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

Morphology, Histology, and Transcriptome Analysis of Gonadal Development in Octopus minor (Sasaki, 1920)

Octopus minor is an economically important species, but little is known about the histological pattern and regulatory mechanisms during gonadal development. In this study, we investigated the annual changes in total body weight (TW), gonad somatic index (GSI), gonadal histological features, and transcriptome of O. minor. The results indicated that both females and males showed a similar TW trend. The GSI peaked in June in females, while it remained constant at around 3% in males. Nine and four histological stages were observed in ovaries and testes, respectively. Our field sampling results implied that O. minor might have overwintering periods for both eggs and larvae. Transcriptome analysis revealed that a total of 1095 and 2468 genes were significantly expressed during ovarian and testicular development, separately. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis displayed that 126 GO terms and 5 KEGG pathways were significantly enriched in the ovarian group of advanced vitellogenic oocytes vs vitellogenic oocytes (AVO vs VO). The pathways "Ribosomal", "Cell cycle", and "Progesterone-mediated oocyte maturation" were predicted to promote yolk deposition. Additionally, the testicular comparison group of spent vs mature (Spent vs Mature) showed significant enrichment in 674 GO terms and 13 KEGG pathways, suggesting that energy metabolism and cell repair pathways may be involved in the spermatogenesis process. This work revealed the development process of the gonads and shed light on the potential regulatory pathways of O. minor, providing novel insights and laying a molecular basis for artificial breeding.

Differential Expression of miRNAs, lncRNAs, and circRNAs between Ovaries and Testes in Common Carp (Cyprinus carpio)

Female common carp grow faster than male individuals, implying that rearing females could be more profitable in aquaculture. Non-coding RNAs (ncRNAs) serve as versatile regulators with multiple functions in diverse biological processes. However, the roles of ncRNAs in the sex differentiation of common carp are less studied. In this study, we investigated the expression profiles of ncRNAs, including miRNAs, lncRNAs, and circRNAs, in the gonads to comprehend the roles of ncRNAs in sex differentiation in common carp. A substantial number of differentially expressed (DE) ncRNAs in ovaries and testes were identified. Some miRNAs, notably miR-205, miR-214, and miR-460-5p, might modulate hormone synthesis and thus maintain sex. A novel miRNA, novel_158, was predicted to suppress the expression of foxl3. DE lncRNAs were associated with oocyte meiosis, GnRH signaling pathways, and steroid biosynthesis, while DE circRNA target genes were enriched in the WNT signaling pathway and MAPK signaling pathway. We also analyzed ncRNA-mRNA interactions to shed light on the crosstalk between competing endogenous RNAs (ceRNAs), which is the critical mechanism by which lncRNAs and circRNAs function. Some lncRNAs and circRNAs may be able to competitively bind novel_313, a new miRNA, and thus regulate hsd17β3. Our research will provide a valuable resource for understanding the genetic basis of gonadal differentiation and development in common carp.

Bioinformatics approaches and big data analytics opportunities in improving fisheries and aquaculture

Aquaculture has witnessed an excellent growth rate during the last two decades and offers huge potential to provide nutritional as well as livelihood security. Genomic research has contributed significantly toward the development of beneficial technologies for aquaculture. The existing high throughput technologies like next-generation technologies generate oceanic data which requires extensive analysis using appropriate tools. Bioinformatics is a rapidly evolving science that involves integrating gene based information and computational technology to produce new knowledge for the benefit of aquaculture. Bioinformatics provides new opportunities as well as challenges for information and data processing in new generation aquaculture. Rapid technical advancements have opened up a world of possibilities for using current genomics to improve aquaculture performance. Understanding the genes that govern economically relevant characteristics, necessitates a significant amount of additional research. The various dimensions of data sources includes next-generation DNA sequencing, protein sequencing, RNA sequencing gene expression profiles, metabolic pathways, molecular markers, and so on. Appropriate bioinformatics tools are developed to mine the biologically relevant and commercially useful results. The purpose of this scoping review is to present various arms of diverse bioinformatics tools with special emphasis on practical translation to the aquaculture industry.

