Proteome and Transcriptome Analysis of Ovary, Intersex Gonads, and Testis Reveals Potential Key Sex Reversal/Differentiation Genes and Mechanism in Scallop Chlamys nobilis

Proteome analysis provides insights into sex differences in Holothuria Scabra

Sex-determining mechanism is still ambiguous for sea cucumber Holothuria scabra which only manifests gonochorism in gonad. In this study, proteomic analysis was employed to delineate sex-related proteins and genes in gonads of H. scabra, subsequently validated through Quantitative real-time polymerase chain reaction (qRT-PCR). A total of 5,313 proteins were identified via proteome sequencing. Among these, 817 proteins exhibited expression in both the ovary and testis, with 445 proteins displaying up-regulation and 372 proteins showing down-regulation (ovary vs testis). Furthermore, 136 and 69 proteins were identified as ovary-specific and testis-specific Differentially Abundant Proteins (DAPs), respectively. And 9 DAP coding genes which play crucial role in ovary and testis were verified by qRT-PCR. Notably, 24 ovary-bias proteins enriched in ribosome pathway strongly indicated the crucial role of ribosome in ovary. This study serves to furnish novel evidence pertaining to sex differences in H. scabra.

Genome-wide identification and expression analysis of Dmrt gene family and their role in gonad development of Pacific oyster (Crassostrea gigas)

Doublesex and Mab-3-related transcription factor (Dmrt) is a type of transcription factor with a zinc-finger DM structural domain, which plays a significant role in sex determination and differentiation in animals. Although Dmrt has been reported in many vertebrates and invertebrates, it has rarely been studied in bivalves. In this study, a total of three members of the Dmrt gene family were identified and characterized in Crassostrea gigas, and all these CgDmrt genes contained a conserved DM domain. Analysis of the phylogenetic tree and gene structure revealed that Dmrt genes clustered on one branch may have similar functions in bivalves. Expression profiling of CgDmrt mRNA in different tissues and stages of gonad development indicated that CgDmrt3 exhibited sexually dimorphic expression and played an important role in the development of the male gonad in C. gigas. Furthermore, analysis of CgDmrt mRNA expression between fertile triploids and sterile triploids showed that CgDmrt3 may be involved in sperm production. Collectively, the systematic analysis of the CgDmrt genes will provide potential insights into the function of these genes in gonadal development.

Bivalves as Emerging Model Systems to Study the Mechanisms and Evolution of Sex Determination: A Genomic Point of View

Bivalves are a diverse group of molluscs that have recently attained a central role in plenty of biological research fields, thanks to their peculiar life history traits. Here, we propose that bivalves should be considered as emerging model systems also in sex-determination (SD) studies, since they would allow to investigate: 1) the transition between environmental and genetic SD, with respect to different reproductive backgrounds and sexual systems (from species with strict gonochorism to species with various forms of hermaphroditism); 2) the genomic evolution of sex chromosomes (SCs), considering that no heteromorphic SCs are currently known and that homomorphic SCs have been identified only in a few species of scallops; 3) the putative role of mitochondria at some level of the SD signaling pathway, in a mechanism that may resemble the cytoplasmatic male sterility of plants; 4) the evolutionary history of SD-related gene (SRG) families with respect to other animal groups. In particular, we think that this last topic may lay the foundations for expanding our understanding of bivalve SD, as our current knowledge is quite fragmented and limited to a few species. As a matter of fact, tracing the phylogenetic history and diversity of SRG families (such as the Dmrt, Sox, and Fox genes) would allow not only to perform more targeted functional experiments and genomic analyses, but also to foster the possibility of establishing a solid comparative framework.

Tandem Mass Tag-Based Quantitative Proteomics Analysis of Gonads Reveals New Insight into Sexual Reversal Mechanism in Chinese Soft-Shelled Turtles

Chinese soft-shelled turtles display obvious sex dimorphism. The exogenous application of hormones (estradiol and methyltestosterone) can change the direction of gonadal differentiation of P. sinensis to produce sex reversed individuals. However, the molecular mechanism remains unclear. In this study, TMT-based quantitative proteomics analysis of four types of P. sinensis (female, male, pseudo-female, and pseudo-male) gonads were compared. Quantitative analysis of 6107 labeled proteins in the four types of P. sinensis gonads was performed. We identified 440 downregulated and 423 upregulated proteins between pseudo-females and males, as well as 394 downregulated and 959 upregulated proteins between pseudo-males and females. In the two comparisons, the differentially expressed proteins, including K7FKG1, K7GIQ2, COL4A6, K7F2U2, and K7FF80, were enriched in some important pathways, such as focal adhesion, endocytosis, apoptosis, extracellular matrix-receptor interaction, and the regulation of actin cytoskeleton, which were upregulated in pseudo-female vs. male and downregulated in pseudo-male vs. female. In pathways such as ribosome and spliceosome, the levels of RPL28, SRSF3, SNRNP40, and HNRNPK were increased from male to pseudo-female, while they decreased from female to pseudo-male. All differentially expressed proteins after sexual reversal were divided into six clusters, according to their altered levels in the four types of P. sinensis, and associated with cellular processes, such as embryonic development and catabolic process, that were closely related to sexual reversal. These data will provide clues for the sexual reversal mechanism in P. sinensis.

