Sex determination: why so many ways of doing it?

Effects of maternal smoking on inflammation, autophagy/mitophagy, and miRNAs in endothelial cells: Influence of newborn sex

Maternal smoking (MS) during pregnancy is linked to well-documented adverse health effects for the mother and foetus, however the role of fetal sex was largely overlooked. Primary cultures of male and female human umbilical vein endothelial cells (MHUVECs and FHUVECs, respectively) were used. IL-6, IL-8, and TNF-α levels were measured in HUVECs supernatant. The expression of genes and proteins (oestrogen receptors (ERs), Hsp90, Beclin-1, p62, LC3, LAMP-1 and Parkin), as well as the expression of miR-29a-3p, miR-29b-3p, miR-126-3p, miR-133a-3p, and miR-146a-5p were analysed in cells obtained from foetuses born to non-smoking and smoking mothers. In HUVECs from foetuses born to non-smoking mothers, Beclin-1 protein was higher in MHUVECs (1.8 fold increase), while Parkin, Hsp90 proteins, and miR-146a-5p were elevated in FHUVECs (2.2, 2.6, and 2.1 fold increase, respectively), with no other significant differences. MS amplified these sex differences, with specific effects based on foetus sex. FHUVECs obtained from foetus born to smoking mothers showed higher levels of IL-8 (1399.36 ± 123.96 pg/ml for FHUVECs vs 655.11 ± 215.94; pg/ml for MHUVECs; P < 0.001), Hsp90 gene and protein (3.3 and 2.6 fold increase), and ERβ protein and Beclin-1 gene (2.1, and 4.9 fold increase), and lower levels of miR-29b-3p, miR-133a-3p, and miR-146a-5p than MHUVECs (0.27, 0.68, and 0.1 fold change, respectively). This study shows that primary HUVECs from fetuses born to smoking mothers retain a memory of smoking effects, with sex differences in gene expression, miRNA profiles, and autophagic responses, suggesting that maternal smoking impacts endothelial cell physiology in a sex-dependent manner.

The RNA-binding protein LSM family regulating reproductive development via different RNA metabolism

The LSM (Like-Sm) protein family, characterized by highly conserved LSM domains, is integral to ribonucleic acid (RNA) metabolism. Ubiquitously present in both eukaryotes and select prokaryotes, these proteins bind to RNA molecules with high specificity through their LSM domains. They can also form ring-shaped complexes with other proteins, thereby facilitating various fundamental cellular processes such as mRNA degradation, splicing, and ribosome biogenesis. LSM proteins play crucial roles in gametogenesis, early embryonic development, sex determination, gonadal maturation, and reproductive system formation. In pathological conditions, the absence of LSM14B leads to arrest of oocytes at mid-meiosis, downregulation of LSM4 expression is associated with abnormal spermatogenesis, and aberrant expression of LSM1 protein is linked to the occurrence and progression of breast cancer. This review focuses on the recent advances in the functional research of LSM proteins in reproduction.

Variable organization of repeats and hidden diversity of XY sex chromosomes in Pentatomidae true Bugs (Hemiptera) revealed through comparative genomic hybridization

Sex chromosomes have independently evolved in various species, displaying unique evolutionary patterns, including differentiation, degeneration, and repetitive DNA accumulation. Pentatomidae hemipterans are characterized by a highly conserved diploid number of 2n = 14 with a XX/XY sex chromosome system, i.e. 2n = 14, 12 A + XY. Thus, it represents an interesting group for investigating the reorganization of repeats in conserved karyotypes, i.e. the absence of large chromosomal rearrangements. Using comparative genomic hybridization (CGH) with male and female genomic DNAs (gDNA), this study examined a total of 25 Pentatomidae species to uncover repetitive DNA dynamics and their role in chromosome differentiation, especially sex chromosome differentiation. New karyotype data for nine species reinforces the chromosomal stasis in Pentatomidae for macro-chromosomal structure. However, significant variability in repetitive DNA patterns on autosomes and sex chromosomes has been revealed despite the karyotypic conservation. Autosomal signals varied in intensity and distribution, with some species exhibiting terminal enrichment of repeats, while others displayed dispersed patterns. Sex chromosomes showed distinct hybridization patterns, with the Y chromosome exhibiting more significant variability compared to the X. These findings emphasize the dynamic nature of sex chromosomes and suggest further studies combining genomic sequencing and cytogenetics to uncover sequences and the mechanisms behind their evolution.

