Gonadal transcriptomic analysis of yellow catfish (Pelteobagrus fulvidraco): identification of sex-related genes and genetic markers

Multi-omics analysis identifies sex-specific hepatic protein-metabolite networks in yellow catfish (Pelteobagrus fulvidraco) exposed to chronic hypoxia

Hypoxia disrupts the endocrine system of teleosts. The liver plays important roles in the endocrine system, energy storage, and metabolic processes. The aim of this study was to investigate the sex-specific hepatic response of yellow catfish under chronic hypoxia at the multi-omics level. Common hepatic responses in both sexes included the HIF-1 signaling pathway, glycolysis/gluconeogenesis, and steroid biosynthesis. Hypoxia dysregulated primary bile acid biosynthesis, lipid metabolism, and vitellogenin levels in female fish. Endoplasmic reticulum function in females also tended to be disrupted by hypoxia, as evidenced by significantly enriched pathways, including ribosome, protein processing in the endoplasmic reticulum, and RNA degradation. Other pathways, including the TCA cycle, oxidative phosphorylation, and Parkinson's and Huntington's disease, were highly enriched by hypoxia in male fish, suggesting that mitochondrial function was dysregulated. In both sexes of yellow catfish, the cell cycle was arrested and apoptosis was inhibited under chronic hypoxia. Multi-omics suggested that SLC2A5, CD209, LGMN, and NEDD8 served as sex-specific markers in these fish under chronic hypoxia. Our results provide insights into hepatic adaptation to chronic hypoxia and facilitate our understanding of sex-specific responses in fish.

De novo assembly, characterization and comparative transcriptome analysis of gonads reveals sex-biased genes in Coreoperca whiteheadi

The wild Coreoperca whiteheadi is considered as the primordial species in sinipercine fish, which has valuable genetic information. Unfortunately, C. whiteheadi was listed as a near-threatened species because of the environmental pollution, over-exploitation and species invasion. Therefore, more genetic information is needed to have a better understanding of gonadal development in C. whiteheadi. Here, the first gonadal transcriptomes analysis of C. whiteheadi was conducted and 277.14 million clean reads were generated. A total of 96,753 unigenes were successfully annotated. By comparing ovary and testis transcriptomes, a total of 21,741 differentially expressed genes (DEGs) were identified, of which 12,057 were upregulated and 9684 were downregulated in testes. Among them, we also identified about 53 differentially expressed sex-biased genes. Subsequently, the expression of twenty-four DEGs were confirmed by real-time fluorescence quantitative PCR. Furthermore, the histological analysis was conducted on ovaries and testes of one-year-old C. whiteheadi. Our results provided basic support for further studies on the function of sex-biased genes and the molecular mechanism of sex determination and reproduction in C. whiteheadi.

Comparative transcriptome analysis reveals sex bias in expression patterns of genes related to sex steroids and immunity in the skin of spinyhead croaker Collichthys lucidus

Fish skin is the first barrier against external invasion, and also an important interface for communication between males and females during reproduction. Nonetheless, sexual dimorphism in the physiology of fish skins is still poorly understood. Herein, transcriptomes of skin were comparatively analysed between males and females in spinyhead croaker, Collichthys lucidus. Totally, 170 differentially expressed genes (DEG) were detected, including 79 female-biased genes and 91 male-biased genes. Gene ontology (GO) annotation items of the DEGs were mainly enriched in biological process items (86.2%), including regulation of biological processes, responses to chemical and biological stimuli, transport and secretion, movement, immune response, tissue development, etc. In KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway enrichment analysis, the male-biased genes were enriched in pathways including those related to immunity such as the TNF signalling pathway and IL-17 signalling pathway, whereas the female-biased genes were enriched in pathways including those related to female steroids such as ovarian steroidogenesis and oestrogen signalling pathway. In addition, odf3 was found to be a male-specific expression gene, being a candidate marker for phenotypic sex. Thus, the sexual difference in gene expression in fish skin in spawning season was uncovered by transcriptome analysis for the first time, providing new insights into sexual dimorphism in the physiology and functions of fish skin.

Gonadal transcriptomes reveal sex-biased expression genes associated with sex determination and differentiation in red-tail catfish (Hemibagrus wyckioides)

BACKGROUND

Red-tail catfish (Hemibagrus wyckioides) is an important commercially farmed catfish in southern China. Males of red-tail catfish grow faster than females, suggesting that all-male catfish will produce more significant economic benefits in aquaculture practice. However, little research has been reported on sex determination and gonadal development in red-tail catfish.

RESULTS

In this study, we performed the first transcriptomic analysis of male and female gonads at four developmental stages at 10, 18, 30, and 48 days post hatching (dph) using RNA-seq technology. A total of 23,588 genes were screened in 24 sequenced samples, of which 28, 213, 636, and 1381 differentially expressed genes (DEGs) were detected at four developmental stages, respectively. Seven candidate genes of sex determination and differentiation were further identified. Real-time quantitative PCR (RT-qPCR) further confirmed that anti-Mullerian hormone (amh), growth differentiation factor 6a (gdf6a), testis-specific gene antigen 10 (tsga10), and cytochrome P450 family 17 subfamily A (cyp17a) were highly expressed mainly in the male, while cytochrome P450 family 19 subfamily A polypeptide 1b (cyp19a1b), forkhead box L2 (foxl2), and hydroxysteroid 17-beta dehydrogenase 1 (hsd17b1) were highly expressed in the female. The KEGG pathway enrichment data showed that these identified DEGs were mainly involved in steroid hormone biosynthesis and TGF-β signaling pathways.

CONCLUSIONS

Based on RNA-seq data of gonads at the early developmental stages, seven DEGs shared by the four developmental stages were identified, among which amh and gdf6a may be the male-biased expression genes, while foxl2, cyp19a1b and hsd17b1 may be the female-biased expression genes in red-tail catfish. Our study will provide crucial genetic information for the research on sex control in red-tail catfish, as well as for exploring the evolutionary processes of sex determination mechanisms in fish.

