation of O. bidens were identified. Overall, our findings provide important data for future studies of the molecular mechanisms of sex differentiation and gonad development of O. bidens and will aid the breeding of all-male species.

As an important member of global aquaculture, oysters (Crassostrea gigas) have significant economic value. With the development of commercial aquaculture, the frequent occurrence of diseases caused by Vibrio alginolyticus has become a hindrance to high-density aquaculture. Gill tissue, as an important component of immune system of the oysters, plays the key point in the face of invasion by foreign substances. Compared to the diploid oyster, the triploid oyster presents a higher growth rate and lower growth investment, making it a more ideal model for studying oyster immune defense. In this study, triploid oysters were as the research subject, and gill tissues attacked by V. alginolyticus were sequenced. By analyzing samples from different time points, 1746 DEGs were obtained. The KEGG and GO functional enrichment analysis showed that gill tissues mainly participate in immune function through the PIK3-Akt signaling pathway and the MAPK signaling pathway. The protein interaction network revealed three genes (CASP8, CASP9 and PIK3CA) that play core roles in immune defense by analyzing the interaction relationship between genes. Finally, qRT-PCR verified the expression of key genes. This study provides a more effective scientific basis for disease prevention and control of oysters and other bivalve shellfish, and helps to promote the sustainable development of aquaculture.