Identification and comparison of gonadal transcripts of testis and ovary of adult common carp Cyprinus carpio using suppression subtractive hybridization

Analysis of Chromatin Accessibility and DNA Methylation to Reveal the Functions of Epigenetic Modifications in Cyprinus carpio Gonads

Epigenetic modifications are critical in precisely regulating gene expression. The common carp (Cyprinus carpio) is an economically important fish species, and females exhibit faster growth rates than males. However, the studies related to epigenetic modifications in the common carp gonads are limited. In this study, we conducted the Assay for Transposase Accessible Chromatin sequencing (ATAC-seq) and Bisulfite sequencing (BS-seq) to explore the roles of epigenetic modifications in the common carp gonads. We identified 84,207 more accessible regions and 77,922 less accessible regions in ovaries compared to testes, and some sex-biased genes showed differential chromatin accessibility in their promoter regions, such as sox9a and zp3. Motif enrichment analysis showed that transcription factors (TFs) associated with embryonic development and cell proliferation were heavily enriched in ovaries, and the TFs Foxl2 and SF1 were only identified in ovaries. We also analyzed the possible regulations between chromatin accessibility and gene expression. By BS-seq, we identified 2087 promoter differentially methylated genes (promoter-DMGs) and 5264 gene body differentially methylated genes (genebody-DMGs) in CG contexts. These genebody-DMGs were significantly enriched in the Wnt signaling pathway, TGF-beta signaling pathway, and GnRH signaling pathway, indicating that methylation in gene body regions could play an essential role in sex maintenance, just like methylation in promoter regions. Combined with transcriptomes, we revealed that the expression of dmrtb1-like, spag6, and fels was negatively correlated with their methylation levels in promoter regions. Our study on the epigenetic modifications of gonads contributes to elucidating the molecular mechanism of sex differentiation and sex maintenance in the common carp.

Exposure of Cyprinus carpio var. larvae to PVC microplastics reveals significant immunological alterations and irreversible histological organ damage

Microplastics have become pervasive in ambient aquatic ecosystems over the last decade and are currently a serious global scale concern. To evaluate the potential toxic effects of PVC (polyvinyl chloride) microplastics on the immune functions of freshwater fish, this study undertook a conducted chronic 60-day dietary exposure experiment with Cyprinus carpio var. larvae. We exposed the fish to four microplastic treatments of different concentrations (food rationed diets): no-plastic (control), 10%, 20% and 30%. At the end of the experimental period the impacts of microplastics on the histology, biochemistry, ROS (reactive oxygen species) levels and gene transcription of immune organs were investigated. The results revealed that PVC microplastics induced cytoplasmic vacuolation in the liver, damaged villi in the intestine, inflammatory cell infiltration, hemosiderosis and vacuolar degeneration in the spleen, glomeruli tuft shrinkage and aggregation of melanin macrophage cells in the kidney. Moreover, following PVC microplastics exposure, ROS levels in the liver and protein levels of pro-inflammatory cytokines including IL-6, IL-8, and TNFα in the liver and serum were increased. Furthermore, modifications in the activities of non-specific immunoenzyme ACP (Acid phosphatase), AKP (alkaline phosphatase), LZM (lysozyme), and expression levels of a range of immune-related genes were observed. Using various techniques at the histological, biochemical and molecular levels, our findings demonstrated the effects of PVC microplastics on changes and imbalances in the immune status of carp. The results of this study provide basic toxicological data toward elucidating and quantifying the impacts of microplastics immunotoxicity on aquatic organisms.

GWAS on Imputed Whole-Genome Sequence Variants Reveal Genes Associated with Resistance to Piscirickettsia salmonis in Rainbow Trout (Oncorhynchus mykiss)

Genome-wide association studies (GWAS) allow the identification of associations between genetic variants and important phenotypes in domestic animals, including disease-resistance traits. Whole Genome Sequencing (WGS) data can help increase the resolution and statistical power of association mapping. Here, we conduced GWAS to asses he facultative intracellular bacterium Piscirickettsia salmonis, which affects farmed rainbow trout, Oncorhynchus mykiss, in Chile using imputed genotypes at the sequence level and searched for candidate genes located in genomic regions associated with the trait. A total of 2130 rainbow trout were intraperitoneally challenged with P. salmonis under controlled conditions and genotyped using a 57K single nucleotide polymorphism (SNP) panel. Genotype imputation was performed in all the genotyped animals using WGS data from 102 individuals. A total of 488,979 imputed WGS variants were available in the 2130 individuals after quality control. GWAS revealed genome-wide significant quantitative trait loci (QTL) in Omy02, Omy03, Omy25, Omy26 and Omy27 for time to death and in Omy26 for binary survival. Twenty-four (24) candidate genes associated with P. salmonis resistance were identified, which were mainly related to phagocytosis, innate immune response, inflammation, oxidative response, lipid metabolism and apoptotic process. Our results provide further knowledge on the genetic variants and genes associated with resistance to intracellular bacterial infection in rainbow trout.