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.

De Novo Assembly, Characterization and Comparative Transcriptome Analysis of the Mature Gonads in Spinibarbus hollandi

Spinibarbus hollandi is an important commercial aquaculture species in southeastern China, but with long maturity period and low egg laying amount. However, there has been little study of its gonad development and reproductive regulation, which limits aquaculture production. Here, for the first time, gonadal transcriptomes of male and female S. hollandi were analyzed. A total of 167,152 unigenes were assembled, with only 48,275 annotated successfully. After comparison, a total of 21,903 differentially expressed genes were identified between male and female gonads, of which 16,395 were upregulated and 5508 were downregulated in the testis. In addition, a large number of differentially expressed genes participating in reproduction, gonad formation and differentiation, and gametogenesis were screened out and the differential expression profiles of partial genes were further validated using quantitative real-time PCR. These results will provide basic information for further research on gonad differentiation and development in S. hollandi.

Variation in immuno-reproductive milieu of testis in Clarias magur from pre-spawning to spawning phase: An indication towards non-canonical role of immune elements in testes

Immune mechanisms are major players in ensuring the normal functioning of testicular functions. However, apart from their role in active defence against pathogens, prior studies have also suggested a possibility for reproduction-related (non-immune) functions of certain immune elements. This study employs a comparative transcriptomics approach followed by network analysis for tracking the variation in the immuno-reproductive milieu of Clarias magur testis in spawning versus pre-spawning phase. The results show a significant modulation of both reproduction and immune-relevant genes in spawning versus pre-spawning phase. The functional enrichment of the upregulated reproduction-relevant gene network also shows immune-related biological processes which indicates a probability of involvement of these candidates in spermatogenesis-related events for switching from pre-spawning to spawning phase. The upregulated immune network is highly dense with 40 hubs, 10 cluster sub-networks and 142 functionally enriched pathways in comparison to its downregulated counterpart with only 5 hubs, 1 cluster and 1 enriched pathway. These findings indicate that the synchronisation in modulation of both reproductive and immune-related factors is critical for progression of testicular events guiding the switch from pre-spawning to spawning phase. The reproductive phase-dependent variation in plasma sex steroid levels and the selected genes for quantitative PCR also corroborated this hypothesis. The study also serves as a preliminary screening step for probable immune candidates that may be involved in reproductive functions of testis in addition to defence.

Sex-specific markers undetected in green sunfish Lepomis cyanellus using restriction-site associated DNA sequencing

We used restriction-site associated DNA sequencing for SNP discovery and genotyping of known-sex green sunfish Lepomis cyanellus DNA samples to search for sex-diagnostic single nucleotide polymorphisms (SNPs) and restriction-site associated sequences present in one sex and absent in the other. The bioinformatic analyses discovered candidate SNPs and sex-specific restriction-site associated sequences that fit patterns of male or female heterogametic sex determination systems. However, when primers were developed and tested, no candidates reliably identified phenotypic sex. The top performing SNP candidate (ZW_218) correlated with phenotypic sex 63.0% of the time and the presence-absence loci universally amplified in both sexes. We recommend further investigations that interrogate a larger fraction of the L. cyanellus genome. Additionally, studies on the effect of temperature and rearing density on sex determination, as well as breeding of sex-reversed individuals, could provide more insights into the sex determination system of L. cyanellus.

A time-course transcriptome analysis of gonads from yellow catfish (Pelteobagrus fulvidraco) reveals genes associated with gonad development

Background

The yellow catfish, Pelteobagrus fulvidraco, is a commercially important fish species. It is widely distributed in the fresh water areas of China, including rivers, lakes, and reservoirs. Like many other aquaculture fish species, people have observed significant size dimorphism between male and female yellow catfish and it shows a growth advantage in males.

Results

Here, at the first time, the time-course transcriptome was used to explore the various expression profiles of genes in different gonad developmental stages and genders. A total of 2696 different expression genes (DEGs) were identified from different stages. Based on these DEGs, 13 gonad development related genes were identified which showed time-specific or sex biased expression patterns.

Conclusion

This study will provide the crucial information on the molecular mechanism of gonad development of female and male yellow catfish. Especially, during the different gonad development stages, these 13 gonad development related genes exhibit various expression patterns in female and male individual respectively. These results could inspire and facilitate us to understanding the various roles of these genes play in different gonad development stages and genders.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08651-0.

Integrated analysis of the miRNA and mRNA expression profiles in Leiocassis longirostris at gonadal maturation

Leiocassis longirostris is a commercially important fish species that shows a sexually dimorphic growth pattern. A lack of molecular data from the gonads of this species has hindered research and selective breeding efforts. In this study, we conducted a comprehensive analysis of the expression profile of miRNA and mRNA to explore their regulatory roles in the gonadal maturation stage of L. longirostris. We identified 60 differentially expressed miRNAs and 20,752 differentially expressed genes by sequencing. A total of 90 miRNAs and 21 target genes involved in gonad development and sex determination were identified. Overall, the results of this study enhance our understanding of the molecular mechanisms underlying sex determination and differentiation and provide valuable genomic information for the selective breeding of L. longirostris.

