Plasticity of gene-regulatory networks controlling sex determination: of masters, slaves, usual suspects, newcomers, and usurpators

AMHY and sex determination in egg-laying mammals

BACKGROUND

Egg-laying mammals (monotremes) evolved multiple sex chromosomes independently of therian mammals and lack the sex-determining gene SRY. The Y-localized anti-Müllerian hormone gene (AMHY) is the candidate sex-determination gene in monotremes. Here, we describe the evolution of monotreme AMHX and AMHY gametologues and for the first time, investigate their expression during gonad sexual differentiation in a monotreme.

RESULTS

Monotreme AMHX and AMHY have significant sequence divergence at the promoter, gene, and protein level, likely following an original allele inversion in the early stages of monotreme sex chromosome differentiation but retaining the conserved features of TGF-β molecules. We show that the expression of sexual differentiation genes in the echidna fetal gonad, including DMRT1 and SOX9, is significantly different from that of therian mammals. Importantly, AMHY is expressed exclusively in the male gonad during sexual differentiation consistent with a role as the primary sex-determination gene whereas AMHX is expressed in both sexes. Experimental ectopic expression of platypus AMHX or AMHY in the chicken embryo did not masculinize the female urogenital system, as does chicken AMH, a possible result of mammalian-specific changes to AMH proteins preventing function in the chicken.

CONCLUSIONS

Our results provide insight into the early steps of monotreme sex chromosome evolution and sex determination with developmental expression data strongly supporting AMHY as the primary male sex-determination gene of platypus and echidna.

Mosquito sex determination: recent advances and applications

Mosquitoes have evolved divergent sex-determining chromosomes and they employ diverse primary signals for sex-determination. As only females feed on vertebrate blood, manipulating genes involved in sex determination can facilitate genetic control measures for mosquito-borne infectious diseases such as dengue and malaria. We highlight new advances in mosquito sex determination, describe innovative applications, and discuss relevant evolutionary insights and future directions.

In-depth investigation of genome to refine QTL positions for spontaneous sex-reversal in XX rainbow trout

Sex determination is a flexible process in fish, controlled by genetics or environmental factors or a combination of both depending on the species. Revealing the underlying molecular mechanisms may have important implications for research on reproductive development in vertebrates, as well as sex-ratio control and selective breeding in fish. Phenotypic sex in rainbow trout (Oncorhynchus mykiss) is primarily controlled by a XX/XY male heterogametic sex determination system. Unexpectedly in genetically XX all-female farmed populations, a small proportion of males or intersex individuals are regularly observed. Spontaneous masculinisation is a highly heritable trait, controlled by minor sex-modifier genes that remain unknown, although several Quantitative Trait Loci (QTL) were detected in previous studies. In the current work we used genome-based approaches and various statistical methods to further investigate these QTL. DNA markers that were previously identified in a French commercial population on chromosomes Omy1, Omy12 and Omy20 were validated in six different farmed trout populations. Functional candidate genes that may be involved in spontaneous masculinisation by reducing germ cell proliferation and repressing oogenesis of XX-rainbow trout in the absence of the master sex determining gene were identified. In particular, syndig1, tlx1 and hells on Omy1, as well as khdrbs2 and csmd1 on Omy20 deserve further investigation to validate their potential sex-modifier roles as well as their interaction with rearing temperature. Those findings could be used to produce all-female populations that are preferred by farmers due to a delayed maturation of females and higher susceptibility of male trout to diseases.

Allelic variation and duplication of the dmrt1 were associated with sex chromosome turnover in three representative Scatophagidae fish species

Fish species of the family Scatophagidae possessing known candidate sex-determining genes (male-specific dmrt1Ys), offer suitable models for studying sex chromosome evolution. Here, we analyzed sex chromosome turnover events in three representative fish species of the family Scatophagidae, belonging to the genera Scatophagus and Selenotoca, which diverged 12.8 million years ago (Mya). Prior to the divergence of Sc. argus and Sc. tetracanthus 7.2 Mya, their dmrt1Y was differentiated from its locus, the truncated dmrt1ΔX, through allelic variation. The Y chromosome (Chr1) of Sc. tetracanthus is the result of the fusion of the original Y chromosome (Chr4) with an autosome (Chr13). The Se. multifasciata dmrt1Y arose from a duplication of dmrt1 on Chr4 and then translocated to the new Y chromosome (Chr18). The divergent evolutionary trajectories of the dmrt1Ys were accompanied by sex chromosome turnover in these three species. The sex chromosomes of the Scatophagidae family have evolved rapidly, albeit not randomly.

The Cause-Effect Model of Master Sex Determination Gene Acquisition and the Evolution of Sex Chromosomes

The canonical model of vertebrate sex chromosome evolution predicts a one-way trend toward degradation. However, most sex chromosomes in lower vertebrates are homomorphic. Recent progress in studies of sex determination has resulted in the discovery of more than 30 master sex determination (MSD) genes, most of which are from teleost fish. An analysis of MSD gene acquisition, recombination suppression, and sex chromosome-specific sequences revealed correlations in the modes of MSD gene acquisition and the evolution of sex chromosomes. Sex chromosomes remain homomorphic with MSD genes acquired by simple mutations, gene duplications, allelic variations, or neofunctionalization; in contrast, they become heteromorphic with MSD genes acquired by chromosomal inversion, fusion, and fission. There is no recombination suppression with sex chromosomes carrying MSD genes gained through simple mutations. In contrast, there is extensive recombination suppression with sex chromosomes carrying MSD genes gained through chromosome inversion. There is limited recombination suppression with sex chromosomes carrying MSD genes gained through transposition or translocation. We propose a cause-effect model that predicts sex chromosome evolution as a consequence of the acquisition modes of MSD genes, which explains the evolution of sex chromosomes in various vertebrates. A key factor determining the trend of sex chromosome evolution is whether non-homologous regions are created during the acquisition of MSD genes. Chromosome inversion creates inversely homologous but directly non-homologous sequences, which lead to recombination suppression but retain recombination potential. Over time, recurrent recombination in the inverted regions leads to the formation of strata and may cause the degradation of sex chromosomes. Depending on the nature of deletions in the inverted regions, sex chromosomes may evolve with dosage compensation, or the selective retention of haplo-insufficient genes may be used as an alternative strategy.

Disrupting Amh and androgen signaling reveals their distinct roles in zebrafish gonadal differentiation and gametogenesis

Sex determination and differentiation in zebrafish involve a complex interaction of male and female-promoting factors. While Dmrt1 has been established as a critical male-promoting factor, the roles of Anti-Müllerian hormone (Amh) and androgen signaling remain less clear. This study employed an estrogen-deficient zebrafish model (cyp19a1a-/-) to dissect individual and combined roles of Amh and androgen receptor (Ar) signaling in gonadal differentiation and gametogenesis. Loss of amh, but not ar, could rescue all-male phenotype of cyp19a1a-/-, leading to female or intersex, confirming the role of Amh in promoting male differentiation. This rescue was recapitulated in bmpr2a-/- but not bmpr2b-/-, supporting Bmpr2a as the type II receptor for Amh in zebrafish. Interestingly, while disruption of amh or ar had delayed spermatogenesis, the double mutant (amh-/-;ar-/-) exhibited severely impaired spermatogenesis, highlighting their compensatory roles. While Amh deficiency led to testis hypertrophy, likely involving a compensatory increase in Ar signaling, Ar deficiency resulted in reduced hypertrophy in double mutant males. Furthermore, phenotype analysis of triple mutant (amh-/-;ar-/-;cyp19a1a-/-) provided evidence that Ar participated in early follicle development. This study provides novel insights into complex interplay between Amh and androgen signaling in zebrafish sex differentiation and gametogenesis, highlighting their distinct but cooperative roles in male development.