Transcriptome sequencing reveals ovarian immune response and development during female sperm storage in viviparous black rockfish (Sebastes schlegelii)

Black rockfish (Sebastes schlegelii) is a viviparous teleost fish whose spermatozoa were transferred into the female ovary cavity and stored for up to five months and then fertilized with the matured eggs. There is no clarity about the molecular characteristics of ovarian follicles during female sperm storage in Sebastes schlegelii. In this study, histological observation, transcriptomic analysis and hormone level detection were performed in ovaries at stages of pre-mating (PRM), post-mating (POM) and pre-fertilization (PRF). Histological observation displayed that oocytes developed from the primary growth (PG) stage to the mature stage during the three stages. Furthermore, somatic cells around the oocyte were proliferated and spermatozoa were found near the layer of epithelial cells. Transcriptomic analysis showed that there were 437 and 747 differentially expressed genes (DEGs) in ovarian comparison of PRM-vs-POM and POM-vs-PRF, respectively. GO enrichment and KEGG analysis revealed that lots of DEGs from PRM-vs-POM were linked to immune-related pathways, such as antigen processing and presentation, immune response, and complement and coagulation cascade. Meanwhile, seven DEGs associated with immune response were differentially expressed after spermatozoa treatment in ovarian tissue in vitro. While the DEGs from POM-vs-PRF were mostly enriched in the pathways related to homeostasis maintenance and cellular junction and metabolism. In addition, we found increased estrogen (E2) and 11-ketotestosterone (11-KT) level and decreased testosterone level in ovarian follicles during the sperm storage period by ELISA, suggesting that sex hormones are involved in the dynamic change of ovarian follicles. In total, this study could provide new hints for understanding the immune adaption and developmental signatures of ovarian follicles post copulation in black rockfish and other viviparous fish.

Transcriptomes of Testes at Different Developmental Stages in the Opsariichthys bidens Predict Key Genes for Testis Development and Spermatogenesis

Testis development is a complex process involving multiple genes, and the molecular mechanisms underlying testis development in Opsariichthys bidens remain unclear. We performed transcriptome sequencing analysis on a total of 12 samples of testes from stages II, III, IV, and V of O. bidens and obtained a total of 79.52 Gb clean data, as well as 288,573 transcripts and 116,215 unigenes. Differential expression analysis showed that 22,857 differentially expressed genes (DEGs) were screened in six comparison groups (III vs. II, IV vs. II, V vs. II, IV vs. III, V vs. III, and V vs. IV). Kyoto Encyclopedia of Genes and Genomes enrichment analysis of DEGs showed that six comparison groups were significantly enriched for a total of 20 significantly up- or down-regulated pathways, including six pathways related to signal transduction, three pathways related to energy metabolism, five pathways related to disease, and two pathways related to ribosomes. Furthermore, our investigation revealed that DEGs were enriched in several important functional pathways, such as Huntington's disease signaling pathway, TGF-β signaling pathway, and ribosome signaling pathway. Protein-protein interaction network analysis of DEGs identified 63 up-regulated hub genes, including 9 kinesin genes and 2 cytoplasmic dynein genes, and 39 down-regulated hub genes, including 13 ribosomal protein genes. This result contributes to the knowledge of spermatogenesis and testis development in O. bidens.

Transcriptome analysis of flathead grey mullet (Mugil cephalus) ovarian development induced by recombinant gonadotropin hormones

Background: Treatment with recombinant gonadotropin hormones (rGths), follicle-stimulating hormone (rFsh) and luteinizing hormone (rLh), was shown to induce and complete vitellogenesis to finally obtain viable eggs and larvae in the flathead grey mullet (Mugil cephalus), a teleost arrested at early stages of gametogenesis in intensive captivity conditions. This study aimed to investigate the transcriptomic changes that occur in the ovary of females during the rGths-induced vitellogenesis. Methods: Ovarian samples were collected through biopsies from the same five females at four stages of ovarian development. RNASeq libraries were constructed for all stages studied, sequenced on an Illumina HiSeq4000, and a de novo transcriptome was constructed. Differentially expressed genes (DEGs) were identified between stages and the functional properties of DEGs were characterized by comparison with the gene ontology and Kyoto Encyclopedia. An enrichment analysis of molecular pathways was performed. Results: The de novo transcriptome comprised 287,089 transcripts after filtering. As vitellogenesis progressed, more genes were significantly upregulated than downregulated. The rFsh application induced ovarian development from previtellogenesis to early-to-mid-vitellogenesis with associated pathways enriched from upregulated DEGs related to ovarian steroidogenesis and reproductive development, cholesterol metabolism, ovarian growth and differentiation, lipid accumulation, and cell-to-cell adhesion pathways. The application of rFsh and rLh at early-to-mid-vitellogenesis induced the growth of oocytes to late-vitellogenesis and, with it, the enrichment of pathways from upregulated DEGs related to the production of energy, such as the lysosomes activity. The application of rLh at late-vitellogenesis induced the completion of vitellogenesis with the enrichment of pathways linked with the switch from vitellogenesis to oocyte maturation. Conclusion: The DEGs and enriched molecular pathways described during the induced vitellogenesis of flathead grey mullet with rGths were typical of natural oogenesis reported for other fish species. Present results add new knowledge to the rGths action to further raise the possibility of using rGths in species that present similar reproductive disorders in aquaculture, the aquarium industry as well as the conservation of endangered species.