The Ovarian Transcriptome at the Early Stage of Testis Removal-Induced Male-To-Female Sex Change in the Protandrous Black Porgy Acanthopagrus schlegelii

Unlike gonochoristic fishes, sex is fixed after gonadal differentiation (primary sex determination), and sex can be altered in adults (secondary sex determination) of hermaphroditic fish species. The secondary sex determination of hermaphroditic fish has focused on the differences between testicular tissue and ovarian tissue during the sex change process. However, comprehensive studies analyzing ovarian tissue or testicular tissue independently have not been performed. Hermaphroditic black porgy shows a digonic gonad (ovarian tissue with testicular tissue separated by connective tissue). Protandrous black porgy has stable maleness during the first two reproductive cycles (<2 years old), and approximately 50% enter femaleness (natural sex change) during the third reproductive cycle. Precocious femaleness is rarely observed in the estradiol-17β (E2)-induced female phase (oocytes maintained at the primary oocyte stage), and a reversible female-to-male sex change is found after E2 is withdrawn in <2-year-old fish. However, precocious femaleness (oocytes entering the vitellogenic oocyte stage) is observed in testis-removed fish in <2-year-old fish. We used this characteristic to study secondary sex determination (femaleness) in ovarian tissue via transcriptomic analysis. Cell proliferation analysis showed that BrdU (5-bromo-2′-deoxyuridine)-incorporated germline cells were significantly increased in the testis-removed fish (female) compared to the control (sham) fish (male) during the nonspawning season (2 months after surgery). qPCR analysis showed that there were no differences in pituitary-releasing hormones (lhb and gtha) in pituitary and ovarian steroidogenesis-related factors (star, cyp11a1, hsd3b1, and cyp19a1a) or female-related genes (wnt4a, bmp15, gdf9, figla, and foxl2) in ovarian tissues between intact and testis-removed fish (2 months after surgery). Low expression of pituitary fshb and ovarian cyp17a1 was found after 2 months of surgery. However, we did find small numbers of genes (289 genes) showing sexual fate dimorphic expression in both groups by transcriptomic analysis (1 month after surgery). The expression profiles of these differentially expressed genes were further examined by qPCR. Our present work identified several candidate genes in ovarian tissue that may be involved in the early period of secondary sex determination (femaleness) in black porgy. The data confirmed our previous suggestion that testicular tissue plays an important role in secondary sex determination in protandrous black porgy.

Distribution of simple sequence repeats, transcription factors, and differentially expressed genes in the NGS-based transcriptome of male and female seabuckthorn (Hippophae salicifolia)

Seabuckthorn (Hippophae salicifolia) is a perennial, multipurpose wonder plant, popular for its immense medicinal, nutritional, and therapeutic properties. However, due to the lack of whole-genome-based studies, the molecular mechanism governing distinct sexual phenotypes is still not clear. We employed the high-throughput NGS Illumina NovaSeq paired-end technology to generate whole transcriptome profiles of male and female plants of H. salicifolia. In total, 3.2 million raw short reads were generated with an average length of 150 bp, including 50911358 reads from the male leaf tissue samples and 45850364 reads from the female leaf tissue samples. Clustering of the high-quality reads yielded de novo short read assembly of 50259 transcripts of >100 bp length. The final transcripts were assigned Gene Ontology (GO) terms. The digital expression of genes was studied using the DESeq2 of R package that identified 7180 differentially expressed genes (DEGs) between the male and female plant samples. Further, 10,850 simple sequence repeats, and 8,351 transcription factors, distributed in more than 85 transcription families, were also mined from the final assembled transcriptome. Next, COG and KEGG pathway analyses were performed to assign biological functional terms to the DEGs. The findings of the present study will provide a valuable resource for gene expression discovery and other functional genomics studies aiming towards the selection of candidate genes for the development of sex-specific markers in seabuckthorn and other closely related species.Communicated by Ramaswamy H. Sarma.

Comparative transcriptomic analysis of gonadal development and renewal in the ovoviviparous black rockfish (Sebastes schlegelii)

BACKGROUND

The black rockfish (Sebastes schlegelii) has an ovoviviparous reproductive pattern and long-term sperm storage, resulting in asynchronous gonadal development between the sexes. However, the comprehensive understanding of gonadal development in black rockfish has not yet been achieved. Here, we studied gonadal development and germ cell renewal using histology and RNA-seq.

RESULTS

In this study, RNA-seq was performed on testes and ovaries to characterize key pathways and genes that are active during development and gamete maturation in black rockfish. Differentially expressed genes (DEGs) were identified and annotated in 4 comparisons (F_III vs. F_IV, F_IV vs. F_V, M_III vs. M_IV and M_IV vs. M_V). Based on analysis of DEGs enriched in the testis, 11 and 14 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were mapped to the M_III vs. M_IV group and the M_IV vs. M_V group, respectively. DEGs in ovarian development were also classified into 10 groups according to their biological functions. The expression patterns of the selected genes determined by qPCR were significantly correlated with the RNA-Seq results, supporting the reliability and accuracy of the RNA-Seq analysis. E2 levels showed down regulation from previtellogenesis to mature stage in female and T level showed down regulation from spermatogenesis to regressed stage in the male.

CONCLUSIONS

The categories "intercellular interaction and cytoskeleton", "molecule amplification" and "repair in the cell cycle" were revealed to be crucial in testis development and spermatogenesis, as was the biosynthesis of a series of metabolites. Our results provide comprehensive insight into black rockfish gonadal development and provide a basis for further study of reproductive physiology and molecular biology in ovoviviparity teleosts.

Advances in Reproductive Endocrinology and Neuroendocrine Research Using Catfish Models

Catfishes, belonging to the order siluriformes, represent one of the largest groups of freshwater fishes with more than 4000 species and almost 12% of teleostean population. Due to their worldwide distribution and diversity, catfishes are interesting models for ecologists and evolutionary biologists. Incidentally, catfish emerged as an excellent animal model for aquaculture research because of economic importance, availability, disease resistance, adaptability to artificial spawning, handling, culture, high fecundity, hatchability, hypoxia tolerance and their ability to acclimate to laboratory conditions. Reproductive system in catfish is orchestrated by complex network of nervous, endocrine system and environmental factors during gonadal growth as well as recrudescence. Lot of new information on the molecular mechanism of gonadal development have been obtained over several decades which are evident from significant number of scientific publications pertaining to reproductive biology and neuroendocrine research in catfish. This review aims to synthesize key findings and compile highly relevant aspects on how catfish can offer insight into fundamental mechanisms of all the areas of reproduction and its neuroendocrine regulation, from gametogenesis to spawning including seasonal reproductive cycle. In addition, the state-of-knowledge surrounding gonadal development and neuroendocrine control of gonadal sex differentiation in catfish are comprehensively summarized in comparison with other fish models.

