Transcriptomic analysis of female and male gonads in juvenile snakeskin gourami (Trichopodus pectoralis)

Comparative transcriptome analysis identified genes involved in testicular development in Takifugu rubripes

To identify candidate genes and pathways involved in testicular development in Takifugu rubripes, a comparative transcription analysis was conducted across the various developmental stages of the testis (stages II to V). A total of 9520 differentially expressed genes (DEGs) were identified among the different stages, and they were significantly clustered into six clusters (P < 0.05). One thousand four hundred eleven DEGs such as gndf, wnt1, and cyp17b1 were found to be decreased from stage II to V. In contrast, 994 DEGs such as fn1, ift81, and cdc25a were found to be increased from stage II to V. Six thousand three hundred eighteen DEGs (e.g., dmrt1, sdk2, and chrna1) were identified as being expressed at similar levels at stages II and III. However, they were subsequently found to be decreased from stage III to IV. Four hundred one DEGs exhibited a significant upregulation trend from stage II to III. These genes were expressed at similar levels in stages III, IV, and V, including chrnd, wnt4a, and cyp7a1. The highest expression levels of 200 DEGs (e.g., ccnb2, cdk1, and sycp2) were observed in stage IV, while 196 DEGs (e.g., chmp1b, hsd17b3, and zp3) exhibited the highest expression level in stage III. Those DEGs were mainly enriched in the pathways (e.g., neuroactive ligand-receptor interaction, cell adhesion molecules, and calcium signaling pathways) associated with testicular development. Quantitative polymerase chain reaction of eight randomly selected genes validated the RNA sequencing results. This study may provide new insights into the molecular regulatory mechanisms governing testicular development and spermatogenesis in T. rubripes.

Revisiting the specific and potentially independent role of the gonad in hormone regulation and reproductive behavior

Gonadal sex steroid hormones are well-studied modulators of reproductive physiology and behavior. Recent behavioral endocrinology research has focused on how the brain dynamically responds to - and may even produce - sex steroids, but the gonadal tissues that primarily release these hormones receive much less attention as a potential mediator of behavioral variation. This Commentary revisits mechanisms by which the reproductive hypothalamic-pituitary-gonadal (HPG) axis can be modulated specifically at the gonadal level. These mechanisms include those that may allow the gonad to be regulated independently of the HPG axis, such as receptors for non-HPG hormones, neural inputs and local production of conventional 'neuropeptides'. Here, I highlight studies that examine variation in these gonadal mechanisms in diverse taxa, with an emphasis on recent transcriptomic work. I then outline how future work can establish functional roles of gonadal mechanisms in reproductive behavior and evaluate gonad responsiveness to environmental cues. When integrated with neural mechanisms, further investigation of gonadal hormone regulation can yield new insight into the control and evolution of steroid-mediated traits, including behavior.

Single-nucleus transcriptional and chromatin accessible profiles reveal critical cell types and molecular architecture underlying chicken sex determination

INTRODUCTION

Understanding the sex determination mechanisms in birds has great significance for the biological sciences and production in the poultry industry. Sex determination in chickens is a complex process that involves fate decisions of supporting cells such as granulosa or Sertoli cells. However, a systematic understanding of the genetic regulation and cell commitment process underlying sex determination in chickens is still lacking.

OBJECTIVES

We aimed to dissect the molecular characteristics associated with sex determination in the gonads of chicken embryos.

METHODS

Single-nucleus RNA-seq (snRNA-seq) and ATAC-seq (snATAC-seq) analysis were conducted on the gonads of female and male chickens at embryonic day 3.5 (E3.5), E4.5, and E5.5.

RESULTS

Here, we provided a time-course transcriptional and chromatin accessible profiling of gonads during chicken sex determination at single-cell resolution. We uncovered differences in cell composition and developmental trajectories between female and male gonads and found that the divergence of transcription and accessibility in gonadal cells first emerged at E5.5. Furthermore, we revealed key cell-type-specific transcription factors (TFs) and regulatory networks that drive lineage commitment. Sex determination signaling pathways, dominated by BMP signaling, are preferentially activated in males during gonadal development. Further pseudotime analysis of the supporting cells indicated that granulosa cells were regulated mainly by the TEAD gene family and that Sertoli cells were driven by the DMRT1 regulons. Cross-species analysis suggested high conservation of both cell types and cell-lineage-specific TFs across the six vertebrates.

CONCLUSIONS

Overall, our study will contribute to accelerating the development of sex manipulation technology in the poultry industry and the application of chickens as a unique model for studying cell fate decisions.