The origin, evolution, and translocation of sex chromosomes in Silurus catfish mediated by transposons

BACKGROUND

Sex chromosome (SC) evolution is a longstanding topic of focus in evolutionary biology. Teleosts often exhibit rapid turnover of SCs and sex-determining (SD) genes, alongside a diverse range of SC differentiation mechanisms.

RESULTS

On the basis of new chromosome-scale assemblies of three Silurus species (S. microdorsalis, S. glanis, and S. lanzhouensis) and two outgroup species (Pterocryptis cochinchinensis and Kryptopterus bicirrhis), along with our previous assemblies of S. meridionalis and S. asotus, we traced the evolution of SC in the Silurus genus (Siluriformes), following the fate of the known SD gene amhr2y. Phylogenetic analysis showed that amhr2y occurred at least before the divergence of Pterocryptis, Kryptopterus, and Silurus and lost in P. cochinchinensis and K. bicirrhis. Chr24 has become the SC in the ancestor of five Silurus species due to the duplication-and-translocation of amhr2 mediated by LTR transposon. Then, a proto Y was formed and maintained with a shared 60 kb male-specific region of the Y chromosome (MSY) by transposable elements (TEs) expansion and gene gathering. Due to the continuous TEs accumulation, genes other than amhr2y in MSYs have degenerated or been lost, while non-recombinant regions continue to expend, forming MSYs of different sizes in different Silurus species (from 320 to 550 kb). Two turnover events, one homologous (from the left arm to the right arm of Chr24) and one nonhomologous (from Chr24 to Chr5), occurring among five Silurus species were possibly mediated by hAT and Helitron transposons.

CONCLUSIONS

Our results on the dynamic evolutionary trajectory of SD gene amhr2y, MSYs, and SCs in Silurus catfish indicated the variability and diversity of fish SCs and confirmed that frequent turnover is an important way to maintain the homology and low differentiation of fish SCs.

Identification and functional analysis of sex-determining genes in the spongy moth, Lymantria dispar (lepidoptera: Erebidae)

The spongy moth (Lymantria dispar) employs a female heterogametic sex-determination system, where the female sex-determining factor (F factor) is located on the W chromosome, and the male sex-determining factor (M factor) is located on the Z chromosome. The sex-determining capabilities of the F factor and M factor vary among subspecies. Consequently, L. dispar serves as an excellent model for studying the mechanisms underlying the evolution and diversity of sex-determining genes. However, the genes encoding the F and M factors, as well as the molecular functions of their translation products, remain unidentified. In this study, we identified a L. dispar Masculinizer ortholog (LdMasc) and found that this gene is highly expressed in male embryos during the sex-determination stage. When LdMasc expression was silenced using embryonic RNA interference (RNAi), the expression pattern of L. dispar doublesex (Lddsx), the master regulatory gene for sex differentiation, shifted from the male-specific form to the female-specific form in male embryos. To identify potential F factors, we screened for genes that were exclusively expressed in females across multiple tissues and located only within the female genome. This screening yielded four unigenes with sequences displaying high homology to each other. These unigenes formed a tandem repeat, comprising approximately 100 copies within a 200 kbp region of the W chromosome-derived contig. We designated these unigenes as Fet-W (female-specifically expressed transcript from the W chromosome). RT-PCR analysis revealed that Fet-W was expressed in a female-specific manner during the sex-determination stage. Suppression of Fet-W expression by embryonic RNAi led to an increase in LdMasc expression in females and a corresponding shift in dsx expression patterns from the female-specific to the male-specific form. These findings strongly suggest that the F factor in L. dispar is Fet-W, whereas the M factor is LdMasc.

Reference genome provide insights into sex determination of silver aworana (Osteoglossum bicirrhosum)

BACKGROUND

Silver arowana (Osteoglossum bicirrhosum) is a basal fish species with sexual monomorphism, while its sex determination mechanism has been poorly understood, posing a significant challenge to its captive breeding efforts.

RESULTS

We constructed two high-quality chromosome-level genome assemblies for both female and male silver arowana, with scaffold N50 values over 10 Mb. Combining re-sequencing data of 109 individuals, we identified a female-specific region, which was localized in a non-coding region, i.e., around 26-kb upstream of foxl2 gene (encoding forkhead box L2). Its strong interaction with the neighboring foxl2 on the same chromosome suggests foxl2 as a candidate sex-related gene in silver arowana. We subsequently propose a complex gene network in the sex determination process of silver arowana, with foxl2 acting as the central contributor. Transcriptome sequencing of gonads support our hypothesis that the regulation of foxl2 can be influenced by the spatial proximity of the female-specific fragment, thereby promoting ovarian function or inhibiting testicular function to stimulate gonadal differentiation. Furthermore, we found the sex chromosomes to be homomorphic with a potentially recent origin, as a linkage disequilibrium analysis proved minor recombination suppression.

CONCLUSIONS

These results taken together serve as a crucial foundation for conducting extensive investigations on the evolution and differentiation of sex-determining mechanisms, as well as the emergence and development of sex chromosomes in various fishes.

The master male sex determinant Gdf6Y of the turquoise killifish arose through allelic neofunctionalization

Although sex determination is a fundamental process in vertebrate development, it is very plastic. Diverse genes became major sex determinants in teleost fishes. Deciphering how individual sex-determining genes orchestrate sex determination can reveal new actors in sexual development. Here, we demonstrate that the Y-chromosomal copy of the TGF-β family member gdf6 (gdf6Y) in Nothobranchius furzeri, an emerging model organism in aging research, gained the function of the male sex determinant through allelic diversification while retaining the skeletal developmental function shared with the X-chromosomal gdf6 allele (gdf6X). Concerning sex determination, gdf6Y is expressed by somatic supporting cells of the developing testes. There it induces the male sex in a germ cell-independent manner in contrast to sex determination in zebrafish and the medaka. Looking for downstream effectors of Gdf6Y, we identified besides TGF-β signaling modulators, especially the inhibitor of DNA binding genes id1/2/3, the mRNA decay activator zfp36l2 as a new GDF6 signaling target.

Evolution and regulation of animal sex chromosomes

Animal sex chromosomes typically carry the upstream sex-determining gene that triggers testis or ovary development and, in some species, are regulated by global dosage compensation in response to functional decay of the Y chromosome. Despite the importance of these pathways, they exhibit striking differences across species, raising fundamental questions regarding the mechanisms underlying their evolutionary turnover. Recent studies of non-model organisms, including insects, reptiles and teleosts, have yielded a broad view of the diversity of sex chromosomes that challenges established theories. Moreover, continued studies in model organisms with recently developed technologies have characterized the dynamics of sex determination and dosage compensation in three-dimensional nuclear space and at single-cell resolution. Here, we synthesize recent insights into sex chromosomes from a variety of species to review their evolutionary dynamics with respect to the canonical model, as well as their diverse mechanisms of regulation.

Yes, polygenic sex determination is a thing!

The process of sexual development in animals is modulated by a variety of mechanisms. Some species respond to environmental cues, while, in others, sex determination is thought to be controlled by a single 'master regulator' gene. However, many animals respond to a combination of environmental cues (e.g., temperature) and genetic factors (e.g., sex chromosomes). Even among species in which genetic factors predominate, there is a continuum between monofactorial and polygenic systems. The perception that polygenic systems are rare may result from experiments that lack the statistical power to detect multiple loci. Intellectual biases against the existence of polygenic sex determination (PSD) may further arise from misconceptions about the regulation of developmental processes and a misreading of theoretical results on the stability of polygenic systems of sex determination.