De Novo Transcriptomic Characterization Enables Novel Microsatellite Identification and Marker Development in Betta splendens

The wild populations of the commercially valuable ornamental fish species, Betta splendens, and its germplasm resources have long been threatened by habitat degradation and contamination with artificially bred fish. Because of the lack of effective marker resources, population genetics research projects are severely hampered. To generate genetic data for developing polymorphic simple sequence repeat (SSR) markers and identifying functional genes, transcriptomic analysis was performed. Illumina paired-end sequencing yielded 105,505,486 clean reads, which were then de novo assembled into 69,836 unigenes. Of these, 35,751 were annotated in the non-redundant, EuKaryotic Orthologous Group, Swiss-Prot, Kyoto Encyclopedia of Genes and Genomes and Gene Ontology databases. A total of 12,751 SSR loci were identified from the transcripts and 7970 primer pairs were designed. One hundred primer pairs were randomly selected for PCR validation and 53 successfully generated target amplification products. Further validation demonstrated that 36% (n = 19) of the 53 amplified loci were polymorphic. These data could not only enrich the genetic information for the identification of functional genes but also effectively facilitate the development of SSR markers. Such knowledge would accelerate further studies on the genetic variation and evolution, comparative genomics, linkage mapping and molecular breeding in B. splendens.

Comparison of Gonadal Transcriptomes Uncovers Reproduction-Related Genes with Sexually Dimorphic Expression Patterns in Diodon hystrix

Diodon hystrix is a new and emerging aquaculture species in south China. However, due to the lack of understanding of reproductive regulation, the management of breeding and reproduction under captivity remains a barrier for the commercial aquaculture of D. hystrix. More genetic information is needed to identify genes critical for gonadal development. Here, the first gonadal transcriptomes of D. hystrix were analyzed and 151.89 million clean reads were generated. All reads were assembled into 57,077 unigenes, and 24,574 could be annotated. By comparing the gonad transcriptomes, 11,487 differentially expressed genes were obtained, of which 4599 were upregulated and 6888 were downregulated in the ovaries. Using enrichment analyses, many functional pathways were found to be associated with reproduction regulation. A set of sex-biased genes putatively involved in gonad development and gametogenesis were identified and their sexually dimorphic expression patterns were characterized. The detailed transcriptomic data provide a useful resource for further research on D. hystrix reproductive manipulation.

Differential expression analysis and identification of sex-related genes by gonad transcriptome sequencing in estradiol-treated and non-treated Ussuri catfish Pseudobagrus ussuriensis

The Ussuri catfish (Pseudobagrus ussuriensis) has an XX/XY sex determination system but its sex determination gene(s) remain unknown. To better understand the molecular sex determination mechanism, transcriptome analysis was conducted to obtain sex-related gene expression profiles. Transcriptome analyses were made of male and female developing/differentiating gonads by high-throughput RNA sequencing, including gonads from fish given an estradiol-induced sex reversal treatment. A total of 81,569 unigenes were assembled and 39,904 were significantly matched to known unique proteins by comparison with public databases. Twenty specifically expressed and 142 differentially expressed sex-related genes were extracted from annotated data by comparing the treatment groups. These genes are involved in spermatogenesis (e.g., Dnali1, nectin3, klhl10, mybl1, Katnal1, Eno4, Mns1, Spag6, Tsga10, Septin7), oogenesis (e.g., Lagr5, Fmn2, Npm2, zar1, Fbxo5, Fbxo43, Prdx4, Nrip1, Lfng, Atrip), gonadal development/differentiation (e.g., Cxcr4b, Hmgb2, Cftr, Ch25h, brip1, Prdm9, Tdrd1, Star, dmrt1, Tut4, Hsd17b12a, gdf9, dnd, arf1, Spata22), and estradiol response (e.g., Mmp14, Lhcgr, vtg1, vtg2, esr2b, Piwil1, Aifm1, Hsf1, gdf9). Dmrt1 and gdf9 may play an essential role in sex determination in P. ussuriensis. The expression patterns of six random genes were validated by quantitative real-time PCR, which confirmed the reliability and accuracy of the RNA-seq results. These data provide a valuable resource for future studies of gene expression and for understanding the molecular mechanism of sex determination/differentiation and gonadal development/differentiation (including hormone-induced sexual reversal) in Ussuri catfish. This has the potential to assist in producing monosex Ussuri catfish to increase aquacultural productivity.

Genome-Wide DNA Methylation and Transcriptome Analyses Reveal Epigenetic and Genetic Mechanisms Underlying Sex Maintenance of Adult Chinese Alligator

The sexes of Chinese alligators are determined during embryonic development and remain fixed thereafter. In this study, we investigated the genetic and epigenetic mechanisms underlying sex maintenance in Chinese alligators through RNA sequencing and bisulfite sequencing data analyses of the adult gonads. We identified the genes and pathways (e. g., DMRT1-SOX9-AMH pathway for males and oocyte meiotic maturation pathway for females) involved in male and female sex maintenance and gonadal development of adult Chinese alligators. In contrast to their expression patterns in the embryo, both DMRT1 and the steroid hormone biosynthesis related genes showed a male-biased expression in adult gonads. The overall DNA methylation density and level were higher in testes than in ovaries. Hypermethylation in the gene bodies enhanced the expression of male-biased genes (such as DMRT1-SOX9-AMH and steroid hormone biosynthesis related genes) in the testis, as opposed to the normalization of gene expression. Our results provide insights into the genetic and epigenetic mechanisms underlying sex maintenance in adult Chinese alligators, and are expected to contribute to the development of scientific programs for the successful conservation of this endangered species.