Screening of temperature-responsive signalling molecules during sex differentiation in Asian yellow pond turtle (Mauremys mutica)

BACKGROUND

The Asian yellow pond turtle (Mauremys mutica) is an important commercial freshwater aquaculture species in China. This species is a highly sexually dimorphic species, with males growing at a faster rate than females and exhibits temperature-dependent sex determination (TSD), in which the incubation temperature during embryonic development determines the sexual fate. However, the mechanisms of the sex determination or sex differentiation in the Asian yellow pond turtle are remain a mystery.

RESULTS

Temperature-specific gonadal transcriptomics of the Asian yellow pond turtle were performed during the thermosensitive period (stage 15) using RNA-seq technology to identify candidate genes that initiate gonadal differentiation. We uncovered candidates that were the first to respond to temperature. These candidates were sexually dimorphic in expression, reflecting differences in gonadal (Cirbp, Runx1) and germline differentiation (Vasa, Nanos1, Piwil2), gametogenesis (Hmgb3, Zar1, Ovoinhibitor-like, Kif4), steroid hormone biosynthesis (Hsd17b5, Hsd17b6), heat shock (Dnajb6, Hsp90b1, Hsp90aa1) and transient receptor potential channel genes (Trpm1, Trpm4, Trpm6, Trpv1).

CONCLUSIONS

Our work will provide important genetic information to elucidate the mechanisms of sex control in the Asian yellow pond turtles, and will contribute important genetic resources for further studies of temperature-dependent sex determination in turtles.

Epididymal segment-specific miRNA and mRNA regulatory network at the single cell level

Spermatozoa released from the testis cannot fertilize an egg before becoming mature and motile in the epididymis. Based on three bulk and one single-cell RNA-seq (scRNA-seq) data series, we compared mRNA or miRNA expression between epididymal segment-specific samples and the other samples. Hereby, we identified 570 differentially expressed mRNAs (DE-mRNAs) and 23 differentially expressed miRNAs (DE-miRNAs) in the caput, 175 DE-mRNAs and 15 DE-miRNAs in the corpus, 946 DE-mRNAs and 12 DE-miRNAs in the cauda. In accordance with respective DE-miRNAs, we predicted upstream transcription factors (TFs) and downstream target genes. Subsequently, we intersected target genes of respective DE-miRNAs with corresponding DE-mRNAs, thereby obtaining 127 upregulated genes in the caput and 92 upregulated genes in cauda. Enriched upregulated pathways included cell motility-related pathways for the caput, smooth muscle-related pathways for the corpus, and immune-associated pathways for the cauda. Protein-protein interaction (PPI) network was constructed to extract key module for the caput and cauda, followed by identifying hub genes through cytohubba. Epididymis tissues from six mice were applied to validate hub genes expression using qRT-PCR, and 7 of the 10 genes displayed identical expression trends in mice caput/cauda. These hub genes were found to be predominantly distributed in spermatozoa using scRNA-seq data. In addition, target genes of DE-miRNAs were intersected with genes in the PPI network for each segment. Subsequently, the miRNA and mRNA regulatory networks for the caput and cauda were constructed. Conclusively, we uncover segment-specific miRNA-mRNA regulatory network, upstream TFs, and downstream pathways of the human epididymis, warranting further investigation into epididymal segment-specific functions.

Effects of dietary supplementation of estradiol-17β during fry stage on growth, physiological and immune parameters and gonadal gene expression in adult snakeskin gourami