Hydin as the Candidate Master Sex Determination Gene in Channel Catfish (Ictalurus punctatus) and Its Epigenetic Regulation

Sex determination is a fascinating area of research. To date, more than 20 master sex determination (SD) genes have been reported from vertebrate animals. With channel catfish (Ictalurus punctatus), much work has been conducted to determine its master SD gene, ranging from genetic linkage mapping, genome-wide association (GWA) analysis, genome sequencing, comparative genome analysis, epigenomic analysis, transcriptome analysis, and functional studies. Here in this mini review, we provide positional, expression, regulatory, and functional evidence supporting hydin (hydrocephalus-inducing protein or HYDIN axonemal central pair apparatus protein-like) as a master SD gene in channel catfish. Hydin is located within the sex determination region (SDR) within a mapped 8.9-Mb non-recombinational segment on chromosome 4 of channel catfish. It is highly expressed in genetic males, but not in genetic females. The alleles of X and Y are highly differentially methylated with the X chromosome being hypermethylated and the Y chromosome hypomethylated. The hypomethylated Y allele of hydin is expressed while the hypermethylated X allele is not expressed. Such allelic expression fits well with the XY sex determination system of channel catfish. Functional analysis using a methylation blocker, 5-aza-dC, demonstrated that demethylation, especially within the SDR, is accompanied with increased expression of hydin, which led to sex reversal of genetic females into phenotypic males. These evidences support the candidacy of hydin as a master SD gene in channel catfish. Future knockout and analysis of affected genes after hydin knockout should provide insights into how hydin functions as a master SD gene.

Acquisition of polymorphism in the chordate doliolids

In polymorphic organisms, a single genome is deployed to program numerous, morphologically distinct body plans within a colony. This complex life history trait has evolved independently within a limited subset of animal taxa. Reconstructing the underlying genetic, cellular, and developmental changes that drove the emergence of polymorphic colonies represents a promising avenue for exploring diversifying selection and resulting impacts on developmental gene regulatory networks. Doliolids are the only polymorphic chordate, deploying a single genome to program distinct morphs specialized for locomotion, feeding, asexual, or sexual reproduction. In this review, we provide a detailed summary of doliolid anatomy, development, taxonomy, ecology, life history, and the cellular basis for doliolid polymorphism. In order to frame the potential evolutionary and developmental insights that could be gained by studying doliolids, we provide a broader overview of polymorphism. We then discuss how comparative studies of polymorphic cnidarians have begun to illuminate the genetic basis of this unusual and complex life history strategy. We then provide a summary of life history divergence in the chordates, particularly among doliolids and their polymorphic cousins, the salps and pyrosomes.

Thermal modulation of energy allocation during sex determination in the European sea bass (Dicentrarchus labrax)

Water temperature governs physiological functions such as growth, energy allocation, and sex determination in ectothermic species. The European sea bass (Dicentrarchus labrax) is a major species in European aquaculture, exhibiting early dimorphic growth favoring females. The species has a polygenic sex determination system that interacts with water temperature to determine an individual's sex, with two periods during development that are sensitive to temperature. The current study investigated the influence of water temperature on energy allocation and sex-biased genes during sex determination and differentiation periods. RNA-Sequencing and qPCR analyses were conducted in two separate experiments, of either constant water temperatures typical of aquaculture conditions or natural seasonal thermal regimes, respectively. We focused on eight key genes associated with energy allocation, growth regulation, and sex determination and differentiation. In Experiment 1, cold and warm temperature treatments favored female and male proportions, respectively. The RNA-seq analysis highlighted sex-dependent energy allocation transcripts, with higher levels of nucb1 and pomc1 in future females, and increased levels of egfra and spry1 in future males. In Experiment 2, a warm thermal regime favored females, while a cold regime favored males. qPCR analysis in Experiment 2 revealed that ghrelin and nucb1 were down-regulated by warm temperatures. A significant sex-temperature interaction was observed for pank1a with higher and lower expression for males in the cold and warm regimes respectively, compared to females. Notably, spry1 displayed increased expression in future males at the all-fins stage and in males undergoing molecular sex differentiation in both experimental conditions, indicating that it provides a novel, robust, and consistent marker for masculinization. Overall, our findings emphasize the complex interplay of genes involved in feeding, energy allocation, growth, and sex determination in response to temperature variations in the European sea bass.

Transitions in sex determination mechanisms through parental and sexual antagonism

Sex chromosomes carry the sex-determining locus, causing them to be differently transmitted to and from females and males. These differences lead them to be selected upon in different ways, and hence they are predicted to become enriched for sexually- and parentally-antagonistic genes. Sexually-antagonistic genes have opposing fitness effects in females versus in males; parentally-antagonistic genes have opposing fitness effects when inherited maternally versus paternally. Sexually-antagonistic selection can drive sex determination transitions, whereby an autosome pair becomes a sex chromosome pair in lieu of the ancestral sex chromosomes. Whether parentally-antagonistic selection can similarly drive sex determination transitions remains unknown. I present a model to investigate the potential for transitions in sex determination through parentally-antagonistic selection as compared to sexually-antagonistic selection. This model assumes an ancestral sex-chromosomal sex-determining locus linked to a parentally- or sexually-antagonistic gene, and an autosomal parentally- or sexually-antagonistic gene in whose vicinity a novel sex-determining gene arises. I find that parentally-antagonistic selection can promote the spread of novel sex-determining genes as well as maintain ancestral sex-determining genes when the invasion of the novel sex-determining gene would involve transitions from male to female heterogamety (or vice versa), similar to sexually-antagonistic selection. Transitions between male and female heterogamety are, however, more likely when the ancestral sex-determining locus is linked to a parentally-antagonistic locus. Consequently, parentally-antagonistic selection can enable some highly unusual evolutionary patterns not encountered in other evolutionary models of sex determination. These results provide novel insights into why some sex-determining mechanisms may be so evolutionary labile.

Honeybees' novel complementary sex-determining system: function and origin

Complementary sex determination regulates female and male development in honeybees (Apis mellifera) via heterozygous versus homo-/hemizygous genotypes of the csd (complementary sex determiner) gene involving numerous naturally occurring alleles. This lineage-specific function offers a rare opportunity to understand an undescribed regulatory mechanism and the molecular evolutionary path leading to this mechanism. We reviewed recent advances in understanding how Csd recognizes different versus identical protein variants, how these variants regulate downstream pathways and sexual differentiation, and how this mechanism has evolved and been shaped by evolutionary forces. Finally, we highlighted the shared regulatory principles of sex determination despite the diversity of primary signals and demonstrated that lineage-specific mutations are very informative for characterizing newly evolved functions.

Chamaeleo calyptratus (veiled chameleon) chromosome-scale genome assembly and annotation provides insights into the evolution of reptiles and developmental mechanisms

The family Chamaeleonidae comprises 228 species, boasting an extensive geographic spread and an array of evolutionary novelties and adaptations, but a paucity of genetic and molecular analyses. Veiled chameleon (Chamaeleo calyptratus) has emerged as a tractable research organism for the study of squamate early development and evolution. Here we report a chromosomal-level assembly and annotation of the veiled chameleon genome. We note a remarkable chromosomal conservation across squamates, but comparisons to more distant genomes reveal GC peaks correlating with ancestral chromosome fusion events. We subsequently identified the XX/XY region on chromosome 5, confirming environmental-independent sex determination in veiled chameleons. Furthermore, our analysis of the Hox gene family indicates that veiled chameleons possess the most complete set of 41 Hox genes, retained from an amniote ancestor. Lastly, the veiled chameleon genome has retained both ancestral paralogs of the Nodal gene, but is missing Dand5 and several other genes, recently associated with the loss of motile cilia during the establishment of left-right patterning. Thus, a complete veiled chameleon genome provides opportunities for novel insights into the evolution of reptilian genomes and the molecular mechanisms driving phenotypic variation and ecological adaptation.