Comparative transcriptome analysis on four types of gonadal tissues of blotched snakehead (Channa maculata)

Blotched snakehead (Channa maculata) is an economically important freshwater fish in China, of which males grow much faster than females. To illuminate the molecular mechanism of sex differentiation and gonad development, RNA-Sequencing was performed to identify sex-related genes and pathway in gonads of 6-month-old normal XX females (XX-F), normal XY males (XY-M), XY sex reversal females (XY-F) and YY super-males (YY-M). The analysis showed that many differentially expressed genes (DEGs) had similar expression patterns in XY-F and XX-F, which were different from XY-M and YY-M. qRT-PCR indicated that Amh, Dmrt1, and Sox9 had relatively high expression in testes of XY-M and YY-M. Taking Amh as an example, there was a relative fold change of 1.0 in XX-F, 2.1 fold change in XY-F, 36.1 fold change in XY-M, and 26.0 fold change in YY-M. Cyp19a1a, Figla, and Foxl2 were highly expressive in ovaries of XX-F and XY-F. Taking Figla as an example, there was a relative fold change of 557 in XX-F, 304.5 fold change in XY-F, 5.6 fold change in XY-M, and 4.4 fold change in YY-M. KEGG analysis revealed many DEGs distributed in pathways related to sex differentiation, steroid hormone synthesis and growth, etc. Significant variation and trends in relative expression levels tested by qRT-PCR were consistent with those recorded by RNA-Sequencing. This is the first time that transcriptome of snakehead has been investigated systematically and in an integrated way. Large quantities of candidate genes involved in sex differentiation, gonad development and growth dimorphism were identified. The study provides useful resources for understanding sex differentiation and growth dimorphism, potentially assisting mono-sex production of snakehead in aquaculture.

Transcriptome analysis of Clarias magur brain and gonads suggests neuro-endocrine inhibition of milt release from captive GnRH-induced males

Transcriptome analysis of Clarias magur brain and gonads at preparatory, mature, 6 and 16 h post-GnRH injection (hpi) stages yielded 9.5 GB data with 39,738 contigs. Sequences of 45 reproductive genes were identified for the first time in C. magur along with unique and differentially expressed genes. The expression of 20 genes was validated by qRT-PCR. Upregulation of Cyp11A1, Cyp17A1 and FTZF1 genes in the 16hpi testis accompanied by the 17β-HSD3 expression indicates testosterone (T) synthesis in response to LH surge, while reduced expression of CYP11B1 suggests a high T: 11-KT ratio. It is evident by the gene expression analysis that the inhibitory neurotransmitter GABA, altered T: 11-KT, increased testicular bile acids, and oxytocin-like neuropeptide in the male brain, appear to be involved in arresting the pulsatile motion of testicular smooth muscles. The work generates important leads for an effective induced breeding strategy for silurid catfish.

De novo transcriptome assembly of four organs of Collichthys lucidus and identification of genes involved in sex determination and reproduction

The spinyhead croaker (Collichthys lucidus) is a commercially important fish species, which is mainly distributed in the coastal regions of China. However, little is known about the molecular regulatory mechanism underlying reproduction in C. lucidus. A de novo transcriptome assembly in brain, liver, ovary and testis tissues of C. lucidus was performed. Illumina sequencing generated 60,322,004, 57,044,284, 60,867,978 and 57,087,688 clean reads from brain, liver, ovary and testis tissues of C. lucidus, respectively. Totally, 131,168 unigenes with an average length of 644 bp and an N50 value of 1033 bp were assembled. In addition, 1288 genes were differentially expressed between ovary and testis, including 442 up-regulated and 846 down-regulated in ovary. Functional analysis revealed that the differentially expressed genes between ovary and testis were mainly involved in the function of sexual reproduction, sex differentiation, development of primary male sexual characteristics, female gamete generation, and male sex differentiation. A number of genes which might be involved in the regulation of reproduction and sex determination were found, including HYAL and SYCP3 and BMP15. Furthermore, 35,476 simple sequence repeats (SSRs) were identified in this transcriptome dataset, which would contribute to further genetic and mechanism researches. De novo transcriptome sequencing analysis of four organs of C. lucidus provides rich resources for understanding the mechanism of reproductive development of C. lucidus and further investigation of the molecular regulation of sex determination and reproduction of C. lucidus.

De novo transcriptome assembly and sex-biased gene expression in the gonads of Amur catfish (Silurus asotus)

Amur catfish is extensively distributed and cultured in Asian countries. Despite of economic importance, the genomic information of this species remains limited. A reference transcriptome of Amur catfish was assembled and the sex-biased gene expression in the gonads was characterized using RNA-sequencing. The assembled transcriptome of Amur catfish consisted of 74,840 transcripts. The N50, mean length and max length of transcripts are 1970, 1235 and 16,748 bp. Putative sex-specific transcripts were identified and sex-specific expression of the representative genes was verified by RT-PCR. Differential expression analysis identified 5401 ovary-biased and 5618 testis-biased genes. The ovary-biased genes were mainly enriched in pathways such as RNA transport and ribosome biogenesis in eukaryotes. The testis-biased genes were enriched in calcium signaling and cytokine-cytokine receptor interaction, etc. Our data provide a valuable genomic resource for further investigating the genetic basis of sex determination, sex differentiation and sexual dimorphism of catfish.