The fourspine stickleback (Apeltes quadracus) has an XY sex chromosome system with polymorphic inversions on both X and Y chromosomes

Teleost fish are well-known for possessing a diversity of sex chromosomes and for undergoing frequent turnovers of these sex chromosomes. However, previous studies have mainly focused on variation between species, while comparatively little attention has been given to sex chromosome polymorphisms within species, which may capture early stages of sex chromosome changes. To better understand the evolution of sex chromosomes, we used the fourspine stickleback (Apeltes quadracus) as a model organism. Previous cytogenetic studies suggested that females of this species possessed a ZW heteromorphic sex chromosome system. However, genetic crosses and our whole-genome sequencing of three geographically distinct wild populations revealed that A. quadracus has an XY sex chromosome on chromosome 23. This chromosome has not previously been identified as a sex chromosome in any other stickleback species, indicating a recent sex chromosome turnover. We also identified two genes - rxfp2a and zar1l - as novel candidate sex determination genes. Notably, we observed inversions on both the X and Y chromosomes in different populations, resulting in distinctive patterns of differentiation between the X and Y chromosomes across populations. The new sex chromosome and intraspecies inversion polymorphisms observed in A. quadracus provide an excellent system for future work assessing the relative fitness effects of the inversions, which will enable testing theoretical models about the drivers of sex chromosome evolution and turnover.

Variation in adult sex ratios in tetrapods is linked to sex chromosomes through mortality differences between males and females

Sex chromosomes can determine male and female phenotypes, and the resulting sex differences may have significant impacts on ecology and life history. One manifestation of this link is that ZW/ZZ sex-determination systems are associated with more male-skewed adult sex ratio (ASR, proportion of males in the adult population) than XX/XY systems across tetrapods (amphibians, reptiles, birds, and mammals). Here, we investigate four demographic processes: male and female offspring production, sex differences in juvenile and adult mortalities and in timing of maturation that can contribute to ASR variation between XX/XY and ZW/ZZ systems, using phylogenetic analyses of a large dataset collected from tetrapod species in the wild. We show that sex differences in adult mortality reliably predict ASR that is also more male-biased in XX/XY species than in ZW/ZZ species. Sex differences in juvenile mortality and in maturation time also contribute to ASR skews, but do not differ consistently between XX/XY and ZW/ZZ systems. Phylogenetic path analyses confirm an influence of sex-determination system on ASR through sex-biased adult mortalities. Together these results infer that sex chromosomes can impact, via demographic pathways, frequency-dependent selection emerging from the relative number of males and females. We call for follow-up studies to uncover the potentially complex web of associations between sex determination, population dynamics, and social behavior.

Zglp-1 is a novel essential transcriptional regulator for sex reversal in zebrafish

Sex determination and differentiation play crucial biological roles in sexual reproduction in vertebrates, including zebrafish. Nevertheless, the intricate molecular mechanisms governing these processes have remained enigmatic. In this study, we showed a pivotal role played by zinc finger GATA-like protein-1 (Zglp-1) in sex differentiation in zebrafish. Our findings revealed that homozygous mutants having no Zglp-1 exhibited a female-to-male sex reversal, ultimately resulting in the development of fertile males. Within the pivotal phase of sexual differentiation, zglp-1 -/- zebrafish demonstrated a gene expression pattern that was skewed toward a male phenotype. Notably, the expression of amh was upregulated, while the expression of cyp19a1a was not sustained. Furthermore, our data revealed a direct interaction between the zinc fingers of Zglp-1 and Sf-1, which inhibited the ability of Sf-1 to activate the amh promoter. This interaction was crucial for regulating sex differentiation. Moreover, we observed alterations in gonadal cell proliferation and apoptosis in zglp-1 -/- zebrafish, which partially contributed to the sexual fate selection. Overall, our findings firmly established Zglp-1 as a crucial regulator of sex differentiation in zebrafish, offering deep insights into the intricate molecular mechanisms that govern sex determination and differentiation in vertebrates.

Supplementary Information

The online version contains supplementary material available at 10.1007/s42995-025-00299-5.

Insights into convergent evolution of cosexuality in liverworts from the Marchantia quadrata genome

Sex chromosomes are expected to coevolve with their respective sex, potentially disfavoring their co-occurrence as cosexuality evolves. This effect is expected to be stronger where sex chromosomes are restricted to one sex, such as in plants expressing sex in their haploid stage. We assess this hypothesis in liverworts with U/V sex chromosomes, ancestral dioicy, and several independent transitions to monoicy (cosexuality). We report the chromosome-level genome assembly of Marchantia quadrata, which recently evolved monoicy, and perform comparative genomic analyses with its dioicous relative M. polymorpha. We find that monoicy evolved via retention of the V chromosome as a small ninth chromosome, complete loss of the U chromosome, and translocation of key U-linked genes to autosomes, among which the major sex-determining gene (Feminizer) acquired environmental/developmental regulation. Our findings parallel recent observations on Ricciocarpos natans, which evolved monoicy independently, suggesting genetic constraints that may make transitions to monoicy predictable in liverworts.