Small RNA sequencing reveals sex-related miRNAs in Collichthys lucidus

Collichthys lucidus (C. lucidus) is an economically important fish species, exhibiting sexual dimorphism in its growth rate. However, there is a lack of research on its underlying sex-related mechanisms. Therefore, small RNA sequencing was performed to better comprehend these sex-related molecular mechanisms. In total, 171 differentially expressed miRNAs (DE-miRNAs) were identified between the ovaries and testes. Functional enrichment analysis revealed that the target genes of DE-miRNAs were considerably enriched in the p53 signaling, PI3K–Akt signaling, and TGF-beta signaling pathways. In addition, sex-related miRNAs were identified, and the expression of miR-430c-3p and miR-430f-3p was specifically observed in the gonads compared with other organs and their expression was markedly upregulated in the testes relative to the ovaries. Bmp15 was a target of miR-430c-3p and was greatly expressed in the ovaries compared with the testes. Importantly, miR-430c-3p and bmp15 co-expressed in the ovaries and testes. This research provides the first detailed miRNA profiles for C. lucidus concerning sex, likely laying the basis for further studies on sex differentiation in C. lucidus.

Pervasive male-biased expression throughout the germline-specific regions of the sea lamprey genome supports key roles in sex differentiation and spermatogenesis

Sea lamprey undergo programmed genome rearrangement (PGR) in which ∼20% of the genome is jettisoned from somatic cells during embryogenesis. Although the role of PGR in embryonic development has been studied, the role of the germline-specific region (GSR) in gonad development is unknown. We analysed RNA-sequence data from 28 sea lamprey gonads sampled across life-history stages, generated a genome-guided de novo superTranscriptome with annotations, and identified germline-specific genes (GSGs). Overall, we identified 638 GSGs that are enriched for reproductive processes and exhibit 36x greater odds of being expressed in testes than ovaries. Next, while 55% of the GSGs have putative somatic paralogs, the somatic paralogs are not differentially expressed between sexes. Further, putative orthologs of some the male-biased GSGs have known functions in sex determination or differentiation in other vertebrates. We conclude that the GSR of sea lamprey plays an important role in testicular differentiation and potentially sex determination.

RNA-sequencing of sea lamprey gonads at different life-history stage identifies germline-specific genes which are highly expressed in males during spermatogenesis. This suggests a link between male-biased germline expression and sex differentiation in the sea lamprey.

A Transcriptomic Analysis of Gonads from the Low-Temperature-Induced Masculinization of Takifugu rubripes

Simple Summary

Our study analyzed the differentiation of transcriptomes in normal and sex-reverse Takifugu rubripes, and screened out 13 differentially expressed genes related to sex differentiation. This is the first report on the gonadal transcriptome of pseudo-males in Takifugu rubripes. Our results provide an important contribution to the molecular mechanism of masculinization in a cultured fish subject to low-temperature treatment.