Proteome and Transcriptome Analysis of Gonads Reveals Intersex in Gigantidas haimaensis

Sex has proven to be one of the most intriguing areas of research across evolution, development, and ecology. Intersex or sex change occurs frequently in molluscs. The deep-sea mussel Gigantidas haimaensis often dominates within Haima cold seep ecosystems, but details of their reproduction remain unknown. Herein, we conducted a combined proteomic and transcriptomic analysis of G. haimaensis gonads to provide a systematic understanding of sexual development in deep-sea bivalves. A total of 2,452 out of 42,238 genes (5.81%) and 288 out of 7,089 proteins (4.06%) were significantly differentially expressed between ovaries and testes with a false discovery rate (FDR) <0.05. Candidate genes involved in sexual development were identified; among 12 differentially expressed genes between sexes, four ovary-biased genes (β-catenin, fem-1, forkhead box L2 and membrane progestin receptor α) were expressed significantly higher in males than females. Combining histological characteristics, we speculate that the males maybe intersex undergoing sex change, and implied that these genes may be involved in the process of male testis converting into female gonads in G. haimaensis. The results suggest that this adaptation may be based on local environmental factors, sedentary lifestyles, and patchy distribution, and sex change may facilitate adaptation to a changing environment and expansion of the population. The findings provide a valuable genetic resource to better understand the mechanisms of sex change and survival strategies in deep-sea bivalves.

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.

Identification and Functional Analysis of the Sex-Determiner Transformer-2 Homologue in the Freshwater Pearl Mussel, Hyriopsis cumingii

Transformer-2 (Tra-2) is an upstream regulatory element of the sex regulation mechanism in insects and plays a critical role in sex formation. To understand the role of tra-2 in Hyriopsis cumingii, the full-length Hctra-2 (1867 bp) was obtained from the gonads, and sequence alignment with other species showed that HCTRA-2 protein had a highly conserved RRM domain. Phylogenetic analysis showed that the HCTRA-2 protein was a close relative to of the mollusks TRA-2 protein. The qRT-PCR of tissue-specific expression pattern showed that the Hctra-2 was abundant in gonads, and the expression in testes was higher than that in ovaries (p < 0.01). It suggests that Hctra-2 may play a potential regulatory role in gonadal development of H. cumingii. In the early gonadal development, the Hctra-2 expression was the highest on the third day after fertilization and increased slightly from 4 months to 5 months, which may be related to the embryonic sex determination and early gonadal development. In situ hybridization showed that Hctra-2 mRNA signals were present in both male and female gonads. After silencing Hctra-2 by RNAi, the expression levels of Hcfem-1b and Hcdmrt were changed. It is speculated that there may be a certain relationship between them, which plays an important role in the sex regulation of H. cumingii. Our research will help to deepen our understanding of the shellfish sex determination mechanisms.

Identification and functional analysis of a sex-biased transcriptional factor Foxl2 in the bay scallop Argopecten irradians irradians

Transcription factor Foxl2 is an evolutionarily conserved gene playing pivotal roles in regulation of early ovarian differentiation and maintenance in animals. However, the Foxl2 gene has not been thoroughly studied in hermaphroditic scallops. In this study, we cloned and characterized a Foxl2 (designated as AiFoxl2) from the bay scallop Argopecten irradians irradians. The open reading frame of AiFoxl2 was 1122 bp encoding 373 amino acids residues and contained a conserved forkhead box domain. Quantitative real-time PCR showed that AiFoxl2 was mainly expressed in the ovary. Moreover, the highest expression of AiFoxl2 in the ovary was detected at proliferative stage and growing stage, while the lowest level was found at resting stage. During the embryonic and larval development, expression of AiFoxl2 was found first in fertilized eggs, increased significantly at the blastula stage, and reached peak value at the D-larvae stage. When AiFoxl2 was knocked down, testis development-related genes (Dmrt1, Sox7 and Sox9) were up-regulated significantly while the ovary development-related genes (Vg, HSD14, and GATA-1) were down-regulated manifestly. These findings suggested that AiFoxl2 was a female-related gene in A. i. irradians and may be involved in regulation of ovarian development and differentiation.