Hybridization between Aedes aegypti and Aedes mascarensis mosquitoes leads to disruption of male sex determination

Understanding the sex determination pathway and its disruptions in mosquitoes is critical for the effective control of disease vectors through genetic manipulations based on sex separation. When male hybrids of Aedes aegypti females and Ae. mascarensis males are backcrossed to Ae. aegypti females, a portion of the backcross progeny manifests as males with abnormal sexual differentiation. We discovered a significant correlation between pupal abnormalities and the feminization of subsequent adults exemplified by the relative abundance of ovarian and testicular tissues. All intersex individuals were genetic males as they expressed a male determining factor, Nix. Further, our analysis of the sex-specific splicing of doublesex and fruitless transcripts demonstrated the presence of both male and female splice variants indicating that sex determination is disrupted. A comparative transcriptomic analysis revealed similar expression levels of most female-associated genes in reproductive organs and carcasses between intersexual males and normal females. Moreover, intersexes had largely normal gene expression in testes but significant gene downregulation in male accessory glands when compared with normal males. We conclude that evolving hybrid incompatibilities between Ae. aegypti and Ae. mascarensis involve disruption of sex determination and are accompanied by changes in gene expression associated with sexual differentiation.

A candidate sex determination locus in amphibians which evolved by structural variation between X- and Y-chromosomes

Most vertebrates develop distinct females and males, where sex is determined by repeatedly evolved environmental or genetic triggers. Undifferentiated sex chromosomes and large genomes have caused major knowledge gaps in amphibians. Only a single master sex-determining gene, the dmrt1-paralogue (dm-w) of female-heterogametic clawed frogs (Xenopus; ZW♀/ZZ♂), is known across >8740 species of amphibians. In this study, by combining chromosome-scale female and male genomes of a non-model amphibian, the European green toad, Bufo(tes) viridis, with ddRAD- and whole genome pool-sequencing, we reveal a candidate master locus, governing a male-heterogametic system (XX♀/XY♂). Targeted sequencing across multiple taxa uncovered structural X/Y-variation in the 5'-regulatory region of the gene bod1l, where a Y-specific non-coding RNA (ncRNA-Y), only expressed in males, suggests that this locus initiates sex-specific differentiation. Developmental transcriptomes and RNA in-situ hybridization show timely and spatially relevant sex-specific ncRNA-Y and bod1l-gene expression in primordial gonads. This coincided with differential H3K4me-methylation in pre-granulosa/pre-Sertoli cells, pointing to a specific mechanism of amphibian sex determination.

Genetics of flight in spongy moths (Lymantria dispar ssp.): functionally integrated profiling of a complex invasive trait

BACKGROUND

Flight can drastically enhance dispersal capacity and is a key trait defining the potential of exotic insect species to spread and invade new habitats. The phytophagous European spongy moths (ESM, Lymantria dispar dispar) and Asian spongy moths (ASM; a multi-species group represented here by L. d. asiatica and L. d. japonica), are globally invasive species that vary in adult female flight capability-female ASM are typically flight capable, whereas female ESM are typically flightless. Genetic markers of flight capability would supply a powerful tool for flight profiling of these species at any intercepted life stage. To assess the functional complexity of spongy moth flight and to identify potential markers of flight capability, we used multiple genetic approaches aimed at capturing complementary signals of putative flight-relevant genetic divergence between ESM and ASM: reduced representation genome-wide association studies, whole genome sequence comparisons, and developmental transcriptomics. We then judged the candidacy of flight-associated genes through functional analyses aimed at addressing the proximate demands of flight and salient features of the ecological context of spongy moth flight evolution.

RESULTS

Candidate gene sets were typically non-overlapping across different genetic approaches, with only nine gene annotations shared between any pair of approaches. We detected an array of flight-relevant functional themes across gene sets that collectively suggest divergence in flight capability between European and Asian spongy moth lineages has coincided with evolutionary differentiation in multiple aspects of flight development, execution, and surrounding life history. Overall, our results indicate that spongy moth flight evolution has shaped or been influenced by a large and functionally broad network of traits.

CONCLUSIONS

Our study identified a suite of flight-associated genes in spongy moths suited to exploration of the genetic architecture and evolution of flight, or validation for flight profiling purposes. This work illustrates how complementary genetic approaches combined with phenotypically targeted functional analyses can help to characterize genetically complex traits.

Repeated co-option of HMG-box genes for sex determination in brown algae and animals

In many eukaryotes, genetic sex determination is not governed by XX/XY or ZW/ZZ systems but by a specialized region on the poorly studied U (female) or V (male) sex chromosomes. Previous studies have hinted at the existence of a dominant male-sex factor on the V chromosome in brown algae, a group of multicellular eukaryotes distantly related to animals and plants. The nature of this factor has remained elusive. Here, we demonstrate that an HMG-box gene acts as the male-determining factor in brown algae, mirroring the role HMG-box genes play in sex determination in animals. Over a billion-year evolutionary timeline, these lineages have independently co-opted the HMG box for male determination, representing a paradigm for evolution's ability to recurrently use the same genetic "toolkit" to accomplish similar tasks.

Direct male development in chromosomally ZZ zebrafish

The genetics of sex determination varies across taxa, sometimes even within a species. Major domesticated strains of zebrafish (Danio rerio), including AB and TU, lack a strong genetic sex determining locus, but strains more recently derived from nature, like Nadia (NA), possess a ZZ male/ZW female chromosomal sex-determination system. AB fish pass through a juvenile ovary stage, forming oocytes that survive in fish that become females but die in fish that become males. To understand mechanisms of gonad development in NA zebrafish, we studied histology and single cell transcriptomics in developing ZZ and ZW fish. ZW fish developed oocytes by 22 days post-fertilization (dpf) but ZZ fish directly formed testes, avoiding a juvenile ovary phase. Gonads of some ZW and WW fish, however, developed oocytes that died as the gonad became a testis, mimicking AB fish, suggesting that the gynogenetically derived AB strain is chromosomally WW. Single-cell RNA-seq of 19dpf gonads showed similar cell types in ZZ and ZW fish, including germ cells, precursors of gonadal support cells, steroidogenic cells, interstitial/stromal cells, and immune cells, consistent with a bipotential juvenile gonad. In contrast, scRNA-seq of 30dpf gonads revealed that cells in ZZ gonads had transcriptomes characteristic of testicular Sertoli, Leydig, and germ cells while ZW gonads had granulosa cells, theca cells, and developing oocytes. Hematopoietic and vascular cells were similar in both sex genotypes. These results show that juvenile NA zebrafish initially develop a bipotential gonad; that a factor on the NA W chromosome, or fewer than two Z chromosomes, is essential to initiate oocyte development; and without the W factor, or with two Z doses, NA gonads develop directly into testes without passing through the juvenile ovary stage. Sex determination in AB and TU strains mimics NA ZW and WW zebrafish, suggesting loss of the Z chromosome during domestication. Genetic analysis of the NA strain will facilitate our understanding of the evolution of sex determination mechanisms.

Dmrt1 is the only male pathway gene tested indispensable for sex determination and functional testis development in tilapia

Sex is determined by multiple factors derived from somatic and germ cells in vertebrates. We have identified amhy, dmrt1, gsdf as male and foxl2, foxl3, cyp19a1a as female sex determination pathway genes in Nile tilapia. However, the relationship among these genes is largely unclear. Here, we found that the gonads of dmrt1;cyp19a1a double mutants developed as ovaries or underdeveloped testes with no germ cells irrespective of their genetic sex. In addition, the gonads of dmrt1;cyp19a1a;cyp19a1b triple mutants still developed as ovaries. The gonads of foxl3;cyp19a1a double mutants developed as testes, while the gonads of dmrt1;cyp19a1a;foxl3 triple mutants eventually developed as ovaries. In contrast, the gonads of amhy;cyp19a1a, gsdf;cyp19a1a, amhy;foxl2, gsdf;foxl2 double and amhy;cyp19a1a;cyp19a1b, gsdf;cyp19a1a;cyp19a1b triple mutants developed as testes with spermatogenesis via up-regulation of dmrt1 in both somatic and germ cells. The gonads of amhy;foxl3 and gsdf;foxl3 double mutants developed as ovaries but with germ cells in spermatogenesis due to up-regulation of dmrt1. Taking the respective ovary and underdeveloped testis of dmrt1;foxl3 and dmrt1;foxl2 double mutants reported previously into consideration, we demonstrated that once dmrt1 mutated, the gonad could not be rescued to functional testis by mutating any female pathway gene. The sex reversal caused by mutation of male pathway genes other than dmrt1, including its upstream amhy and downstream gsdf, could be rescued by mutating female pathway gene. Overall, our data suggested that dmrt1 is the only male pathway gene tested indispensable for sex determination and functional testis development in tilapia.