Evolution, Expression, and Function of Gonadal Somatic Cell-Derived Factor

Fish gonads develop in very diverse ways different from mammalian gonads. This diversity is contributed by species-specific factors. Gonadal somatic cell-derived factor (Gsdf) is one such factor. The gsdf gene exists mostly in teleosts and is absent in many tetrapods, probably as a result of two gene losses during evolution. The gsdf transcript is expressed mainly in gonadal somatic cells, including Sertoli cell in testis and granulosa cells in ovary; however, these gonadal somatic cells can surround many types of germ cells at different developmental stages depending on the fish species. The function of gsdf is also variable. It is involved in germ cell proliferation, testicular formation, ovarian development and even male sex determination. Here, we summarize the common and diverse expression, regulation and functions of gsdf among different fish species with aspect of evolution.

Transwell isolation and difference analysis of capacitated boar sperm proteins based on the iTRAQ technique

During capacitation, proteins in boar sperm are released to maintain the stability of their own state and membrane structure. No studies have analyzed the differences between retained proteins and released proteins during sperm capacitation. In the present study, a Transwell chamber and polycarbonate membrane were used to separate the proteins of boar sperm and their released proteins. Isotopically labeled relative and absolute quantification (iTRAQ) was used to analyze each compartment protein. A total of 108 differential proteins were identified in the upper and lower chambers of the Transwell, among which 27 were significantly upregulated (p-value≤0.05 and |log2 (fold change)|≥1) and 81 were significantly downregulated (p-value≤0.05 and |log2 (fold change)|≤1). These differential proteins were mainly involved in biological processes (e.g., the regulation of cysteine peptidase activity, transmembrane transportation, ion transportation and ATP synthesis) and major signaling pathways (e.g., glutathione/galactose metabolism, cellular adhesion and PI3K-Akt), and most of them interacted with each other to some extent. In conclusion, retained proteins and released proteins of capacitated sperm were effectively separated using a Transwell chamber, and differential proteins were successfully identified from among the proteins. Bioinformatics analysis suggested that these differential proteins affect sperm capacitation mainly by adjusting sperm energy metabolism, motion characteristics and acrosome membrane status.

Down-regulation of SETD6 protects podocyte against high glucose and palmitic acid-induced apoptosis, and mitochondrial dysfunction via activating Nrf2-Keap1 signaling pathway in diabetic nephropathy

Diabetic nephropathy (DN), a serious complication of hyperglycemia, is one of the most common causes of end-stage renal disease (ESRD). Glomerular podocyte injury is a major mechanism that leads to DN. However, the mechanisms underlying podocyte injury are ambiguous. In this study, we sought to investigate the contribution of SET domain-containing protein 6 (SETD6) to the pathogenesis of podocyte injury induced by glucose (GLU) and palmitic acid (PA), as well as the underlying mechanisms. Our results showed that GLU and PA treatment significantly decreased SETD6 expression in mouse podocytes. Besides, Cell Counting Kit-8 (CCK-8) and flow cytometry assay demonstrated that silencing of SETD6 silence obviously enhanced cell viability, and suppressed apoptosis in GLU and PA-induced podocytes. We also discovered that downregulation of SETD6 suppressed GLU and PA-induced ROS generation and podocyte mitochondrial dysfunction. Nrf2-Keap1 signaling pathway was involved in the effect of SETD6 on mitochondrial dysfunction. Taken together, silencing of SETD6 protected mouse podocyte against apoptosis and mitochondrial dysfunction through activating Nrf2-Keap1 signaling pathway. Therefore these data provide new insights into new potential therapeutic targets for DN treatment.

Polyvinyl chloride microplastics induce growth inhibition and oxidative stress in Cyprinus carpio var. larvae

The occurrence and accumulation of microplastics in wildlife and humans have become a serious global scale concern over the last decade. To evaluate the potential toxic effects of PVC (polyvinyl chloride) microplastics in freshwater fish larvae, we conducted chronic 30-day and 60-day dietary exposure using Cyprinus carpio var. larvae. We exposed the larvae to four treatments with different microplastic concentrations (10%, 20%, and 30%) using food rationed diets, in conjunction with a non-plastic control. The results indicated that microplastics significantly inhibited weight gain and growth under all PVC treatments, compared to the control group. SOD (superoxide dismutase) and CAT (catalase) activities were analyzed, and an inverse relationship between them was observed. The activities of GPx (glutathione peroxidase) initially ascended and then descended with increased PVC concentrations following 30 days of exposure. A dose dependent downtrend was observed after 60 days of exposure. Malondialdehyde (MDA) levels were significantly reduced upon exposure to different concentrations of microplastics in various tissues. Altered antioxidant-related gene expression was observed in the livers of larvae exposed to the PVC microplastics. The transcription of CYP1A and GSTa initially increased, and then decreased under higher microplastics concentrations following 30 days of exposure. Furthermore, histological studies revealed cytoplasmic vacuolation in the liver under exposure to 20% and 30% microplastics. This investigation provided basic toxicological data toward elucidating and quantifying the impacts of PVC microplastics on freshwater organisms.