Abstract

The phenotypic sex of fish is usually plastic. Low-temperature treatment induces the masculinization of Takifugu rubripes, resulting in pseudo-males (PM) with the physiological sex of a male (M) and genetic sex of a female (F). For a comparison of gonadal transcriptomes, we collected gonads from three groups of T. rubripes (F, M, and PM) for high-throughput transcriptome sequencing. The results provided 467,640,218 raw reads (70.15 Gb) and a total of 436,151,088 clean reads (65.43 Gb), with an average length of 150 bp. Only 79 differentially expressed genes (DEGs) were identified between F and PM, whereas 12,041 and 11,528 DEGs were identified between F and M, and PM and M, respectively. According to the functional annotation of DEGs, 13 DEGs related to gonadal development were screened (LOC101066759, dgat1, limk1, fbxl3, col6a3, fgfr3, dusp22b, svil, abhd17b, srgap3, tmem88b, bud4, and mustn10) which might participate in formating PM. A quantitative PCR of the DEGs confirmed the reliability of the RNA-seq. Our results provide an important contribution to the genome sequence resources for T. rubripes and insight into the molecular mechanism of masculinization in a cultured fish subject to low-temperature treatment.

Comparison of differential expression genes in ovaries and testes of Pearlscale angelfish Centropyge vrolikii based on RNA-Seq analysis

Pearlscale angelfish Centropyge vrolikii is a kind of protogynous hermaphrodite fish with a natural sexual reversion. Under appropriate social conditions, a female fish can transform into a male fish spontaneously. It is an important prerequisite for artificial breeding to understand the process of its gonadal development and sexual reversion. Gonadal development is regulated by many sex-related genes. In this study, we used unreferenced RNA-Seq technology to sequence the ovary at the perinucleolus stage (O_II), ovary at the yolk vesicle stage (O_IV),IV and testis (T), respectively; screened the gonadal differential expression genes (DEGs); and analyzed the expression of these genes in different developmental stages of ovary and different sex gonads. The results showed that a total of 142,589 all-unigene samples were assembled, and gene annotation was performed by COG, GO, KEGG, KOG, Pfam, Swissprot, eggNOG, and NR functional database. Comparative analysis revealed that there were 1919 genes that were up-regulated and 1289 genes were down-regulated in comparison to O_IV vs O_II, while there were 3653 genes that were up-regulated and 2874 genes were down-regulated in comparison of O_IV vs T, there were 3345 genes that were up-regulated and 2995 genes were down-regulated in comparison of the O_II vs the T. At the same time, the results verified by RT-qPCR were consistent with the variation trend of transcriptome data. Among the results, amh, sox9b, dmrt1, dmrt2, cyp11a, cyp17a, and cyp19a were significantly expressed in the testes, while sox3, sox4, sox11, sox17, and hsd3b7 were significantly expressed in the ovaries. And, the expression of the amh, sox9b, dmrt2, and dmrt1 were low in the O_II and O_IV, while significantly increased during the ovotestis in the hermaphroditic period (O_T), and finally reached the highest level in pure testis after sex reversal. The expression of sox3, sox4, hsd3b7, sox11, and sox17 was significantly reduced during the hermaphroditic period (O_T). These results suggested that these genes may play an important role in the process of sex reversal. This study is helpful to further understand the molecular regulation mechanism of gonadal development and sexual reversion in Pearlscale angelfish and also provide important clues for future studies.

Whole-Genome Re-sequencing and Transcriptome Reveal Oogenesis-Related Genes in Autotetraploid Carassius auratus

Oogenesis involves a series of biochemical and physiological transformations and numerous regulated genes. The autotetraploid Carassius auratus (4nRR) originated from whole-genome duplication of Carassius auratus red var. (RCC), which produces diploid eggs through pairing of diploid-like chromosome during female meiosis. To explore the molecular mechanisms underlying oogenesis in 4nRR, we used the Illumina sequencing platform to characterize the ovaries of 4nRR and RCC. Transcriptome and whole-genome re-sequencing were performed to uncover the key genes and potential genetic mutations related to oogenesis. Each sample produced paired-end reads in the range of 66.97 to 98.36 million via Illumina HiSeq™ 2500. After comparing of the transcriptome profiles between the 4nRR and RCC, we uncovered 8562 differentially expressed genes (DEGs). The DEGs were enriched in oogenesis-related processes, including oogenesis, oocyte development, ubiquitin-mediated proteolysis, the signaling pathways of MAPK and calcium, and oocyte meiosis as investigated by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis. Additionally, whole-genome re-sequencing revealed 34,058,834 SNPs and 6,153,711 InDels, including 6,677,638 non-synonymous variations (SNPs) and 706,210 frame-shift InDels in the 8510 DEGs of 4nRR fish. Subsequently, whole-genome re-sequencing and transcriptomatic analyses revealed the genes that participate in oogenesis associated processes. Specifically, genes involved in ubiquitin-mediated proteolysis (SMURF1, UBE2I), calcium transport (CALM3, CAMK4), and meiosis (MAPK3, GRB2, CPEB1, CCNB2, YWHAE) were related to oogenesis in 4nRR. These findings enrich our understanding of oogenesis in the autopolyploid fish.