It's a trap?! Escape from an ancient, ancestral sex chromosome system and implication of Foxl2 as the putative primary sex-determining gene in a lizard (Anguimorpha; Shinisauridae)

Although sex determination is ubiquitous in vertebrates, mechanisms of sex determination vary from environmentally to genetically influenced. In vertebrates, genetic sex determination is typically accomplished with sex chromosomes. Groups like mammals maintain conserved sex chromosome systems, while sex chromosomes in most vertebrate clades are not conserved across similar evolutionary timescales. One group inferred to have an evolutionarily stable mode of sex determination is Anguimorpha, a clade of charismatic taxa including monitor lizards, Gila monsters, and crocodile lizards. The common ancestor of extant anguimorphs possessed a ZW system that has been retained across the clade. However, the sex chromosome system in the endangered, monotypic family of crocodile lizards (Shinisauridae) has remained elusive. Here, we analyze genomic data to demonstrate that Shinisaurus has replaced the ancestral anguimorph ZW system on LG7 with a novel ZW system on LG3. The linkage group, LG3, corresponds to chromosome 9 in chicken, and this is the first documented use of this syntenic block as a sex chromosome in amniotes. Additionally, this ~1 Mb region harbors approximately 10 genes, including a duplication of the sex-determining transcription factor, Foxl2, critical for the determination and maintenance of sexual differentiation in vertebrates, and thus a putative primary sex-determining gene for Shinisaurus.

Extraordinary variability in gene activation and repression programs during gonadal sex differentiation across vertebrates

Genes involved in gonadal sex differentiation have been traditionally thought to be fairly conserved across vertebrates, but this has been lately questioned. Here, we performed the first comparative analysis of gonadal transcriptomes across vertebrates, from fish to mammals. Our results unambiguously show an extraordinary overall variability in gene activation and repression programs without a phylogenetic pattern. During sex differentiation, genes such as dmrt1, sox9, amh, cyp19a and foxl2 were consistently either male- or female-enriched across species while many genes with the greatest expression change within each sex were not. We also found that downregulation in the opposite sex, which had only been quantified in the mouse model, was also prominent in the rest of vertebrates. Finally, we report 16 novel conserved markers (e.g., fshr and dazl) and 11 signaling pathways. We propose viewing vertebrate gonadal sex differentiation as a hierarchical network, with conserved hub genes such as sox9 and amh alongside less connected and less conserved nodes. This proposed framework implies that evolutionary pressures may impact genes based on their level of connectivity.

On the Origin and Evolution of the Mosquito Male-determining Factor Nix

The mosquito family Culicidae is divided into 2 subfamilies named the Culicinae and Anophelinae. Nix, the dominant male-determining factor, has only been found in the culicines Aedes aegypti and Aedes albopictus, 2 important arboviral vectors that belong to the subgenus Stegomyia. Here we performed sex-specific whole-genome sequencing and RNAseq of divergent mosquito species and explored additional male-inclusive datasets to investigate the distribution of Nix. Except for the Culex genus, Nix homologs were found in all species surveyed from the Culicinae subfamily, including 12 additional species from 3 highly divergent tribes comprising 4 genera, suggesting Nix originated at least 133 to 165 million years ago (MYA). Heterologous expression of 1 of 3 divergent Nix open reading frames (ORFs) in Ae. aegypti resulted in partial masculinization of genetic females as evidenced by morphology and doublesex splicing. Phylogenetic analysis suggests Nix is related to femaleless (fle), a recently described intermediate sex-determining factor found exclusively in anopheline mosquitoes. Nix from all species has a conserved structure, including 3 RNA-recognition motifs (RRMs), as does fle. However, Nix has evolved at a much faster rate than fle. The RRM3 of both Nix and fle are distantly related to the single RRM of a widely distributed and conserved splicing factor transformer-2 (tra2). The RRM3-based phylogenetic analysis suggests this domain in Nix and fle may have evolved from tra2 or a tra2-related gene in a common ancestor of mosquitoes. Our results provide insights into the evolution of sex determination in mosquitoes and will inform broad applications of mosquito-control strategies based on manipulating sex ratios toward nonbiting males.

Direct Male Development in Chromosomally ZZ Zebrafish

The genetics of sex determination varies across taxa, sometimes even within a species. Major domesticated strains of zebrafish ( Danio rerio ), including AB and TU, lack a strong genetic sex determining locus, but strains more recently derived from nature, like Nadia (NA), possess a ZZ male/ZW female chromosomal sex-determination system. AB strain fish pass through a juvenile ovary stage, forming oocytes that survive in fish that become females but die in fish that become males. To understand mechanisms of gonad development in NA zebrafish, we studied histology and single cell transcriptomics in developing ZZ and ZW fish. ZW fish developed oocytes by 22 days post-fertilization (dpf) but ZZ fish directly formed testes, avoiding a juvenile ovary phase. Gonads of some ZW and WW fish, however, developed oocytes that died as the gonad became a testis, mimicking AB fish, suggesting that the gynogenetically derived AB strain is chromosomally WW. Single-cell RNA-seq of 19dpf gonads showed similar cell types in ZZ and ZW fish, including germ cells, precursors of gonadal support cells, steroidogenic cells, interstitial/stromal cells, and immune cells, consistent with a bipotential juvenile gonad. In contrast, scRNA-seq of 30dpf gonads revealed that cells in ZZ gonads had transcriptomes characteristic of testicular Sertoli, Leydig, and germ cells while ZW gonads had granulosa cells, theca cells, and developing oocytes. Hematopoietic and vascular cells were similar in both sex genotypes. These results show that juvenile NA zebrafish initially develop a bipotential gonad; that a factor on the NA W chromosome or fewer than two Z chromosomes is essential to initiate oocyte development; and without the W factor or with two Z doses, NA gonads develop directly into testes without passing through the juvenile ovary stage. Sex determination in AB and TU strains mimics NA ZW and WW zebrafish, suggesting loss of the Z chromosome during domestication. Genetic analysis of the NA strain will facilitate our understanding of the evolution of sex determination mechanisms.

Genetic evidence for differential functions of figla and nobox in zebrafish ovarian differentiation and folliculogenesis

FIGLA and NOBOX are important oocyte-specific transcription factors. Both figla-/- and nobox-/- mutants showed all-male phenotype in zebrafish due to increased dominance of the male-promoting pathway. The early diversion towards males in these mutants has precluded analysis of their roles in folliculogenesis. In this study, we attenuated the male-promoting pathway by deleting dmrt1, a key male-promoting gene, in figla-/- and nobox-/- fish, which allows a sufficient display of defects in folliculogenesis. Germ cells in figla-/-;dmrt1-/- double mutant remained in cysts without forming follicles. In contrast, follicles could form well but exhibited deficient growth in nobox-/-;dmrt1-/- double mutants. Follicles in nobox-/-;dmrt1-/- ovary could progress to previtellogenic (PV) stage but failed to enter vitellogenic growth. Such arrest at PV stage suggested a possible deficiency in estrogen signaling. This was supported by lines of evidence in nobox-/-;dmrt1-/-, including reduced expression of ovarian aromatase (cyp19a1a) and level of serum estradiol (E2), regressed genital papilla (female secondary sex characteristics), and more importantly the resumption of vitellogenic growth by E2 treatment. Expression analysis suggested Nobox might regulate cyp19a1a by controlling Gdf9 and/or Bmp15. Our discoveries indicate that Figla is essential for ovarian differentiation and follicle formation whereas Nobox is important for driving subsequent follicle development.