Gonadal transcriptome analysis of the common carp, Cyprinus carpio: Identification of differentially expressed genes and SSRs

Common carp (Cyprinus carpio) is a world-wide freshwater fish of eutrophic waters. C. carpio, have various reproductive traits, including early sexual maturity, that may make them excellent, large, realistic, aquaculture model species. In the present work, de novo assembly of gonadal (testicular and ovarian) transcriptomes from juvenile common carp was performed to identify genes involved in gonadal development. A total of 81,757 and 43,257 transcripts with average lengths of 769 and 856 bp, were obtained from the immature testicular and ovarian transcriptomes, respectively. About 84,367 unigenes were constructed after removing redundancy involving representation of transcripts in both gonadal transcriptomes. Gene ontology (39,171 unigenes), clusters of orthologous group's analysis (6651 unigenes) and Kyoto encyclopedia of genes, and genomes automatic annotation server analysis (4783 unigenes) were performed to identify potential genes along with their functions. Furthermore, 18,342 (testis) and 8693 (ovary) simple sequence repeats were identified. About 298 differentially expressed genes were identified, of which 171 and 127 genes were up-regulated in testis and ovary, respectively. Quantitative real-time reverse transcription PCR was performed to validate differential expression of selected genes in testis and ovary. Nearly 809 genes related to reproduction were identified, sex-wise expression pattern of genes related to steroid synthesis, endocrine regulation, germ cell maintenance and others factors related to gonadal differentiation was observed, and expression analysis of nanos, ad4bp/sf-1, and gdf9 was performed. The present study identified certain important genes/factors involved in the gonadal development of C. carpio which may provide insights into the understanding of sex-differentiation and gonadal development processes.

Identification of suh gene and evidence for involvement of notch signaling pathway on gonadal differentiation of Yellow River carp (Cyprinus carpio)

The suh gene is crucial in Notch pathway and regulates mammalian gonad development. In this study, the sequences of suh1 and suh2 genes in Yellow River carp (Cyprinus carpio) were verified. The partial 5'-flanking regions of suh1 and suh2 were analyzed and several potential transcription factor-binding sites were identified. Phylogenetic, gene structure, and chromosome synteny analyses revealed that carp suh1 and suh2 were orthologs and homologous to vertebrate suh. Investigation of the expression profiles of suh1 and suh2 with qPCR showed that these genes were abundant in the brain and gonad of carp, with suh1 exhibiting sexual dimorphism expression pattern in gonad. To study the relationship between gonad differentiation and Notch signaling, primordial gonads were exposed to DAPT, an inhibitor of Notch signaling, in vitro and in vivo. The results revealed a significant downregulation of suh1 and other Notch genes in vitro. In addition, expression of male-biased genes, such as amh, dmrt1, etc., was downregulated, whereas that of female-biased genes, such as foxl2, gdf9, etc., was upregulated. When the primordial gonads were subjected to long-term DAPT exposure, an increased proportion of ovary and delay in testis development were observed. These results suggest that suh gene may have a conservative function between teleosts and mammals. Furthermore, Notch signaling was found to be involved in gonad differentiation in Yellow River carp, and DAPT was noted to inhibit and enhance the expression of male- and female-biased genes, respectively, and induce the increase in number of females.

Transcriptome analysis of three critical periods of ovarian development in Yellow River carp (Cyprinus carpio)

Ovary development is a complex process involving numerous genes; the molecular mechanism underlying the ovary development of carp is still unknown. Here we used Illumina HiSeq™ 2500 to explore the transcriptome of undifferentiated gland (PG), juvenile ovary (OJ) and adult ovary (OA) of Yellow River carp (Cyprinus carpio). A total of 58,749 unigenes were obtained, comprising 45,707 known genes and 13,042 new genes. We identified differentially-expressed genes (DEGs) during development and characterized the functional properties of DEGs by comparison with the gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes databases. qRT-PCR was used to analyze the expression of 22 DEGs and the results corresponded with those of RNA-Seq. Among DEGs between PG and OJ, some upstream regulators of gonad development were upregulated in PG, such as cyp19a and sox9, while some oocyte-specific genes were upregulated in OJ, such as nobox, bmp15 and zp2. Among DEGs between OJ and OA, many oocyte physiological function-related genes were upregulated in OA, such as fem-1 and foxl2. GO analysis showed a higher number of DEGs from PG-OJ analysis were assigned to reproduction terms. Furthermore, our investigation has also revealed DEGs identified from PG-OJ analysis were enriched in several important functional pathways, such as Fanconi anemia and the notch signal pathway. These data suggested a dynamic shift in gene expression during ovary development, and DEGs between PG and OJ provided crucial candidate gene data for the study of ovarian differentiation. Additionally, a total of 1,776,769 single nucleotide polymorphisms and 157,279 INDEs were revealed from transcriptome data. This result will contribute to knowledge of ovary differentiation of Yellow River carp.