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.

Repeated Evolution of Transcript Dosage Compensation of Independently Formed Nematode Neo-X Chromosomes

Ohno proposed that, during the origin of X/Y sex chromosomes from a pair of autosomes, X-linked genes must double their per-allele expressions to compensate for the degeneration of their Y homologs. Whether Ohno's hypothesis holds in the nematode Caenorhabditis elegans remains unresolved despite that C. elegans is a model for studying between-sex X chromosome dosage compensation. Genome sequencing revealed independent fusions of an ancestrally autosomal linkage group to the X chromosome in C. elegans and Brugia malayi, two species belonging to different suborders of the order Rhabditida, allowing testing Ohno's hypothesis in repeated origins of neo-X chromosomes from the same autosomal linkage group. For each C. elegans X-linked gene and its autosomal ortholog in Pristionchus pacificus, we computed the X:AA ratio in transcript level and observed a median of ∼1. The same is true for B. malayi X-linked genes when compared with their autosomal orthologs in Dirofilaria immitis. We find a significant enrichment of presumably dosage-sensitive transcription factor genes among the autosomal genes of P. pacificus (or D. immitis) that become X-linked in C. elegans (or B. malayi), but the results are mixed for other groups of presumably dosage-sensitive genes, providing a partial support to the hypothesis that X upregulation depends on the prevalence of dosage-sensitive genes in the proto-X. We conclude that, unlike the virtual absence of X upregulation at the transcript level in eutherian mammals, Ohno's hypothesis is strongly supported in both nematode lineages investigated.

Phylogenomics resolves key relationships in Rumex and uncovers a dynamic history of independently evolving sex chromosomes

Sex chromosomes have evolved independently many times across eukaryotes. Despite a considerable body of literature on sex chromosome evolution, the causes and consequences of variation in their formation, degeneration, and turnover remain poorly understood. Chromosomal rearrangements are thought to play an important role in these processes by promoting or extending the suppression of recombination on sex chromosomes. Sex chromosome variation may also contribute to barriers to gene flow, limiting introgression among species. Comparative approaches in groups with sexual system variation can be valuable for understanding these questions. Rumex is a diverse genus of flowering plants harboring significant sexual system and karyotypic variation, including hermaphroditic and dioecious clades with XY (and XYY) sex chromosomes. Previous disagreement in the phylogenetic relationships among key species has rendered the history of sex chromosome evolution uncertain. Resolving this history is important for investigating the interplay of chromosomal rearrangements, introgression, and sex chromosome evolution in the genus. Here, we use new transcriptome assemblies from 11 species representing major clades in the genus, along with a whole-genome assembly generated for a key hermaphroditic species. Using phylogenomic approaches, we find evidence for the independent evolution of sex chromosomes across two major clades, and introgression from unsampled lineages likely predating the formation of sex chromosomes in the genus. Comparative genomic approaches revealed high rates of chromosomal rearrangement, especially in dioecious species, with evidence for a complex origin of the sex chromosomes through multiple chromosomal fusions. However, we found no evidence of elevated rates of fusion on the sex chromosomes in comparison with autosomes, providing no support for an adaptive hypothesis of sex chromosome expansion due to sexually antagonistic selection. Overall, our results highlight a complex history of karyotypic evolution in Rumex, raising questions about the role that chromosomal rearrangements might play in the evolution of large heteromorphic sex chromosomes.

Discovery of XY Sex Chromosomes in Mauremys mutica Provides Insights Into the Role of KDM6B Gene in Coexistence of Temperature-Dependent and Genetic Sex Determination

The Asian yellow pond turtle (Mauremys mutica) has long been thought to lack dimorphic sex chromosomes, with prevailing theories suggesting a solely temperature-dependent sex determination (TSD) system. In this study, a male chromosome-level genomic sequence with a contig N50 of ~23.59 Mb was generated using a combination of both Nanopore and Hi-C sequencing technologies. We utilise a combination of bioinformatics and cytogenetic experimental validation to demonstrate that this species indeed possesses XY chromosomes, thereby correcting a longstanding misconception. The results suggest that the X chromosome of the Asian yellow pond turtle originated independently during later stages of evolution and underwent chromosomal rearrangements. Notably, it was observed that the sex chromosomes exhibited a significant repeat expansion, with 95.9% comprising repetitive sequences. This expansion is primarily driven by LINE/CR1 repeats, which account for 55.2% of the total length of the X chromosome. We found that the X chromosome underwent a lower rate of adaptive evolution, supporting the concept of the "slower-X" effect. We present a novel model concerning the KDM6B, which is located on both XY chromosomes, mediates a sex determination mechanism that coexists with TSD + XY in turtles. This study paves the way for further exploration into the complexities of sex determination and the evolutionary dynamics of sex chromosomes in turtles and potentially other reptiles.