In snakeskin gourami (Trichopodus pectoralis), females are generally larger than males, and estradiol-17β (E2)-sex reversal to produce female monosex has gained interest in this species. In this study, we aimed to investigate the effects of E2-induced sex reversal on growth, physiological and immune parameters, and gonadal gene expression in adult snakeskin gourami. Fry (7 days posthatching) were divided into different experimental groups based on the dose of E2: control (no E2 (0 mg kg-1) supplementation), E2-100 (100 mg kg-1), E2-200 (200 mg kg-1), and E2-300 (300 mg kg-1), fed with the E2 doses for 90 d and cultured for 11 months (adult stage). The findings revealed that E2 supplementation produced 88.89-100% of female population. After 11 months of culture, the effects of sexual dimorphism on the growth performance of the E2-100 group were not significant compared to that on the growth performance of the control male and female groups; however, it improved significantly in the E2-200 and E2-300 groups (P < 0.05). E2 elevated the CP and fat contents in body in E2-200 and E2-300 groups (P < 0.05) compared to that in the control group. No sex differences in blood metabolites, haematological values, or immune parameters were identified. Nevertheless, E2-200 and E2-300 groups showed increased blood glucose, triglyceride, haemoglobin, and total immunoglobulin (P < 0.05) compared to control male fish. In addition, all concentrations of E2 increased alternative complement 50 (P < 0.05). Several genes, including bHLH, cyp19a1, daz, deadend, esrb, esrrg, gnrhr, gpa, gsg1l, hsd17β, mospd1, nanos2, p53, piwi2, rerg, rps6ka, tgfb, and vgr, showed differential expression between testis and ovary in control female and E2-treated groups. The expression patterns of the genes were similar in the ovary of the control female and E2-200-treated fish. In conclusion, the findings demonstrate that a feminisation duration of 7-97 days and two doses of E2 at 200 or 300 mg kg-1 successfully produced all-female stocks in snakeskin gourami. Furthermore, the findings showed that E2-treated females were maintained throughout adulthood and exhibited several superior characteristics to male fish. Together with the information generated on differentially expressed sex-related genes, these findings could enable the culturing of faster-growing sex to increase productivity and contribute to the development of intensive snakeskin gourami farming.

High production of transfer RNAs identifies the presence of developing oocytes in ovaries and intersex testes of teleost fish

5S rRNA is highly transcribed in fish oocytes and this transcription levels can be used to identify the presence of oocytes in the intersex testes of fish exposed to xenoestrogens. Similar to 5S rRNA, tRNAs are transcribed by RNA polymerase III (Pol-III) in eukaryotes, so this study focuses in the analysis of the levels of expression of tRNAs in the gonads (ovaries and testes) of eight teleost species as a possible new oocyte molecular marker. Total RNA extracted from gonads of six commercial teleost species in the Biscay Bay, from the pollution sentinel species thicklip grey mullet (Chelon labrosus) known present intersex testes in response to xenoestrogens in Gernika estuary and from the laboratory model species Danio rerio were analysed through capillary electrophoresis. Bioanalyzer electropherograms were used to quantify the concentrations of tRNAs, 5S and 5.8S rRNA. All studied ovaries expressed significantly higher levels of tRNAs and 5S rRNA than testes. A tRNA to 5.8S rRNA index was calculated which differentiates ovaries from testes, and identifies some intersex testes in between testes and ovaries in mullets. The tRNA/5.8S ratio was highest in ovaries in previtellogenic stage, decreasing towards maturity. Thus, strong oocyte expression of tRNAs is an additional proof of high activity levels of Pol-III during early stages of oocyte development in teleost ovaries. Incidentally, we observed that miRNA concentrations were always higher in testes than ovaries. The indexing approach developed in the present study could have multiple applications in teleost reproduction research and in the development of early molecular markers of intersex condition.

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.

Sex steroid profile during oocyte development and maturation in the intertidal worm Marphysa madrasi (Polychaeta: Eunicidae) from the east coast of India

Marphysa madrasi is a commercially valuable maturation diet in crustacean aquaculture. This study presents the first detailed investigation of oogenesis in the intertidal polychaete worm M. madrasi and reports the steroid profile during oocyte growth and development. Oogenesis is extraovarian type I, originating from coelomic epithelial cells, with four stages of development - primary growth, early vitellogenic, late vitellogenic, and maturation. The primary growth phase contains oogonial cells and previtellogenic oocyte clusters in the early, mid, and late stages of development form a dispersed ovary attached to blood vessels. The late previtellogenic oocytes detach from the ovary at the onset of vitellogenesis. The detached oocytes complete vitellogenesis and final maturation in the coelomic fluid as solitary free-floating cells without any connection with follicle cells. The worms display asynchronous reproduction with a heterogeneous population of developing oocytes. Steroid extracts from the polychaete homogenates in different stages of oogenesis were identified by HPLC and confirmed by LC-MS/MS. In M. madrasi, two vertebrate-type steroids, pregnenolone (P5) and 17α-hydroxyprogesterone (17-OHP) were detected and quantified. The P5 levels were low in immature worms but increased significantly by ∼ 8.3-fold in the previtellogenic stage and peaked during oocyte maturation. 17-OHP levels were low in immature worms but gradually increase as the oogenesis progress to the primary growth and early vitellogenic phase, with a significant increase (p < 0.001) during the late vitellogenic phase. Although an increase in the concentration of P5 and 17-OHP during vitellogenesis and maturation of oocytes points to a possible role in reproduction, the absence of other vertebrate-type steroids in the investigated polychaete signifies a plausible uptake of P5 and 17-OHP from the environment.