Construction of High-Density Genetic Map and Mapping of Sex-Related Loci in the Yellow Catfish (Pelteobagrus fulvidraco)

The yellow catfish (Pelteobagrus fulvidraco) is a very important aquaculture species distributed in freshwater area of China. All-male yellow catfish is very popular in aquaculture because of their significant sex dimorphism phenomena. The males grow much faster than females in full-sibling family. However, the sex dimorphism mechanism is still unclear in yellow catfish. In order to better understand the genetic basis of yellow catfish sexual dimorphism, it is vital to map the sex-related traits and localize the candidate genes across yellow catfish whole genome. Here, we constructed a high-density linkage map of yellow catfish using genotyping-by-sequencing (GBS) strategy. A total of 5705 single-nucleotide polymorphism (SNP) markers were mapped to 26 different linkage groups (LGs) using 184 F1 offspring. The total genetic map length was 3071.59 cM, with an average interlocus distance of 0.54 cM. Eleven significant sex-related QTLs in yellow catfish were identified. Six sex-related genes were identified from the region of reference genome near these QTLs including amh, gnrhr, vasa, lnnr1, foxl2, and bmp15. The high-density genetic linkage map provides valuable resources for yellow catfish molecular assistant breeding and elucidating sex differentiation process. Moreover, the comparative genomic study was analyzed among yellow catfish, channel catfish, and zebrafish. It revealed highly conserved chromosomal distribution between yellow catfish and channel catfish.

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.

Comparative transcriptome analyses reveal changes of gene expression in fresh and cryopreserved yellow catfish (Pelteobagrus fulvidraco) sperm and the effects of Cryoprotectant Me2SO

This study, for the first time in fish, compared the transcriptome of fresh and frozen-thawed sperm, and would help to better understand the effect of cryopreservation on fish sperm and then better preserve the aquatic germplasm resources. Here, we employed high-throughput sequencing technology to obtain the transcriptome of yellow catfish from fresh sperm, cryopreserved sperm with and without cryoprotectant. When cryoprotectant (Me₂SO) was excluded, down-regulated genes were significantly enriched into calcium ion binding, cytoskeletal protein binding, microfilament motor activity, calmodulin binding and carnitine O-acyltransferase activity, which affected Ca²⁺ regulation, cellular morphology, motility and metabolism. Moreover, heat shock proteins and genes associated with regulation of cholesterol, HCO₃^- and protein tyrosine phosphorylation (PTP) were down-regulated, and thus would impair ability against stress, membrane rigidity, pH regulation and signal transduction of cryopreserved sperm. After Me₂SO was added, the amounts of DEGs decreased significantly and down-regulation of genes were found mainly in cytoskeleton and heat shock proteins, thereby suggesting that Me₂SO effectively reduced the impact caused by low temperature on gene expression. Whether adding Me₂SO or not, the up-regulated genes were mainly found in ribosomal proteins genes. However, when Me₂SO was added, over-expression of some genes might contribute to maintain normal function of cryopreserved sperm.

De novo transcriptome assembly and analysis of differential gene expression following lipopolysaccharide challenge in Pelteobagrus fulvidraco

The yellow catfish, Pelteobagrus fulvidraco, has been recognized as an important freshwater aquaculture species in Eastern and Southeast Asia. To gain a better understanding of the immune response in P. fulvidraco, we analyzed its transcriptome following stimulation with lipopolysaccharide (LPS). Phosphate buffer saline (PBS) was used as control. Following assembly and annotation, 72,152 unigenes with an average length of 1090 bp were identified. A total of 370 differentially expressed genes (DEGs) in the P. fulvidraco were observed at 12 h post LPS treatment, including 197 up-regulated genes and 173 down-regulated genes. Clusters of Orthologous Groups of proteins (KOG/COG) annotation demonstrated that a total of 18,819 unigenes classified into 26 categories. Gene ontology (GO) analysis revealed 20 biological process subcategories, 7 cellular component subcategories and 20 molecular function subcategories. The Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis identified immune responses pathways. Quantitative reverse transcription polymerase chain reaction measured the expression of 18 genes involved in the immune response. CXCL2-like chemokine (CXCL2), goose-type lysozyme (LYZ G), and cathepsin K (CTSK) were significantly up-regulated. This study enriches the P. fulvidraco transcriptome database and provides insight into the immune response of P. fulvidraco against infection.

De novo transcriptome sequencing and analysis of male and female swimming crab (Portunus trituberculatus) reproductive systems during mating embrace (stage II)

Background

The swimming crab Portunus trituberculatus is one of the most commonly farmed crustaceans in China. As one of the most widely known and high-value edible crabs, it crab supports large crab fishery and aquaculture in China. Only large and sexually mature crabs can provide the greatest economic benefits, suggesting the considerable effect of reproductive system development on fishery. Studies are rarely conducted on the molecular regulatory mechanism underlying the development of the reproductive system during the mating embrace stage in this species. In this study, we used high-throughput sequencing to sequence all transcriptomes of the P. trituberculatus reproductive system.

Results

Transcriptome sequencing of the reproductive system produced 81,688,878 raw reads (38,801,152 and 42,887,726 reads from female and male crabs, respectively). Low-quality (quality <20) reads were trimmed and removed, leaving only high-quality reads (37,020,664 and 41,021,030 from female and male crabs, respectively). A total of 126,188 (female) and 164,616 (male) transcripts were then generated by de novo transcriptome assembly using Trinity. Functional annotation of the obtained unigenes revealed that a large number of key genes and some important pathways may participate in cell proliferation and signal transduction. On the basis of our transcriptome analyses and as confirmed by quantitative real-time PCR, a number of genes potentially involved in the regulation of gonadal development and reproduction of P. trituberculatus were identified: ADRA1B, BAP1, ARL3, and TRPA1.

Conclusion

This study is the first to report on the whole reproductive system transcriptome information in stage II of P. trituberculatus gonadal development and provides rich resources for further studies to elucidate the molecular basis of the development of reproductive systems and reproduction in crabs. The current study can be used to further investigate functional genomics in this species.

Electronic supplementary material

The online version of this article (10.1186/s12863-017-0592-5) contains supplementary material, which is available to authorized users.