Heterozygosity at a conserved candidate sex determination locus is associated with female development in the clonal raider ant (Ooceraea biroi)

Sex determination is a developmental switch that triggers sex-specific developmental programs. This switch is "flipped" by the expression of genes that promote male- or female-specific development. Many lineages have evolved sex chromosomes that act as primary signals for sex determination. However, haplodiploidy (males are haploid and females are diploid), which occurs in ca. 12% of animal species, is incompatible with sex chromosomes. Haplodiploid taxa must, therefore, rely on other strategies for sex determination. One mechanism, "complementary sex determination" (CSD), uses heterozygosity as a proxy for diploidy. In CSD, heterozygosity at a sex determination locus triggers female development, while hemizygosity or homozygosity permits male development. CSD loci have been mapped in honeybees and two ant species, but we know little about their evolutionary history. Here, we investigate sex determination in the clonal raider ant, Ooceraea biroi. We identified a 46kb candidate CSD locus at which all females are heterozygous, but most diploid males are homozygous for either allele. As expected for CSD loci, the candidate locus has more alleles than most other loci, resulting in a peak of nucleotide diversity. This peak negligibly affects the amino acid sequences of protein-coding genes, suggesting that heterozygosity of a non-coding genomic sequence triggers female development. This locus is distinct from the CSD locus in honeybees but homologous to a CSD locus mapped in two distantly related ant species, implying that this molecular mechanism has been conserved since a common ancestor that lived approximately 112 million years ago.

Molecular Determination of Sex from Down and Feather in Wild and Reared Monomorphic and Dimorphic Birds at Juvenile Age

The inability to distinguish males from females in young birds is a major obstacle for pair formation in reintroduction-restocking programs and commercial-amateur breeding. Several techniques are employed to address this problem, but not all of them are suitable for juvenile subjects. Among the various tests applied for sex determination, polymerase chain reaction (PCR) is one of the genetic tools that seems to be most effective (rapid, not invasive and cheaper). In this study, DNA was extracted from down and feathers to make the procedure less stressful for nestlings. The DNA was amplified by PCR, and the amplicon was subjected to the restriction endonucleases procedure when the gender was not clearly identified by PCR alone. One hundred and fifty-three avian species were sexed using this procedure, including 27 for the first time. In all the nestlings and juveniles tested, sex was correctly identified; in fact, all pairs that reached sexual maturity during this study gave offspring.

Deciphering the genetic basis of sex differentiation in silver-lipped pearl oyster ( Pinctada maxima) based on integrative transcriptomic analysis

The silver-lipped pearl oyster ( Pinctada maxima) is the largest and most commercially valuable pearl-producing oyster, renowned for its ability to generate large, lustrous pearls. This species is a sequential hermaphrodite, with pearl production displaying notable sexual dimorphism. Consequently, understanding the molecular mechanisms governing sex determination and differentiation is crucial for advancing breeding strategies in the pearl oyster industry. To elucidate these mechanisms, this study conducted integrative transcriptomic analyses of P. maxima gonadal tissues using isoform sequencing (Iso-seq) and RNA sequencing (RNA-seq). Comparative analysis of ovarian and testicular tissues identified 2 768 differentially expressed genes (DEGs). Gene co-expression network analysis delineated four key modules, including three sex-specific modules and one shared module. Key genes implicated in sex determination and maintenance were identified, including FOXL2, NANOS1, and β-catenin, important for ovarian maintenance, and DMRT, SOX30, FEM1, and FOXJ1, crucial for testicular maintenance. These genes, widely studied in other taxa, were confirmed as hub genes in the sex-related modules of P. maxima. Interestingly, genes within the shared module were significantly enriched in the spliceosome pathway. Alternative splicing analysis highlighted its extensive role in gonadal tissues, with more pronounced activity observed in the testis compared to the ovary. Nearly half (47.83%, 375) of the identified genes undergoing differential alternative splicing (DASGs) also exhibited differential transcript usage (DTUGs), while only 17% of DTUGs overlapped with DEGs. Genes associated with sex differentiation, such as DMRT, β-catenin, and U2AF2, displayed sex-specific and/or sex-biased isoforms. These findings offer novel insights into the molecular basis of sex differentiation in P. maxima, which could inform the development of targeted breeding strategies aimed at sex control, thereby enhancing pearl quality and yield in aquaculture. This study offers a robust molecular foundation for advancing breeding programs and optimizing production in the pearl oyster industry.