Comparative Transcriptomic and Expression Profiles Between the Foot Muscle and Mantle Tissues in the Giant Triton Snail Charonia tritonis

The giant triton snail (Charonia tritonis), an endangered gastropod species of ecological and economic importance, is widely distributed in coral reef ecosystems of the Indo-West Pacific region and the tropical waters of the South China Sea. Limited research on molecular mechanisms can be conducted because the complete genomic information on this species is unavailable. Hence, we performed transcriptome sequencing of the C. tritonis foot muscle and mantle using the Illumina HiSeq sequencing platform. In 109,722 unigenes, we detected 7,994 (3,196 up-regulated and 4,798 down-regulated) differentially expressed genes (DEGs) from the C. tritonis foot muscle and mantle transcriptomes. These DEGs will provide valuable resources to improve the understanding of molecular mechanisms involved in biomineralization of C. tritonis. In the Gene Ontology (GO) database, DEGs were clustered into three main categories (biological processes, molecular functions, and cellular components) and were involved in 50 functional subcategories. The top 20 GO terms in the molecular function category included sulfotransferase activity, transferring sulfur-containing groups, and calcium ion binding, which are terms considered to be related to biomineralization. In KEGG classifications, transcriptomic DEGs were mainly enriched in glycosaminoglycan biosynthesis-chondroitin sulfate/dermatan sulfate, and sulfur metabolism pathway, which may be related to biomineralization. The results of qPCR showed that three of the eight genes examined were significantly up-regulated in the mantle. The phylogenetic tree of BMP1 suggested a significant divergence between homologous genes in C. tritonis. Our results improve the understanding of biomineralization in C. tritonis and provide fundamental transcriptome information to study other molecular mechanisms such as reproduction.

Comparative transcriptome analysis of three gonadal development stages reveals potential genes involved in gametogenesis of the fluted giant clam (Tridacna squamosa)

BACKGROUND

Gonad development and differentiation is an essential function for all sexually reproducing species, and many aspects of these developmental processes are highly conserved among the metazoa. However, the mechanisms underlying gonad development and gametogenesis remain unclear in Tridacna squamosa, a large-size bivalve of great ecological value. They are protandrous simultaneous hermaphrodites, with the male gonad maturing first, eventually followed by the female gonads. In this study, nine gonad libraries representing resting, male and hermaphrodite stages in T. squamosa were performed to identify the molecular mechanisms.

RESULTS

Sixteen thousand four hundred ninety-one unigenes were annotated in the NCBI non-redundant protein database. Among the annotated unigenes, 5091 and 7328 unigenes were assigned to Gene Ontology categories and the Kyoto Encyclopedia of Genes and Genomes (KEGG) Pathway database, respectively. A total of 4763 differentially expressed genes (DEGs) were identified by comparing male to resting gonads, consisting of 3499 which were comparatively upregulated in males and 1264 which were downregulated in males. Six hundred-ninteen DEGs between male and hermaphroditic gonads were identified, with 518 DEGs more strongly expressed in hermaphrodites and 101 more strongly expressed in males. GO (Gene Ontology) and KEGG pathway analyses revealed that various biological functions and processes, including functions related to the endocrine system, oocyte meiosis, carbon metabolism, and the cell cycle, were involved in regulating gonadal development and gametogenesis in T. squamosa. Testis-specific serine/threonine kinases 1 (TSSK1), TSSK4, TSSK5, Doublesex- and mab-3-related transcription factor 1 (DMRT1), SOX, Sperm surface protein 17 (SP17) and other genes were involved in male gonadal development in Tridacna squamosal. Both spermatogenesis- (TSSK4, spermatogenesis-associated protein 17, spermatogenesis-associated protein 8, sperm motility kinase X, SP17) and oogenesis-related genes (zona pellucida protein, Forkhead Box L2, Vitellogenin, Vitellogenin receptor, 5-hydroxytryptamine, 5-hydroxytryptamine receptor) were simultaneously highly expressed in the hermaphroditic gonad to maintain the hermaphroditism of T. squamosa.

CONCLUSION

All these results from our study will facilitate better understanding of the molecular mechanisms underlying giant clam gonad development and gametogenesis, which can provided a base on obtaining excellent gametes during the seed production process for giant clams.