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

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

It's a Trap?! Escape from an ancient, ancestral sex chromosome system and implication of Foxl2 as the putative primary sex determining gene in a lizard (Anguimorpha; Shinisauridae)

Although sex determination is ubiquitous in vertebrates, mechanisms of sex determination vary from environmentally- to genetically-influenced. In vertebrates, genetic sex determination is typically accomplished with sex chromosomes. Groups like mammals maintain conserved sex chromosome systems, while sex chromosomes in most vertebrate clades aren't conserved across similar evolutionary timescales. One group inferred to have an evolutionarily stable mode of sex determination is Anguimorpha, a clade of charismatic taxa including: monitor lizards, Gila monsters, and crocodile lizards. The common ancestor of extant anguimorphs possessed a ZW system that has been retained across the clade. However, the sex chromosome system in the endangered, monotypic family of crocodile lizards (Shinisauridae) has remained elusive. Here, we analyze genomic data to demonstrate that Shinisaurus has replaced the ancestral anguimorph ZW system on LG7 chromosome with a novel ZW system on LG3. The linkage group LG3 corresponds to chromosome 9 in chicken, and this is the first documented use of this syntenic block as a sex chromosome in amniotes. Additionally, this ~1Mb region harbors approximately 10 genes, including a duplication of the sex-determining transcription factor, Foxl2-critical for the determination and maintenance of sexual differentiation in vertebrates, and thus a putative primary sex determining gene for Shinisaurus.

Recognition of polymorphic Csd proteins determines sex in the honeybee

Sex in honeybees, Apis mellifera, is genetically determined by heterozygous versus homo/hemizygous genotypes involving numerous alleles at the single complementary sex determination locus. The molecular mechanism of sex determination is however unknown because there are more than 4950 known possible allele combinations, but only two sexes in the species. We show how protein variants expressed from complementary sex determiner (csd) gene determine sex. In females, the amino acid differences between Csd variants at the potential-specifying domain (PSD) direct the selection of a conserved coiled-coil domain for binding and protein complexation. This recognition mechanism activates Csd proteins and, thus, the female pathway. In males, the absence of polymorphisms establishes other binding elements at PSD for binding and complexation of identical Csd proteins. This second recognition mechanism inactivates Csd proteins and commits male development via default pathway. Our results demonstrate that the recognition of different versus identical variants of a single protein is a mechanism to determine sex.

The use of in silico extreme pathway (ExPa) analysis to identify conserved reproductive transcriptional-regulatory networks in humans, mice, and zebrafish

Vertebrate sex determination and differentiation are coordinated by the activations and maintenance of reproductive transcriptional-regulatory networks (TRNs). There is considerable interest in studying the conserved design principles and functions of reproductive TRNs given that their intricate regulation is susceptible to disruption by gene mutations or exposures to exogenous endocrine disrupting chemicals (or EDCs). In this manuscript, the Boolean rules describing reproductive TRNs in humans, mice, and zebrafish, were represented as a pseudo-stoichiometric matrix model. This model mathematically described the interactions of 35 transcription factors with 21 sex determination and differentiation genes across the three species. The in silico approach of Extreme Pathway (ExPa) analysis was used to predict the extent of TRN gene activations subject to the species-specific transcriptomics data, from across various developmental life-stages. A goal of this work was to identify conserved and functional reproductive TRNs across the three species. ExPa analyses predicted the sex differentiation genes, DHH, DMRT1, and AR, to be highly active in male humans, mice, and zebrafish. Whereas FOXL2 was the most active gene in female humans and mice; and CYP19A1A in female zebrafish. These results agree with the expectation that regardless of a lack of sex determination genes in zebrafish, the TRNs responsible for canalizing male vs. female sexual differentiation are conserved with mammalian taxa. ExPa analysis therefore provides a framework with which to study the TRNs that influence the development of sexual phenotypes. And the in silico predicted conservation of sex differentiation TRNs between mammals and zebrafish identifies the piscine species as an effective in vivo model to study mammalian reproductive systems under normal or perturbed pathologies.

Sex blind: bridging the gap between drug exposure and sex-related gene expression in Danio rerio using next-generation sequencing (NGS) data and a literature review to find the missing links in pharmaceutical and environmental toxicology studies

The sex of both humans and Danio rerio has previously been shown to affect the way individuals respond to drug exposure. Genes which allow identification of sex in juvenile zebrafish show potential to reveal these confounding variables between sex in toxicological and preclinical trials but the link between these is so far missing. These sex-specific, early expressed genes where expression is not altered by drug exposure must be carefully selected for this purpose. We aimed to discover genes which can be used in pharmaceutical trials and environmental toxicology studies to uncover sex-related variations in gene expression with drug application using the model organism Danio rerio. Previously published early sex determining genes from King et al. were evaluated as well as additional genes selected from our zebrafish Next-generation sequencing (NGS) data which are known from previously published works not to be susceptible to changes in expression with drug exposure. NGS revealed a further ten female-specific genes (vtg1, cyp17a1, cyp19a1a, igf3, ftz-f1, gdf9, foxl2a, Nr0b1, ipo4, lhcgr) and five male related candidate genes (FKBP5, apobb1, hbaa1, dmrt1, spata6) which are also expressed in juvenile zebrafish, 28 days post fertilisation (dpf). Following this, a literature review was performed to classify which of these early-expressed sex specific genes are already known to be affected by drug exposure in order to determine candidate genes to be used in pharmaceutical trials or environmental toxicology testing studies. Discovery of these early sex-determining genes in Danio rerio will allow identification of sex-related responses to drug testing to improve sex-specific healthcare and the medical treatment of human patients.

Transformer gene regulates feminization under two complementary sex determination loci in the ant, Vollenhovia emeryi

Organisms that reproduce sexually have evolved well-organized mechanisms to determine two sexes. Some hymenopterans (such as ants, bees, and wasps) have a complementary sex-determination system in which heterozygosity at one CSD locus induces female development, whereas hemi- or homozygosity at the locus induces male development. This system can generate a high cost of inbreeding, as individuals that are homozygous at the locus become sterile, diploid males. On the other hand, some hymenopterans have evolved a multi-locus, complementary, sex-determination system in which heterozygosity in at least one CSD locus induces female development. This system effectively reduces the proportion of sterile diploid males; however, how these multiple
primary signals based on CSD pass through a molecular cascade to regulate downstream genes has remained unclear. To clarify this matter, we used a backcross to investigate the molecular cascade in the ant, Vollenhovia emeryi, with two CSD loci. Here we show by gene disruption that transformer (tra) is necessary for proper feminization. Expression analysis of tra and doublesex (dsx) showed that heterozygosity in at least one of the two CSD loci is sufficient to promote female sex determination. Analysis of overexpression suggested that female-type Tra protein promotes splicing of tra pre-mRNA to female isoform by a positive-regulatory-feedback loop. Our data also showed that tra affects splicing of dsx. We conclude that two-loci sex determination system in V. emeryi evolved based on tra-dsx splicing cascade that is well conserved in other insect species. Finally, we suggest a cascade model to arrive at a binary determination of sex under multiple primary signals.

CRISPR Cas9 mediated knockout of sex determination pathway genes in Aedes aegypti

The vector role of Aedes aegypti for viral diseases including dengue and dengue hemorrhagic fever makes it imperative for its proper control. Despite various adopted control strategies, genetic control measures have been recently focused against this vector. CRISPR Cas9 system is a recent and most efficient gene editing tool to target the sex determination pathway genes in Ae. aegypti. In the present study, CRISPR Cas9 system was used to knockout Ae. aegypti doublesex (Aaedsx) and Ae. aegypti sexlethal (AaeSxl) genes in Ae. aegypti embryos. The injection mixes with Cas9 protein (333 ng ul^-1) and gRNAs (each at 100 ng ul^-1) were injected into eggs. Injected eggs were allowed to hatch at 26 ± 1°C, 60 ± 10% RH. The survival and mortality rate was recorded in knockout Aaedsx and AaeSxl. The results revealed that knockout produced low survival and high mortality. A significant percentage of eggs (38.33%) did not hatch as compared to control groups (P value 0.00). Highest larval mortality (11.66%) was found in the knockout of Aaedsx female isoform, whereas, the emergence of only male adults also showed that the knockout of Aaedsx (female isoform) does not produce male lethality. The survival (3.33%) of knockout for AaeSxl eggs to the normal adults suggested further study to investigate AaeSxl as an efficient upstream of Aaedsx to target for sex transformation in Ae. aegypti mosquitoes.