The role of unbalanced segmental duplication in sex chromosome evolution in Australian ridge-tailed goannas

Varanids are known for conserved sex chromosomes, but there are differences in the size of the W chromosome but not in morphology among species representing varying stages of sex chromosome evolution. We tested for homology of the ZW sex chromosome system with size differences in varanids among four species from two lineages in Australia, the Odatria and the Gouldii. We found that while DNA sequences of the sex chromosomes are conserved in the species we tested, we also identified a homologous region on an enlarged autosomal microchromosome that shares sequences with the W chromosome in some isolated populations of V. acanthurus and V. citrinus from the Odatria lineage. The enlarged microchromosome was unpaired in all individuals tested and is likely an unbalanced segmental duplication translocated between chromosome 1, the W, and another microchromosome. This suggests an ancient balanced duplication homologous to the W and the terminal region of the long arm of chromosome 1. The most parsimonious explanation is that the duplicated region likely originated on chromosome 1. We hypothesised in our reconstruction that genes and related DNA sequences associated with the sex-linkage group have likely originated on an autosome. Subsequently, the sequences may have undergone duplication and translocation to the W chromosome, followed by the accumulation of lineage specific repeat elements and amplifications on the W at different rates in various lineages. Lastly, these sequences are likely to have undergone duplication and translocation to another autosomal microchromosome. Given the role of segmental duplications and translocations as important evolutionary drivers of speciation in other taxa, together with the rapid speciation that has occurred in Australian varanids, our findings provide broader insight into the evolutionary pathway leading to rapid chromosomal and genic divergence of species.

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 dynamic regulatory network of stamens and pistils in papaya

BACKGROUND

Papaya exhibits three sex types: female (XX), male (XY), and hermaphrodite (XYh), making it an unusual trioecious model for studying sex determination. A critical aspect of papaya sex determination is the pistil abortion in male flowers. However, the regulatory networks that control the development of pistils and stamens in papaya remain incompletely understood.

RESULTS

In this study, we identified three organ-specific clusters involved in papaya pistils and stamens development. We found that pistil development is primarily characterized by the significant expression of auxin-related genes, while the pistil abortion genes in males is mainly associated with cytokinin, gibberellin, and auxin pathways. Additionally, we constructed expression regulatory networks for the development of female pistils, aborted pistils and stamens in male flowers, revealing key regulatory genes and signaling pathways involved in papaya organ development. Furthermore, we systematically identified 65 members of the MADS-box gene family and 10 ABCDE subfamily MADS-box genes in papaya. By constructing a phylogenetic tree of the ABCDE subfamily, we uncovered gene contraction and expansion in papaya, providing an improved understanding of the developmental mechanisms and evolutionary history of papaya floral organs.

CONCLUSIONS

These findings provide a robust framework for identifying candidate sex-determining genes and constructing the sex determination regulatory network in papaya, providing insights and genomic resources for papaya breeding.

Full-Length Transcriptome Sequencing and Comparative Transcriptomics Reveal the Molecular Mechanisms Underlying Gonadal Development in Sleepy Cod (Oxyeleotris lineolata)

Sleepy cod (Oxyeleotris lineolata) is native to Australia and is now an economically valuable fish cultured in China and Southern Asian countries. Its growth rate exhibits as sexually dimorphic, with males generally growing more rapidly and attaining a larger body size compared to females. Thus, the effective development of sex control breeding can significantly contribute to increased yields and output value. Nevertheless, due to the lack of genomic and transcriptomic data, the molecular mechanisms underlying sex determination and gonadal differentiation in sleepy cod remain poorly understood. In this study, long-read PacBio isoform sequencing (Iso-Seq) was performed to obtain a full-length transcriptome from a pooled sample of eight tissues (kidney, brain, liver, muscle, heart, spleen, ovary and testis). A total of 30.41 G subread bases were generated and 49,113 non-redundant full-length transcripts with an average length of 2948 bp were produced. Using the full-length transcriptome as a reference, short-read Illumina sequencing was performed to investigate the differences in gene expression at the transcriptome level between ovaries and testes from 12-month-old individuals. A total of 19,102 differentially expressed transcripts (DETs) were identified, of which 8510 (44.55%) were up-regulated in the ovary and 10,592 (55.45%) were up-regulated in the testis. The DETs were mainly clustered into 241 KEGG pathways, in which oocyte meiosis and arachidonic acid metabolism were the most relevant pathways involved in gonadal differentiation. To verify the validity of the transcriptomic data, 20 DETs were selected to investigate the gonad expression profiles based on qPCR. The expression levels of all 20 screened genes were consistent with the transcriptome sequencing results. The present study provides new genetic resources-including full-length transcriptome sequences and annotation information-as a coding genomic-level reference for sleepy cod-yielding valuable insights into the genetic mechanisms of sex determination and gonadal differentiation in this economically important species.