Transcriptome Profiling and Analysis of Genes Associated with High Temperature-Induced Masculinization in Sex-Undifferentiated Nile Tilapia Gonad

Artificially high temperatures during critical thermosensitive periods (TSPs) can induce the sex reversal of Nile tilapia (Oreochromis niloticus) females into pseudomales; Nile tilapia is a GSD + TE (genotypic plus temperature effects) fish species. Previous studies have shown that water temperature affects the expression levels of many genes in the gonad or brain in various teleost species. However, few studies on the effect of temperature at the whole-gonad transcriptomic level in the early stage of sex differentiation have been reported in fish species exhibiting GSD + TE. In this study, RNA-Seq was performed to characterize the transcriptomic profile and identify genes exhibiting temperature- and sex-biased expressions in the Nile tilapia gonad at 21 dpf. A total of 42 genes were found to be associated with both high-temperature treatment and sex development, as the expression levels of these genes differed in both FC (female control) vs MC (male control) and FC vs FT (high temperature-treated females in the TSP). Among these genes, the transcriptional alterations of many male sex determination and differentiation genes, such as Dmrt1, Gsdf, and the DNA damage-inducible protein GADD45 alpha, suggested that the male pathway is initiated after high-temperature treatment and that its initiation may play a role in high temperature-induced masculinization in Nile tilapia. The qRT-PCR validation results for thirteen differentially expressed genes showed that the Pearson's correlation of the log₁₀ fold change values between the qPCR and RNA-Seq results was 0.70 (p < 0.001), indicating the accuracy and reliability of the RNA-Seq results. Our study provides insights into how high-temperature treatment induces the sex reversal of Nile tilapia females.

Genome-Wide Characterization of Alternative Splicing Events and Their Responses to Cold Stress in Tilapia

Alternative splicing (AS) is an important post-transcriptional regulatory mechanism for cells to generate transcript variability and proteome diversity. No systematic investigation of AS events among different tissues in response to stressors is available for tilapia currently. In this study, AS among different tissues was identified and the cold stress-related AS events were explored in a Nile tilapia (Oreochromis niloticus) line based on 42 RNA-seq datasets using a bioinformatics pipeline. 14,796 (82.76%; SD = 2,840) of the expression genes showed AS events. The two most abundant AS types were alternative transcription start site (TSS) and terminal site (TTS) in tilapia. Testis, brain and kidney possess the most abundant AS gene number, while the blood, muscle and liver possess the least number in each tissue. Furthermore, 208 differentially alternative splicing (DAS) genes in heart and 483 DAS in brain in response to cold stress. The number of AS types for alternative exon end, exon skipping and retention of single intron increased significantly under cold stress. GO enrichment and pathway overrepresentation analysis indicated that many DAS genes, e.g., genes in circadian clock pathway, may influence expression of downstream genes under cold stress. Our study revealed that AS exists extensively in tilapia and plays an important role in cold adaption.

Putative Mitochondrial Sex Determination in the Bivalvia: Insights From a Hybrid Transcriptome Assembly in Freshwater Mussels

Bivalves exhibit an astonishing diversity of sexual systems, with genetic and environmental determinants of sex, and possibly the only example of mitochondrial genes influencing sex determination pathways in animals. In contrast to all other animal species in which strict maternal inheritance (SMI) of mitochondria is the rule, bivalves possess a system known as doubly uniparental inheritance (DUI) of mitochondria in which maternal and paternal mitochondria (and their corresponding female-transmitted or F mtDNA and male-transmitted or M mtDNA genomes) are transmitted within a species. Species with DUI also possess sex-associated mtDNA-encoded proteins (in addition to the typical set of 13), which have been hypothesized to play a role in sex determination. In this study, we analyzed the sex-biased transcriptome in gonads of two closely-related freshwater mussel species with different reproductive and mitochondrial transmission modes: the gonochoric, DUI species, Utterbackia peninsularis, and the hermaphroditic, SMI species, Utterbackia imbecillis. Through comparative analysis with other DUI and non-DUI bivalve transcriptomes already available, we identify common male and female-specific genes, as well as SMI and DUI-related genes, that are probably involved in sex determination and mitochondrial inheritance in this animal group. Our results contribute to the understanding of what could be the first animal sex determination system involving the mitochondrial genome.

Transcriptomics analysis revealing candidate genes and networks for sex differentiation of yesso scallop (Patinopecten yessoensis)

Background

The Yesso scallop, Patinopecten (Mizuhopecten) yessoensis, is a commercially important bivalve in the coastal countries of Northeast Asia. It has complex modes of sex differentiation, but knowledge of the mechanisms underlying this sex determination and differentiation is limited.