Development of Ovaries and Sex Change in Fish: Bringing Potential into Action

BACKGROUND

Encompassing about half of the 60,000 species of vertebrates, fish display the greatest diversity of sex determination mechanisms among metazoans. As such that phylum offers a unique playground to study the impressive variety of gonadal morphogenetic strategies, ranging from gonochorism, with either genetic or environmental sex determination, to unisexuality, with either simultaneous or consecutive hermaphroditism.

SUMMARY

From the two main types of gonads, the ovaries embrace the important role to produce the larger and non-motile gametes, which is the basis for the development of a future organism. The production of the egg cells is complex and involves the formation of follicular cells, which are necessary for the maturation of the oocytes and the production of feminine hormones. In this vein, our review focuses on the development of ovaries in fish with special emphasis on the germ cells, including those that transition from one sex to the other as part of their life cycle and those that are capable of transitioning to the opposite sex depending on environmental cues.

KEY MESSAGES

Clearly, establishing an individual as either a female or a male is not accomplished by the sole development of two types of gonads. In most cases, that dichotomy, be it final or transient, is accompanied by coordinated transformations across the entire organism, leading to changes in the physiological sex as a whole. These coordinated transformations require both molecular and neuroendocrine networks, but also anatomical and behavioural adjustments. Remarkably, fish managed to tame the ins and outs of sex reversal mechanisms to take the most advantages of changing sex as adaptive strategies in some situations.

Identification of sex-specific splicing via comparative transcriptome analysis of gonads from sea cucumber Apostichopus japonicus

Alternative splicing (AS) is an essential post-transcriptional regulation mechanism for sex differentiation and gonadal development, which has rarely been reported in marine invertebrates. Sea cucumber (Apostichopus japonicus) is an economically important marine benthic echinoderm with a potential XX/XY sex determination mechanism, whose molecular mechanism in the gonadal differentiation has not been clearly understood. In this study, we analyzed available RNA-seq datasets of male and female gonads to explore if AS mechanism exerts an essential function in sex differentiation and gonadal development of A. japonicus. In our results, a total of 20,338 AS events from 7219 alternatively spliced genes, and 189 sexually differential alternative splicing (DAS) events from 156 genes were identified in gonadal transcriptome of sea cucumber. Gene Ontology analysis indicated that these DAS genes were significantly enriched in spermatogenesis-related GO terms. Maximal Clique Centrality (MCC) was then applied for protein-protein interaction (PPI) analysis to search for protein interactions and hub DAS gene. Among all DAS genes, we identified 10 DAS genes closely related to spermatogenesis and (or) sperm motility and a hub gene dnah1. Thus, this study revealed that alternative isoforms were generated from certain genes in female and male gonads through alternative splicing, which may provide direct evidence that alternative splicing mechanisms participate in female and male gonads. These results suggested a novel perspective for explaining the molecular mechanisms underlying gonadal differentiation between male and female sea cucumbers.

Theme and variation in the evolution of insect sex determination

The development of dimorphic adult sexes is a critical process for most animals, one that is subject to intense selection. Work in vertebrate and insect model species has revealed that sex determination mechanisms vary widely among animal groups. However, this variation is not uniform, with a limited number of conserved factors. Therefore, sex determination offers an excellent context to consider themes and variations in gene network evolution. Here we review the literature describing sex determination in diverse insects. We have screened public genomic sequence databases for orthologs and duplicates of 25 genes involved in insect sex determination, identifying patterns of presence and absence. These genes and a 3.5 reference set of 43 others were used to infer phylogenies and compared to accepted organismal relationships to examine patterns of congruence and divergence. The function of candidate genes for roles in sex determination (virilizer, female-lethal-2-d, transformer-2) and sex chromosome dosage compensation (male specific lethal-1, msl-2, msl-3) were tested using RNA interference in the milkweed bug, Oncopeltus fasciatus. None of these candidate genes exhibited conserved roles in these processes. Amidst this variation we wish to highlight the following themes for the evolution of sex determination: (1) Unique features within taxa influence network evolution. (2) Their position in the network influences a component's evolution. Our analyses also suggest an inverse association of protein sequence conservation with functional conservation.

XY sex determination in a cnidarian

BACKGROUND

Sex determination occurs across animal species, but most of our knowledge about its mechanisms comes from only a handful of bilaterian taxa. This limits our ability to infer the evolutionary history of sex determination within animals.

RESULTS

In this study, we generated a linkage map of the genome of the colonial cnidarian Hydractinia symbiolongicarpus and used it to demonstrate that this species has an XX/XY sex determination system. We demonstrate that the X and Y chromosomes have pseudoautosomal and non-recombining regions. We then use the linkage map and a method based on the depth of sequencing coverage to identify genes encoded in the non-recombining region and show that many of them have male gonad-specific expression. In addition, we demonstrate that recombination rates are enhanced in the female genome and that the haploid chromosome number in Hydractinia is n = 15.

CONCLUSIONS

These findings establish Hydractinia as a tractable non-bilaterian model system for the study of sex determination and the evolution of sex chromosomes.

Distinct developmental mechanisms influence sexual dimorphisms in the milkweed bug Oncopeltus fasciatus

Sexual dimorphism is common in animals. The most complete model of sex determination comes from Drosophila melanogaster, where the relative dosage of autosomes and X chromosomes leads indirectly to sex-specific transcripts of doublesex (dsx). Female Dsx interacts with a mediator complex protein encoded by intersex (ix) to activate female development. In males, the transcription factor encoded by fruitless (fru) promotes male-specific behaviour. The genetics of sex determination have been examined in a small number of other insects, yet several questions remain about the plesiomorphic state. Is dsx required for female and male development? Is fru conserved in male behaviour or morphology? Are other components such as ix functionally conserved? To address these questions, we report expression and functional tests of dsx, ix and fru in the hemipteran Oncopeltus fasciatus, characterizing three sexual dimorphisms. dsx prevents ix phenotypes in all sexes and dimorphic traits in the milkweed bug. ix and fru are expressed across the body, in females and males. fru and ix also affect the genitalia of both sexes, but have effects limited to different dimorphic structures in different sexes. These results reveal roles for ix and fru distinct from other insects, and demonstrate distinct development mechanisms in different sexually dimorphic structures.

Three dimensions of thermolabile sex determination

The molecular mechanism of temperature-dependent sex determination (TSD) is a long-standing mystery. How is the thermal signal sensed, captured and transduced to regulate key sex genes? Although there is compelling evidence for pathways via which cells capture the temperature signal, there is no known mechanism by which cells transduce those thermal signals to affect gene expression. Here we propose a novel hypothesis we call 3D-TSD (the three dimensions of thermolabile sex determination). We postulate that the genome has capacity to remodel in response to temperature by changing 3D chromatin conformation, perhaps via temperature-sensitive transcriptional condensates. This could rewire enhancer-promoter interactions to alter the expression of key sex-determining genes. This hypothesis can accommodate monogenic or multigenic thermolabile sex-determining systems, and could be combined with upstream thermal sensing and transduction to the epigenome to commit gonadal fate.