Virtual Grid Engine: a simulated grid engine environment for large-scale supercomputers

Background

Supercomputers have become indispensable infrastructures in science and industries. In particular, most state-of-the-art scientific results utilize massively parallel supercomputers ranked in TOP500. However, their use is still limited in the bioinformatics field due to the fundamental fact that the asynchronous parallel processing service of Grid Engine is not provided on them. To encourage the use of massively parallel supercomputers in bioinformatics, we developed middleware called Virtual Grid Engine, which enables software pipelines to automatically perform their tasks as MPI programs.

Result

We conducted basic tests to check the time required to assign jobs to workers by VGE. The results showed that the overhead of the employed algorithm was 246 microseconds and our software can manage thousands of jobs smoothly on the K computer. We also tried a practical test in the bioinformatics field. This test included two tasks, the split and BWA alignment of input FASTQ data. 25,055 nodes (2,000,440 cores) were used for this calculation and accomplished it in three hours.

Conclusion

We considered that there were four important requirements for this kind of software, non-privilege server program, multiple job handling, dependency control, and usability. We carefully designed and checked all requirements. And this software fulfilled all the requirements and achieved good performance in a large scale analysis.

Pig Hsd17b3: Alternative splice variants expression, insertion/deletion (indel) in promoter region and their associations with male reproductive traits

Hydroxysteroid 17-Beta Dehydrogenase 3 (Hsd17b3), primarily expressed in Leydig cells (LCs) of the mammalian testes, is essential for testosterone biosynthesis and male fertility. The aim of our study was to profile the expression, splice variants (SV) and novel insertion/deletion (indel) of Hsd17b3 in boars. Quantitative analysis showed that the expression level of Hsd17b3 in the testis was significantly highest. Among different testicular cell types, the Hsd17b3 mRNA expression level of LCs was significantly higher than that of SSCs (spermatogonial stem cells) and SCs (Sertoli cells). Furthermore, the SV was firstly identified in pigs and it was highly expressed in LCs comparing with SSCs and SCs. In addition, two mutations were identified in pig Hsd17b3 gene promotor and intron, respectively, which were associated with male reproductive traits (P <  0.05). In conclusion, both transcripts of Hsd17b3 gene were highly expressed in pig testes and LCs; the two novel indel variants of Hsd17b3 gene can be used as potential DNA makers for the marker-assisted selection in pigs. All these findings would enrich the study of Hsd17b3 gene in pig genetic breeding.

Transcriptomic Analysis Revealed the Regulatory Mechanisms of Oocyte Maturation and Hydration in Orange-Spotted Grouper (Epinephelus coioides)

Oocyte maturation and hydration are regulated by a complex interplay of various hormones and local factors. We have investigated the morphological changes of follicles and serum steroid levels during the HCG (human choionic gonadotophin)-induced oocyte maturation in the orange-spotted grouper. For the first time, a large-scale transcriptomic analysis of follicles during the maturation has been conducted in a fish species which produce pelagic oocytes. Eight cDNA libraries of follicle samples, from full-grown immature follicles to mature follicles, were constructed. A total of 402,530,284 high-quality clean reads were obtained after filtering, 79.66% of which perfectly mapped to the orange-spotted grouper genome. Real-time PCR results of 12 representative genes related to oocyte maturation and hydration verified the reliability of the RNA-seq data. A large number of genes related to oocyte maturation and hydration were identified in the transcriptome dataset. And the transcriptomic analysis revealed the dynamic changes of the steroid synthesis pathway and the pathway of hydration during oocyte maturation. The present study will facilitate future study on the oocyte maturation and hydration in the orange-spotted grouper and other marine pelagic egg spawner.

Effects of short-time exposure to atrazine on miRNA expression profiles in the gonad of common carp (Cyprinus carpio)

BACKGROUND

Atrazine is widely used in agriculture and is a known endocrine disrupting chemical. Atrazine can seep into the water body through surface, posing a potential threat to the aquatic ecological environment and human drinking water source. In vertebrate, studies have shown that it can affect reproduction and development seriously, but its molecular mechanism for aquatic animals is unknown. Aquaculture is very common in China, especially common carp, whose females grow faster than males. However, the effects of atrazine on the reproduction of carp, especially miRNA, have not been investigated.