Results

In this study, the gonad tissues from females and males at three developmental stages were used to investigate candidate genes and networks for sex differentiation via RNA-Req. A total of 901,980,606 high quality clean reads were obtained from 18 libraries, of which 417 expressed male-specific genes and 754 expressed female-specific genes. Totally, 10,074 genes differentially expressed in females and males were identified. Weighted gene co-expression network analysis (WGCNA) revealed that turquoise and green gene modules were significantly positively correlated with male gonads, while coral1 and black modules were significantly associated with female gonads. The most important gene for sex determination and differentiation was Pydmrt 1, which was the only gene discovered that determined the male sex phenotype during early gonadal differentiation. Enrichment analyses of GO terms and KEGG pathways revealed that genes involved in metabolism, genetic and environmental information processes or pathways are sex-biased. Forty-nine genes in the five modules involved in sex differentiation or determination were identified and selected to construct a gene co-expression network and a hypothesized sex differentiation pathway.

Conclusions

The current study focused on screening genes of sex differentiation in Yesso scallop, highlighting the potential regulatory mechanisms of gonadal development in P. yessoensis. Our data suggested that WCGNA can facilitate identification of key genes for sex differentiation and determination. Using this method, a hypothesized P. yessoensis sex determination and differentiation pathway was constructed. In this pathway, Pydmrt 1 may have a leading function.

Electronic supplementary material

The online version of this article (10.1186/s12864-019-6021-6) contains supplementary material, which is available to authorized users.

Gonadal microRNA Expression Profiles and Their Potential Role in Sex Differentiation and Gonadal Maturation of Mud Crab Scylla paramamosain

Although the sexual dimorphism in terms of gonadal development and gametogenesis of mud crab has been described, the internal regulating mechanism and sex differentiation process remain unclear. A comparative gonadal miRNA transcriptomic study was conducted to identify miRNAs that are differentially expressed between testes and ovaries, and potentially uncover miRNAs that might be involved in sex differentiation and gonadal maturation mechanisms of mud crabs (Scylla paramamosain). A total of 10 known miRNAs and 130 novel miRNAs were identified, among which 54 were differentially expressed. Target gene prediction revealed a significant enrichment in 30 KEGG pathways, including some reproduction-related pathways, e.g. phosphatidylinositol signalling system and inositol phosphate metabolism pathways. Further analysis on six differentially expressed known miRNAs, six differentially expressed novel miRNAs and their reproduction-related putative target genes shows that both miRNAs and putative target genes showed stage-specific expression during gonadal maturation, suggesting their potential regulatory roles in sex differentiation and reproductive development. This study reveals the sex-biased miRNA profile and establishes a solid foundation for understanding the sex differentiation and gonadal maturation mechanisms of S. paramamosain.

De novo assembly, characterization of tissue-specific transcriptomes and identification of immune related genes from the scallop Argopecten purpuratus

The scallop Argopecten purpuratus is one of the most economically important cultured mollusks on the coasts from Chile and Peru but its production has declined, in part, due to the emergence of mass mortality events of unknown origin. Driven by this scenario, increasing progress has been made in recent years in the comprehension of immune response mechanisms in this species. However, it is still not entirely understood how different mucosal interfaces participate and cooperate with the immune competent cells, the hemocytes, in the immune defense. Thus, in this work we aimed to characterize the transcriptome of three tissues with immune relevance from A. purpuratus by next-generation sequencing and de novo transcriptome assembly. For this, 18 cDNA libraries were constructed from digestive gland, gills and hemocytes tissues of scallops from different immune conditions and sequenced by the Illumina HiSeq4000 platform. A total of 967.964.884 raw reads were obtained and 967.432.652 clean reads were generated. The clean reads were de novo assembled into 46.601 high quality contigs and 32.299 (69.31%) contigs were subsequently annotated. In addition, three de novo specific assemblies were performed from clean reads obtained from each tissue cDNA libraries for their comparison. Gene ontology (GO) and KEGG analyses revealed that annotated sequences from digestive gland, gills and hemocytes could be classified into both general and specific subcategory terms and known biological pathways, respectively, according to the tissue nature. Finally, several immune related candidate genes were identified, and the differential expression of tissue-specific genes was established, suggesting they could display specific roles in the host defense. The data presented in this study provide the first insight into the tissue specific transcriptome profiles of A. purpuratus, which should be considered for further research on the interplay between the hemocytes and mucosal immune responses.