Cephalopod sex determination and its ancient evolutionary origin

Octopuses, squids, and cuttlefishes-the coleoid cephalopods-are a remarkable branch in the tree of life whose members exhibit a repertoire of sophisticated behaviors.1 As a clade, coleoids harbor an incredible variety of novel traits, including the most complex nervous system among invertebrates, derived camera-type eyes, and rapid adaptive camouflage abilities.2,3 The burst of evolutionary novelty that distinguishes cephalopods is even more striking in a phylogenetic context; cephalopods are a deeply diverged lineage that last shared a common ancestor with other extant molluscs in the Cambrian period, roughly 550 million years ago.4,5 With recent advances in genome sequencing technologies, we have the capability to explore the genomic foundations of cephalopod novelties. Here, using PacBio long-read sequencing of genomic DNA and Iso-Seq full-length mRNA sequencing, we provide a novel chromosome-scale reference genome and annotation for a female California two-spot octopus (O. bimaculoides). Our assembly reveals that the female octopus has just one sex chromosome, consistent with a ZO karyotype, whereas the male has two (ZZ), providing the first evidence of genetic sex determination in cephalopods. We use our assembly and annotation in combination with existing genomic information from other cephalopods to create the first whole-genome alignments from this group and demonstrate that the sex chromosome is of an ancient origin, before the radiation of extant cephalopods approximately 480 million years ago,4 and has been conserved to the present day in all cephalopod genomes available.

Mechanisms underlining Kelp (Saccharina japonica) adaptation to relative high seawater temperature

Saccharina japonica has been cultivated in China for almost a century. From Dalian to Fujian, the lowest and the highest seawater temperatures in the period of cultivation increased by 14℃ and 8℃, respectively. Its adaptation to elevated seawater temperature is an example of securing the natural habitats of a species. To decipher the mechanisms underlining S. japonica adaptation to relative high seawater temperature, we assembled ~ 516.3 Mb female gametophyte genome and ~ 540.3 Mb of the male, respectively. The gametophytes isolated from southern China kelp cultivars acclimated to the relative high seawater temperature by transforming amino acids, glycosylating protein, maintaining osmotic pressure, intensifying the innate immune system, and exhausting energy and reduction power through the PEP-pyruvate-oxaloacetate node and the iodine cycle. They adapted to the relative high seawater temperature by transforming amino acids, changing sugar metabolism and intensifying innate immune system. The sex of S. japonica was determined by HMG-sex, and around this male gametophyte determiner the stress tolerant genes become linked to or associated with.

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.

The Silene latifolia genome and its giant Y chromosome

In many species with sex chromosomes, the Y is a tiny chromosome. However, the dioecious plant Silene latifolia has a giant ~550-megabase Y chromosome, which has remained unsequenced so far. We used a long- and short-read hybrid approach to obtain a high-quality male genome. Comparative analysis of the sex chromosomes with their homologs in outgroups showed that the Y is highly rearranged and degenerated. Recombination suppression between X and Y extended in several steps and triggered a massive accumulation of repeats on the Y as well as in the nonrecombining pericentromeric region of the X, leading to giant sex chromosomes. Using sex phenotype mutants, we identified candidate sex-determining genes on the Y in locations consistent with their favoring recombination suppression events 11 and 5 million years ago.

Balancing selfing and outcrossing: the genetics and cell biology of nematodes with three sexual morphs

Trioecy, a rare reproductive system where hermaphrodites, females, and males coexist, is found in certain algae, plants, and animals. Though it has evolved independently multiple times, its rarity suggests it may be an unstable or transitory evolutionary strategy. In the well-studied Caenorhabditis elegans, attempts to engineer a trioecious strain have reverted to the hermaphrodite/male system, reinforcing this view. However, these studies did not consider the sex-determination systems of naturally stable trioecious species. The discovery of free-living nematodes of the Auanema genus, which have naturally stable trioecy, provides an opportunity to study these systems. In Auanema, females produce only oocytes, while hermaphrodites produce both oocytes and sperm for self-fertilization. Crosses between males and females primarily produce daughters (XX hermaphrodites and females), while male-hermaphrodite crosses result in sons only. These skewed sex ratios are due to X-chromosome drive during spermatogenesis, where males produce only X-bearing sperm through asymmetric cell division. The stability of trioecy in Auanema is influenced by maternal control over sex determination and environmental cues. These factors offer insights into the genetic and environmental dynamics that maintain trioecy, potentially explaining its evolutionary stability in certain species.