Identification of differentially-expressed genes in early developmental ovary of Yellow River carp (Cyprinus carpio var) using Suppression Subtractive Hybridization

Ovary development appears to be under polygenic control, and is influenced by multiple genetic factors that may vary from organism to organism. To gain a better insight into the molecular mechanisms of carp ovary development, Suppression Subtractive Hybridization (SSH) DNA libraries in two species of Yellow River carp were analyzed. Primordial gonads and stage II ovaries were used as testers, and adult ovaries as drivers. One hundred and fifty differentially-expressed candidate genes were examined by Southern blot microarray hybridization. We identified 41 differentially-expressed genes in the PG (Primordial gonad) library and 37 in the stage II ovary library. Gene Ontology Biological Pathway analysis showed the genes were involved in signal transduction, proteolysis process, cell differentiation, TGF-β signal and other biological responses. Twenty-two candidate genes were selected and further characterized using qRT-PCR. Pvalb, epd, and MYH were found specifically expressed in PG, while bmp2b, desmin and fp1 were specifically expressed in stage II ovary. Our results indicate that these genes could be used as biomarkers of the early development of carp ovary. This finding will provide a basis for further understanding of the complex gonad developmental molecular mechanisms in Yellow River carp.

De novo assembly, characterization and annotation for the transcriptome of Sarcocheilichthys sinensis

The Chinese lake gudgeon Sarcocheilichthys sinensis is a small cyprinid fish with great aquaculture potential both for its edible and ornamental values. Nevertheless, available genomic and transcriptomic information for this fish is extremely deficient. In this study, a normalized cDNA library was constructed using 13 mixed tissues of an adult male S. sinensis, and was sequenced by the Illumina HiSeq2500 platform. De novo assembly was performed using 38,911,511 obtained clean reads, and a total of 147,282 unigenes with an average length of 900 bp were finally achieved. 96.2% of these unigenes were annotated in 9 public databases, and 16 segments of growth-related genes were identified for future studies. In addition, 28,493 unigenes were assigned to 61 subcategories of Gene Ontology (GO), and 10,483 unigenes were assigned to 25 categories of Cluster of Orthologous Group (COG). Moreover, 14,943 unigenes were classified into 225 pathways of the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. A total of 30,666 microsatellites were detected from 17,627 unigenes with an average distribution density of 1:2405 bp. This transcriptome data set will be valuable for researches on discovery, expression and evolution on genes of interest. Meanwhile, the identified microsatellites would be useful tools for genetic and genomic studies in S. sinensis.

Hypoxic stress -responsive genes in air breathing catfish, Clarias magur (Hamilton 1822) and their possible physiological adaptive function

The Indian catfish, Clarias magur (previous name C. batrachus) is an air breathing fish, inhabitant of aquatic bodies characterized by low dissolved oxygen levels. It is exposed to hypoxic conditions in its natural habitat. Thus, it can be useful model to study the mechanism of hypoxia stress tolerance. In C. magur, molecular processes facilitating its adaptation to hypoxia stress remain largely unexplored, in part due to unavailability of genomic resources. The suppression subtractive hybridization technique (SSH) was employed to compare the differential expression of transcripts under experimental hypoxic conditions, to that of normoxic conditions. Twelve subtracted cDNA libraries (six each forward and reverse) were constructed from brain, heart, liver, muscle, spleen and head kidney tissues. A total of 2020 clones were screened and sequenced, resulting into 1805 high quality expressed sequence tags (ESTs). Annotation of these differentially expressed ESTs resulted into the identification of genes involved in vast majority of pathways/processes affecting metabolism, cellular processes, signal transduction and/or immune functions. Additionally, 18 potential novel genes expressed in hypoxia stress exposed fish were also identified. The study had catalogued the differentially expressed genes from hypoxia stress induced C. magur, where most of them are reported for the first time in a hypoxia-tolerant fish species. The results not only provided insights for the hypoxia stress altered cellular functions in C. magur, but also generated a valuable functional genomics resource to assist targeted studies on functional genomics and future genome projects.