Master-Key Regulators of Sex Determination in Fish and Other Vertebrates-A Review

In vertebrates, mainly single genes with an allele ratio of 1:1 trigger sex-determination (SD), leading to initial equal sex-ratios. Such genes are designated master-key regulators (MKRs) and are frequently associated with DNA structural variations, such as copy-number variation and null-alleles. Most MKR knowledge comes from fish, especially cichlids, which serve as a genetic model for SD. We list 14 MKRs, of which dmrt1 has been identified in taxonomically distant species such as birds and fish. The identification of MKRs with known involvement in SD, such as amh and fshr, indicates that a common network drives SD. We illustrate a network that affects estrogen/androgen equilibrium, suggesting that structural variation may exert over-expression of the gene and thus form an MKR. However, the reason why certain factors constitute MKRs, whereas others do not is unclear. The limited number of conserved MKRs suggests that their heterologous sequences could be used as targets in future searches for MKRs of additional species. Sex-specific mortality, sex reversal, the role of temperature in SD, and multigenic SD are examined, claiming that these phenomena are often consequences of artificial hybridization. We discuss the essentiality of taxonomic authentication of species to validate purebred origin before MKR searches.

Descriptive versus causal morphology: gynandromorphism and intersexuality

In animal species with separate sexes, abnormal individuals with a mix of phenotypically male and phenotypically female body parts are generally indicated as gynandromorphs, whereas individuals with intermediate sexual phenotypic traits are generally indicated as intersexes. However, this distinction, clear as it may seem, is neither universally agreed upon, nor free of critical issues. In consideration of the role of sex anomalies in understanding normal development, we reassess these phenomena of abnormal sexual development, taking into consideration the more recent advances in the study of sex determination and sexual differentiation. We argue that a distinction between gynandromorphism and intersexuality, although useful for descriptive purposes, is not always possible or sensible. We discuss the conceptual and terminological intricacies of the literature on this subject and provide reasons for largely, although not strictly, preferring a terminology based on descriptive rather than causal morphology, that is, on the observed phenotypic patterns rather on the causal process behind them.

Independent Evolution of Sex Chromosomes and Male Pregnancy-Related Genes in Two Seahorse Species

Unlike birds and mammals, many teleosts have homomorphic sex chromosomes, and changes in the chromosome carrying the sex-determining locus, termed "turnovers", are common. Recent turnovers allow studies of several interesting questions. One question is whether the new sex-determining regions evolve to become completely non-recombining, and if so, how and why. Another is whether (as predicted) evolutionary changes that benefit one sex accumulate in the newly sex-linked region. To study these questions, we analyzed the genome sequences of two seahorse species of the Syngnathidae, a fish group in which many species evolved a unique structure, the male brood pouch. We find that both seahorse species have XY sex chromosome systems, but their sex chromosome pairs are not homologs, implying that at least one turnover event has occurred. The Y-linked regions occupy 63.9% and 95.1% of the entire sex chromosome of the two species and do not exhibit extensive sequence divergence with their X-linked homologs. We find evidence for occasional recombination between the extant sex chromosomes that may account for their homomorphism. We argue that these Y-linked regions did not evolve by recombination suppression after the turnover, but by the ancestral nature of the low crossover rates in these chromosome regions. With such an ancestral crossover landscape, a turnover can instantly create an extensive Y-linked region. Finally, we test for adaptive evolution of male pouch-related genes after they became Y-linked in the seahorse.

Loss of growth differentiation factor 9 causes an arrest of early folliculogenesis in zebrafish-A novel insight into its action mechanism

Growth differentiation factor 9 (GDF9) was the first oocyte-specific growth factor identified; however, most information about GDF9 functions comes from studies in the mouse model. In this study, we created a mutant for Gdf9 gene (gdf9-/-) in zebrafish using TALEN approach. The loss of Gdf9 caused a complete arrest of follicle development at primary growth (PG) stage. These follicles eventually degenerated, and all mutant females gradually changed to males through sex reversal, which could be prevented by mutation of the male-promoting gene dmrt1. Interestingly, the phenotypes of gdf9-/- could be rescued by simultaneous mutation of inhibin α (inha-/-) but not estradiol treatment, suggesting a potential role for the activin-inhibin system or its signaling pathway in Gdf9 actions. In gdf9-null follicles, the expression of activin βAa (inhbaa), but not βAb (inhbab) and βB (inhbb), decreased dramatically; however, its expression rebounded in the double mutant (gdf9-/-;inha-/-). These results indicate clearly that the activation of PG follicles to enter the secondary growth (SG) requires intrinsic factors from the oocyte, such as Gdf9, which in turn works on the neighboring follicle cells to trigger follicle activation, probably involving activins. In addition, our data also support the view that estrogens are not involved in follicle activation as recently reported.

Limited evidence of a genetic basis for sex determination in the common creek chub, Semotilus atromaculatus

Sexual reproduction is almost universal in vertebrates; therefore, each animal species which uses it must have a mechanism for designating sex as male or female. Fish, especially, have a wide range of sex determining systems. In the present study, we aimed to identify a genetic basis for sex determination in the common creek chub (Semotilus atromaculatus) using genotyping-by-sequencing data. No sex-associated markers were found by RADSex or a GWAS using GEMMA; however, Weir and Cockerham locus-specific F_ST analysis and discriminant analysis of principal components revealed genetic differentiation between the sexes at several loci. While no explicit sex determination mechanism has been yet discovered in creek chub, these loci are potential candidates for future studies. Incompatible systems are thought to increase reproductive isolation but interspecific hybridization is common among groups such as cyprinid minnows; thus, studies such as ours can provide insight into hybridization and evolutionary diversification of this clade. We also highlight technical challenges involved in studying sex determination in evolutionary groups with extremely variable mechanisms and without heteromorphic sex chromosomes.

Sex Determination and Ovarian Development in Reptiles and Amphibians: From Genetic Pathways to Environmental Influences

BACKGROUND

Reptiles and amphibians provide untapped potential for discovering how a diversity of genetic pathways and environmental conditions are incorporated into developmental processes that can lead to similar functional outcomes. These groups display a multitude of reproductive strategies, and whereas many attributes are conserved within groups and even across vertebrates, several aspects of sexual development show considerable variation.

SUMMARY

In this review, we focus our attention on the development of the reptilian and amphibian ovary. First, we review and describe the events leading to ovarian development, including sex determination and ovarian maturation, through a comparative lens. We then describe how these events are influenced by environmental factors, focusing on temperature and exposure to anthropogenic chemicals. Lastly, we identify critical knowledge gaps and future research directions that will be crucial to moving forward in our understanding of ovarian development and the influences of the environment in reptiles and amphibians.

KEY MESSAGES

Reptiles and amphibians provide excellent models for understanding the diversity of sex determination strategies and reproductive development. However, a greater understanding of the basic biology of these systems is necessary for deciphering the adaptive and potentially disruptive implications of embryo-by-environment interactions in a rapidly changing world.

Molecular Evolution and Inheritance Pattern of Sox Gene Family among Bovidae

Sox genes are an evolutionarily conserved family of transcription factors that play important roles in cellular differentiation and numerous complex developmental processes. In vertebrates, Sox proteins are required for cell fate decisions, morphogenesis, and the control of self-renewal in embryonic and adult stem cells. The Sox gene family has been well-studied in multiple species including humans but there has been scanty or no research into Bovidae. In this study, we conducted a detailed evolutionary analysis of this gene family in Bovidae, including their physicochemical properties, biological functions, and patterns of inheritance. We performed a genome-wide cataloguing procedure to explore the Sox gene family using multiple bioinformatics tools. Our analysis revealed a significant inheritance pattern including conserved motifs that are critical to the ability of Sox proteins to interact with the regulatory regions of target genes and orchestrate multiple developmental and physiological processes. Importantly, we report an important conserved motif, EFDQYL/ELDQYL, found in the SoxE and SoxF groups but not in other Sox groups. Further analysis revealed that this motif sequence accounts for the binding and transactivation potential of Sox proteins. The degree of protein–protein interaction showed significant interactions among Sox genes and related genes implicated in embryonic development and the regulation of cell differentiation. We conclude that the Sox gene family uniquely evolved in Bovidae, with a few exhibiting important motifs that drive several developmental and physiological processes.