Potential Contributions of miR-200a/-200b and Their Target Gene-Leptin to the Sexual Size Dimorphism in Yellow Catfish

Sexual size dimorphism is the consequence of differential expression of sex-biased genes related to feeding and growth. Leptin is known to regulate energy balance by regulating food intake. In order to investigate the molecular mechanism of sexual size dimorphism in yellow catfish (Pelteobagrus fulvidraco), the expression of leptin (lep) and its functional receptor (lepr) were detected during larval development. Both lep and lepr have lower expression in males than in females during 1–4 weeks post hatching. 17a-Methyltestosterone (MT) treatment resulted in decreased expression of lep and lepr in both male and female larval fish. Interestingly, the mRNA levels of lep and lepr in juvenile male were significantly decreased compared with juvenile female during short-term fasting periods. Lep was predicted to be a potential target of miR-200a and miR-200b that had an opposite expression pattern to lep in male and female larvas. The results of luciferase reporter assay suggested that lep is a target of miR-200a/-200b. Subsequently, male hormone and fasting treatment have opposite effects on the expression of miR-200a/-200b and lep between males and females. In summary, our results suggest that sexual size dimorphism in fish species is probably caused by the sexually dimorphic expression of leptin, which could be negatively regulated by miR-200a/-200b.

Comparative transcriptome analysis reveals differentially expressed genes associated with sex expression in garden asparagus (Asparagus officinalis)

BACKGROUND

Garden asparagus (Asparagus officinalis) is a highly valuable vegetable crop of commercial and nutritional interest. It is also commonly used to investigate the mechanisms of sex determination and differentiation in plants. However, the sex expression mechanisms in asparagus remain poorly understood.

RESULTS

De novo transcriptome sequencing via Illumina paired-end sequencing revealed more than 26 billion bases of high-quality sequence data from male and female asparagus flower buds. A total of 72,626 unigenes with an average length of 979 bp were assembled. In comparative transcriptome analysis, 4876 differentially expressed genes (DEGs) were identified in the possible sex-determining stage of female and male/supermale flower buds. Of these DEGs, 433, including 285 male/supermale-biased and 149 female-biased genes, were annotated as flower related. Of the male/supermale-biased flower-related genes, 102 were probably involved in anther development. In addition, 43 DEGs implicated in hormone response and biosynthesis putatively associated with sex expression and reproduction were discovered. Moreover, 128 transcription factor (TF)-related genes belonging to various families were found to be differentially expressed, and this finding implied the essential roles of TF in sex determination or differentiation in asparagus. Correlation analysis indicated that miRNA-DEG pairs were also implicated in asparagus sexual development.

CONCLUSIONS

Our study identified a large number of DEGs involved in the sex expression and reproduction of asparagus, including known genes participating in plant reproduction, plant hormone signaling, TF encoding, and genes with unclear functions. We also found that miRNAs might be involved in the sex differentiation process. Our study could provide a valuable basis for further investigations on the regulatory networks of sex determination and differentiation in asparagus and facilitate further genetic and genomic studies on this dioecious species.

De novo sequencing and comparative analysis of testicular transcriptome from different reproductive phases in freshwater spotted snakehead Channa punctatus

The spotted snakehead Channa punctatus is a seasonally breeding teleost widely distributed in the Indian subcontinent and economically important due to high nutritional value. The declining population of C. punctatus prompted us to focus on genetic regulation of its reproduction. The present study carried out de novo testicular transcriptome sequencing during the four reproductive phases and correlated differential expression of transcripts with various testicular events in C. punctatus. The Illumina paired-end sequencing of testicular transcriptome from resting, preparatory, spawning and postspawning phases generated 41.94, 47.51, 61.81 and 44.45 million reads, and 105526, 105169, 122964 and 106544 transcripts, respectively. Transcripts annotated using Rattus norvegicus reference protein sequences and classified under various subcategories of biological process, molecular function and cellular component showed that the majority of the subcategories had highest number of transcripts during spawning phase. In addition, analysis of transcripts exhibiting differential expression during the four phases revealed an appreciable increase in upregulated transcripts of biological processes such as cell proliferation and differentiation, cytoskeleton organization, response to vitamin A, transcription and translation, regulation of angiogenesis and response to hypoxia during spermatogenically active phases. The study also identified significant differential expression of transcripts relevant to spermatogenesis (mgat3, nqo1, hes2, rgs4, cxcl2, alcam, agmat), steroidogenesis (star, tkt, gipc3), cell proliferation (eef1a2, btg3, pif1, myo16, grik3, trim39, plbd1), cytoskeletal organization (espn, wipf3, cd276), sperm development (klhl10, mast1, hspa1a, slc6a1, ros1, foxj1, hipk1), and sperm transport and motility (hint1, muc13). Analysis of functional annotation and differential expression of testicular transcripts depending on reproductive phases of C. punctatus helped in developing a comprehensive understanding on genetic regulation of spermatogenic and steroidogenic events in seasonally breeding teleosts. Our findings provide the basis for future investigation on the precise role of testicular genes in regulation of seasonal reproduction in male teleosts.

De novo transcriptome sequencing and analysis of male, pseudo-male and female yellow perch, Perca flavescens

Transcriptome sequencing could facilitate discovery of sex-biased genes, biological pathways and molecular markers, which could help clarify the molecular mechanism of sex determination and sexual dimorphism, and assist with selective breeding in aquaculture. Yellow perch has unique gonad system and sexual dimorphism and is an alternative model to study mechanism of sex determination, sexual dimorphism and sexual selection. In this study, we performed the de novo assembly of yellow perch gonads and muscle transcriptomes by high throughput Illumina sequencing. A total of 212,180 contigs were obtained, ranging from 127 to 64,876 bp, and N50 of 1,066 bp. The assembly RNA-Seq contigs (≥200bp) were then used for subsequent analyses, including annotation, pathway analysis, and microsatellites discovery. No female- and pseudo-male-biased genes were involved in any pathways while male-biased genes were involved in 29 pathways, and neuroactive ligand receptor interaction and enzyme of trypsin (enzyme code, EC: 3.4.21.4) was highly involved. Pyruvate kinase (enzyme code, EC: 2.7.1.40), which plays important roles in cell proliferation, was highly expressed in muscles. In addition, a total of 183,939 SNPs, 11,286 InDels and 41,479 microsatellites were identified. This study is the first report on transcriptome information in Percids, and provides rich resources for conducting further studies on understanding the molecular basis of sex determinations, sexual dimorphism, and sexual selection in fish, and for population studies and marker-assisted selection in Percids.