The Role of Transposable Elements in Sexual Development

Up to 50% of most mammalian genomes are made up of transposable elements (TEs) that have the potential to mobilize around the genome. Despite this prevalence, research on TEs is only beginning to gain traction within the field of neuroscience. While TEs have long been regarded as "junk" or parasitic DNA, it has become evident that they are adaptive DNA and RNA regulatory elements. In addition to their vital role in normal development, TEs can also interact with steroid receptors, which are key elements to sexual development. In this review, we provide an overview of the involvement of TEs in processes related to sexual development- from TE activity in the germline to TE accumulation in sex chromosomes. Moreover, we highlight sex differences in TE activity and their regulation of genes related to sexual development. Finally, we speculate on the epigenetic mechanisms that may govern TEs' role in sexual development. In this context, we emphasize the need to further the understanding of sexual development through the lens of TEs including in a variety of organs at different developmental stages, their molecular networks, and evolution.

Whole-genome sequencing reveals the artificial selection and local environmental adaptability of pigeons (Columba livia)

To meet human needs, domestic pigeons (Columba livia) with various phenotypes have been bred to provide genetic material for our research on artificial selection and local environmental adaptation. Seven pigeon breeds were resequenced and can be divided into commercial varieties (Euro-pigeon, Shiqi, Shen King, Taishen, and Silver King), ornamental varieties (High Fliers), and local varieties (Tarim pigeon). Phylogenetic analysis based on population resequencing showed that one group contained local breeds and ornamental pigeons from China, whereas all commercial varieties were clustered together. It is revealed that the traditional Chinese ornamental pigeon is a branch of Tarim pigeon. Runs of homozygosity (ROH) and linkage disequilibrium (LD) analyses revealed significant differences in the genetic diversity of the three types of pigeons. Genome sweep analysis revealed that the selected genes of commercial breeds were related to body size, reproduction, and plumage color. The genomic imprinting genes left by the ornamental pigeon breeds were mostly related to special human facial features and muscular dystrophy. The Tarim pigeon has evolved genes related to chemical ion transport, photoreceptors, oxidative stress, organ development, and olfaction in order to adapt to local environmental stress. This research provides a molecular basis for pigeon genetic resource evaluation and genetic improvement and suggests that the understanding of adaptive evolution should integrate the effects of various natural environmental characteristics.

The Snakeskin Gourami (Trichopodus pectoralis) Tends to Exhibit XX/XY Sex Determination

The snakeskin gourami (Trichopodus pectoralis) has a high meat yield and is one of the top five aquaculture freshwater fishes in Thailand. The species is not externally sexually dimorphic, and its sex determination system is unknown. Understanding the sex determination system of this species will contribute to its full-scale commercialization. In this study, a cytogenetic analysis did not reveal any between-sex differences in chromosomal patterns. However, we used genotyping-by-sequencing to identify 4 male-linked loci and 1 female-linked locus, indicating that the snakeskin gourami tends to exhibit an XX/XY sex determination system. However, we did not find any male-specific loci after filtering the loci for a ratio of 100:0 ratio of males:females. This suggests that the putative Y chromosome is young and that the sex determination region is cryptic. This approach provides solid information that can help identify the sex determination mechanism and potential sex determination regions in the snakeskin gourami, allowing further investigation of genetic improvements in the species.

SPATS1 (spermatogenesis-associated, serine-rich 1) is not essential for spermatogenesis and fertility in mouse

SPATS1 (spermatogenesis-associated, serine-rich 1) is an evolutionarily conserved, testis-specific protein that is differentially expressed during rat male meiotic prophase. Some reports have suggested a link between SPATS1 underexpression/mutation and human pathologies such as male infertility and testicular cancer. Given the absence of functional studies, we generated a Spats1 loss-of-function mouse model using CRISPR/Cas9 technology. The phenotypic analysis showed no overt phenotype in Spats1^-/- mice, with both males and females being fertile. Flow cytometry and histological analyses did not show differences in the testicular content and histology between WT and knockout mice. Moreover, no significant differences in sperm concentration, motility, and morphology, were observed between WT and KO mice. These results were obtained both for young adults and for aged animals. Besides, although an involvement of SPATS1 in the Wnt signaling pathway has been suggested, we did not detect changes in the expression levels of typical Wnt pathway-target genes in mutant individuals. Thus, albeit Spats1 alteration might be a risk factor for male testicular health, we hereby show that this gene is not individually essential for male fertility and spermatogenesis in mouse.