Sex Chromosome Dosage Compensation in Insects

Dosage compensation (DC) is of crucial importance in balancing the sex-linked gene expression between males and females. It serves to guarantee that the proteins or other enzymatic products encoded by the sex chromosome exhibit quantitative parity between the two genders. During the evolutionary process of achieving dose compensation, insects have developed a wide variety of mechanisms. There exist two primary modes of dosage compensation mechanisms, including the up-regulation of heterogametic sex chromosomes in the heterogamety and down-regulation of homogametic sex chromosomes in the homogamety. Although extensive investigations have been conducted on dosage compensation in model insects, many questions still remain unresolved. Meanwhile, research on non-model insects is attracting increasing attention. This paper systematically summarizes the current advances in the field of insect dosage compensation with respect to its types and mechanisms. The principal insects involved in this study include the Drosophila melanogaster, Tribolium castaneum, Bombyx mori, and other lepidopteran insects. This paper analyzes the controversial issues about insect dosage compensation and also provides prospects for future research.

A Genetic Polymorphism Underlying Alternative Reproductive Tactics in Eurycea Salamanders

Alternative reproductive tactics are discrete, intrasexual differences in reproductive behaviour within a population. In some cases, these complex phenotypes are determined by autosomal supergenes or sex chromosomes-both of which exhibit reduced recombination and thus enable the linked inheritance of co-adapted alleles from multiple loci. Most alternative reproductive tactics in amphibians are plastic (and reversible), environmentally determined and lacking morphological differentiation, but a striking exception is found in the two-lined salamander (Eurycea bislineata) species complex. In some populations, two distinct male phenotypes coexist: 'searching' males have mental glands, protruding premaxillary teeth and elongate cirri used in terrestrial courtship, while 'guarding' males lack these traits and instead have hypertrophied jaw musculature used in mate guarding at aquatic nesting sites. These tactics differ in many morphological and behavioural phenotypes, but their proximate cause has not yet been described. Here, we generated genome-wide SNP data from > 130 Eurycea cf. wilderae collected from Highlands Biological Station. We provide evidence for an XY sex determination and for a Y-linked polymorphism underlying alternative reproductive tactics in this population. We then develop and validate a PCR-based genotyping assay and apply it to characterise the sex ratio and relative frequency of male tactics from a sample of larvae. Our results add to the growing body of literature exploring the importance of supergenes and sex chromosomes in complex intraspecific polymorphisms, and we highlight opportunities for future work to continue exploring the genomic architecture of these traits.

Genomic diversity in time and space in the toxic diatom Pseudo-nitzschia multistriata

Understanding the origin and maintenance of genetic diversity is crucial to elucidate population dynamics of unicellular microalgae, their microevolutionary history and their adaptive ability. The planktonic, domoic acid-producing diatom Pseudo-nitzschia multistriata has a ubiquitous distribution in the world oceans and past population genetics studies, based on few genomic loci, have shown a clear temporal structure over different years in the Gulf of Naples (Italy). Despite the ecological and toxicological importance of this organism, detailed information on its diversity across the whole genome and at the population level is still lacking. We collected P. multistriata strains in the Gulf of Naples in five different years, obtained strains from the Adriatic Sea, the Gulf of Mexico and New Zealand coasts, and resequenced the whole genomes of a total of 28 strains at high coverage. While strains from the first three geographical areas were capable of producing the toxin domoic acid, the New Zealand strains had been reported to be non-toxic. A comparison of the domoic acid biosynthetic (dab) genes sequences between toxic and non-toxic strains showed very little variation among the strains, and no disrupting mutation was found in the dab genes in the non-toxic strains. On the other hand, the dab genes showed higher levels of expression in toxic strains than in non-toxic strains, suggesting that, in this species, absence of toxicity is explained by gene regulation rather than dab sequence divergence. Variant analysis showed stronger spatial than temporal genetic structuring and a clear separation was observed between the New Zealand strains and the others, the former having a greater content of genes under selection. Overall, the genomes of the different groups, including strains from a clonal bloom, did not appear to contain major rearrangements. Our findings contribute to enlarging our understanding of diatom diversity, a key factor underlying diatom success, and provide novel data on the longstanding problem of Pseudo-nitzschia toxicity.