Sexually Dimorphic Gene Expression Associated with Growth and Reproduction of Tongue Sole (Cynoglossus semilaevis) Revealed by Brain Transcriptome Analysis

In this study, we performed a comprehensive analysis of the transcriptome of one- and two-year-old male and female brains of Cynoglossus semilaevis by high-throughput Illumina sequencing. A total of 77,066 transcripts, corresponding to 21,475 unigenes, were obtained with a N50 value of 4349 bp. Of these unigenes, 33 genes were found to have significant differential expression and potentially associated with growth, from which 18 genes were down-regulated and 12 genes were up-regulated in two-year-old males, most of these genes had no significant differences in expression among one-year-old males and females and two-year-old females. A similar analysis was conducted to look for genes associated with reproduction; 25 genes were identified, among them, five genes were found to be down regulated and 20 genes up regulated in two-year-old males, again, most of the genes had no significant expression differences among the other three. The performance of up regulated genes in Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis was significantly different between two-year-old males and females. Males had a high gene expression in genetic information processing, while female’s highly expressed genes were mainly enriched on organismal systems. Our work identified a set of sex-biased genes potentially associated with growth and reproduction that might be the candidate factors affecting sexual dimorphism of tongue sole, laying the foundation to understand the complex process of sex determination of this economic valuable species.

The testis and ovary transcriptomes of the rock bream (Oplegnathus fasciatus): A bony fish with a unique neo Y chromosome

The rock bream (Oplegnathus fasciatus) is considerably one of the most economically important marine fish in East Asia and has a unique neo-Y chromosome system that is a good model to study the sex determination and differentiation in fish. In the present study, we used Illumina sequencing technology (HiSeq2000) to sequence, assemble and annotate the transcriptome of the testis and ovary tissues of rock bream. A total of 40,004,378 (NCBI SRA database SRX1406649) and 53,108,992 (NCBI SRA database SRX1406648) high quality reads were obtained from testis and ovary RNA sequencing, respectively, and 60,421 contigs (with average length of 1301 bp) were obtained after de novo assembling with Trinity software. Digital gene expression analysis reveals 14,036 contigs that show gender-enriched expressional profile with either testis-enriched (237 contigs) or ovary-enriched (581 contigs) with RPKM > 100. There are 237 male- and 582 female-abundant expressed genes that show sex dimorphic expression. We hope that the gonad transcriptome and those gender-enriched transcripts of rock bream can provide some insight into the understanding of genome-wide transcriptome profile of teleost gonad tissue and give useful information in fish gonad development.

Transcriptomic Analyses Reveal Novel Genes with Sexually Dimorphic Expression in Yellow Catfish (Pelteobagrus fulvidraco) Brain

Yellow catfish (Pelteobagrus fulvidraco) is a pivotal freshwater aquaculture species in China. It shows sexual size dimorphism favoring male in growth. Whole transcriptome approach is required to get the overview of genetic toolkit for understanding the sex determination mechanism aiming at devising its monosex production. Beside gonads, the brain is also considered as a major organ for vertebrate reproduction. Transcriptomic analyses on the brain and of different developmental stages will provide the dynamic view necessary for better understanding its sex determination. In this regard, we have performed a de novo assembly of yellow catfish brain transcriptome by high throughput Illumina sequencing. A total number of 154,507 contigs were obtained with the lengths ranging from 201 to 27,822 bp and N50 of 2,101 bp, as well as 20,699 unigenes were identified. Of these unigenes, 13 and 54 unigenes were detected to be XY-specifically expressed genes (SEGs) for one and 2-year-old yellow catfish, while the corresponding numbers of XX-SEGs for those two stages were 19 and 13, respectively. Our work identifies a set of annotated genes that are candidate factors affecting sexual dimorphism as well as simple sequence repeat (SSR) and single nucleotide variation (SNV) in yellow catfish. To validate the expression patterns of the sex-related genes, we performed quantitative real-time PCR (qRT-PCR) indicating the reliability and accuracy of our analysis. The results in our study may enhance our understanding of yellow catfish sex determination and potentially help to improve the production of all-male yellow catfish for aquaculture.

Comparative Transcriptome Analysis of Differentially Expressed Genes and Signaling Pathways between XY and YY Testis in Yellow Catfish

YY super-males have rarely been detected in nature and only been artificially created in some fish species including tilapia and yellow catfish (Pelteobagrusfulvidraco), which provides a promising model for testis development and spermatogenesis. In our previous study, significant differences in morphology and miRNA expression were detected between XY and YY testis of yellow catfish. Here, solexa sequencing technology was further performed to compare mRNA expression between XY and YY testis. Compared with unigenes expressed in XY testis, 1146 and 1235 unigenes have significantly higher and lower expression in YY testis, respectively. 605 differentially expressed unigenes were annotated to 1604 GO terms with 319 and 286 genes having relative higher expression in XY and YY testis. KEGG analysis suggested different levels of PI3K-AKT and G protein-coupled receptor (GPCR) signaling pathways between XY and YY testis. Down-regulation of miR-141/429 in YY testis was speculated to promote testis development and maturation, and several factors in PI3K-AKT and GPCR signaling pathways were found as predicted targets of miR-141/429, several of which were confirmed by dual-luciferase reporter assays. Our study provides a comparative transcriptome analysis between XY and YY testis, and reveals interactions between miRNAs and their target genes that are possibly involved in regulating testis development and spermatogenesis.