RESULTS

In this study, common carp (Cyprinus carpio) at two key developmental stages were exposed to atrazine in vitro. Sex ratio was observed to analyze the effect of atrazine on the sex. MiRNA expression profiles were analysed to identify miRNAs related to gonad development and to reveal the atrazine mechanisms interfering with gonad differentiation. The results showed that the sex ratio was biased towards females. Atrazine exposure caused significant alteration of multiple miRNAs. Predicted targets of differently-expressed miRNAs were involved in many reproductive biology signalling pathways.

CONCLUSIONS

Our results indicate that atrazine promoted the expression of female-biased genes by decreasing miRNAs in primordial gonad. In addition, our results indicate that atrazine can up-regulate aromatase expression through miRNAs, which supports the hypothesis that atrazine has endocrine-disrupting activity by altering the gene expression profile of the Hypothalamus-Pituitary-Gonad axis through its corresponding miRNAs.

Characterization of the European Sea Bass (Dicentrarchus labrax) Gonadal Transcriptome During Sexual Development

The European sea bass is one of the most important cultured fish in Europe and has a marked sexual growth dimorphism in favor of females. It is a gonochoristic species with polygenic sex determination, where a combination between still undifferentiated genetic factors and environmental temperature determines sex ratios. The molecular mechanisms responsible for gonadal sex differentiation are still unknown. Here, we sampled fish during the gonadal developmental period (110 to 350 days post fertilization, dpf), and performed a comprehensive transcriptomic study by using a species-specific microarray. This analysis uncovered sex-specific gonadal transcriptomic profiles at each stage of development, identifying larger number of differentially expressed genes in ovaries when compared to testis. The expression patterns of 54 reproduction-related genes were analyzed. We found that hsd17β10 is a reliable marker of early ovarian differentiation. Further, three genes, pdgfb, snx1, and nfy, not previously related to fish sex differentiation, were tightly associated with testis development in the sea bass. Regarding signaling pathways, lysine degradation, bladder cancer, and NOD-like receptor signaling were enriched for ovarian development while eight pathways including basal transcription factors and steroid biosynthesis were enriched for testis development. Analysis of the transcription factor abundance showed an earlier increase in females than in males. Our results show that, although many players in the sex differentiation pathways are conserved among species, there are peculiarities in gene expression worth exploring. The genes identified in this study illustrate the diversity of players involved in fish sex differentiation and can become potential biomarkers for the management of sex ratios in the European sea bass and perhaps other cultured species.

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.

Transcriptomic Analysis for Differentially Expressed Genes in Ovarian Follicle Activation in the Zebrafish

In teleosts, the onset of puberty in females is marked by the appearance of the first wave of pre-vitellogenic (PV) follicles from the pool of primary growth (PG) follicles (follicle activation) in the ovary during sexual maturation. To understand the mechanisms underlying follicle activation and therefore puberty onset, we undertook this transcriptomic study to investigate gene expression profiles in the event. Our analysis revealed a total of 2,027 up-regulated and 859 down-regulated genes during the PG-PV transition. Gene Ontology (GO) analysis showed that in addition to basic cellular functions such as gene transcription, cell differentiation, and cell migration, other biological processes such as steroidogenesis, cell signaling and angiogenesis were also enriched in up-regulated genes; by comparison, some processes were down-regulated including piRNA metabolism, gene silencing and proteolysis. Further Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis identified a variety of signaling pathways that might play pivotal roles in PG-PV transition, including MAPK, TGF-β, Hedgehog, FoxO, VEGF, Jak-STAT, and phosphatidylinositol signaling pathways. Other pathways of particular interest included endocytosis and glycosaminoglycan biosynthesis. We also analyzed expression changes of genes expressed in different compartments viz. oocytes and follicle cells. Interestingly, most oocyte-specific genes remained unchanged in expression during follicle activation whereas a great number of genes specifically expressed in the follicle cells showed significant changes in expression. Overall, this study reported a comprehensive analysis for genes, biological processes and pathways involved in follicle activation, which also marks female puberty onset in the zebrafish when occurring for the first time in sexual maturation.