Dose-dependent role of AMH and AMHR2 signaling in male differentiation and regulation of sex determination in Spotted knifejaw (Oplegnathus punctatus) with X1X1X2X2/X1X2Y chromosome system

Sex determination mechanisms vary significantly across different chromosomal systems and evolutionary contexts. Nonetheless, the regulatory framework governing the multi-sex chromosome system (X1X1X2X2/X1X2Y) remains enigmatic. Through an examination of sex-related genes (dmrt1, hsd11b2, amh, sox9a, sox9b, foxl2, cyp19a), hormonal influences (E2, 11-KT), and histological analyses of gonadal development, we demonstrate that the critical period for sexual differentiation occurs between 35 to 60 days post-hatching (dph). Our multi-omics analysis identified amhr2 as a candidate sex-determining gene, revealing that the males possess three distinct amhr2 transcripts (amhr2ay, amhr2by, amhr2cy), whereas females express only one (amhr2a). In situ hybridization assays demonstrated that amhr2 is predominantly localized to primary spermatocyte and Sertoli cells of male testes. Notably, the specific mRNA expression of amhr2 is significantly enriched in amhr2cy, whose extracellular domain exhibits the highest binding affinity for Amh protein, with sexual expression differences manifesting as early as 5 dph. The outcomes of amhr2 interference (RNAi) experiments indicate that amhr2 knockdown leads to a reduction in the expression of male-related gene (dmrt1, amh, sox9a, sox9b), androgen synthesis genes (hsd11b2, cyp11a), and female-related genes (wnt4, foxl2, cyp19a, cyp19b). Conversely, overexpression of amhr2 yielded contrasting results. Our research supports the role of amhr2 as a pivotal candidate sex-determining gene. Furthermore, the dosage effect of amhr2, reflected in transcript abundance, mRNA expression levels, and binding efficacy, serves as a fundamental mechanism driving male differentiation and regulatory processes in Spotted knifejaw.

Characterization of a novel and testis-specific zinc finger protein during sexual development of Pacific white shrimp Litopenaeus vannamei†

Since females grow faster in penaeid shrimp, all-female aquaculture was proposed. Environmental conditions in the Pacific white shrimp were not found to affect genetic sex determination (ZZ/ZW system). The androgenic gland-secreting insulin-like androgenic gland hormone is a key controlling factor in crustacean male differentiation. However, functional sex reversal (neo-male) in penaeid shrimp has not yet been achieved by manipulating the insulin-like androgenic gland hormone-sexual switch. Therefore, understanding the molecular mechanisms of gonadal differentiation may help build appropriate tools to generate neo-male for all-female breeding. This study describes the potential role of the novel penaeid-specific testicular zinc finger protein (pTZFP) in the gonads of Pacific white shrimp. First, pTZFP transcripts show a male-bias expression pattern in undifferentiated gonads, which is then exclusively expressed in the testis and absent or slightly expressed in the ovary and other tissues. Besides, the knockdown of pTZFP in undifferentiated males results in smaller testes but no sex reversal. Immunohistochemical staining of proliferating cell nuclear antigen further confirmed that the smaller testes in pTZFP-deficient males are due to the lower proliferating activity of spermatogonia. These data reveal that pTZFP may be involved in testicular development but have fewer effects on gonadal differentiation. Moreover, testicular pTZFP transcription levels were not reduced with estradiol-17β (E2) administration or AG excision. Therefore, our data suggest that pTZFP may regulate testicular development through downstream genes regulating spermatogonia proliferation. Moreover, our data provide an appropriate molecular marker for identifying the sex of undifferentiated gonads.

Understanding Genetic Regulation of Sex Differentiation in Hermaphroditic Fish

As a fundamental taxonomic group within vertebrates, fish represent an invaluable resource for investigating the mechanisms underlying sex determination and differentiation owing to their extensive geographical distribution and rich biodiversity. Within this biological cohort, the processes of sex determination and differentiation are intricately governed by both genetic factors and the complex interplay of environmental cues. While variations in external environmental factors, particularly temperature, can exert a modulatory influence on sex differentiation in fish to a limited degree, genetic factors remain the primary determinants of sexual traits. Hermaphroditic fish display three distinct types of sexual transitions: protandry (male to female), protogyny (female-to-male), bidirectional sex change (both directions serially). These fish, characterized by their unique reproductive strategies and sexual plasticity, serve as exemplary natural models for elucidating the mechanisms of sex differentiation and sexual transitions in fish. The present review delves into the histological dynamics during gonadal development across three types of sequential hermaphroditic fish, meticulously delineating the pivotal characteristics at each stage, from the inception of primordial gonads to sexual specialization. Furthermore, it examines the regulatory genes and associated signaling pathways that orchestrate sex determination and differentiation. By systematically synthesizing these research advancements, this paper endeavors to offer a comprehensive and profound insight into the intricate mechanisms governing sex differentiation in sequential hermaphroditic fish.

Identification of genes associated with sex expression and sex determination in hemp (Cannabis sativa L.)

Dioecy in flowering plants has evolved independently many times, and thus the genetic mechanisms underlying sex determination are diverse. In hemp (Cannabis sativa), sex is controlled by a pair of sex chromosomes (XX for females and XY for males). In an attempt to understand the molecular mechanism responsible for sex expression in hemp plants, we carried out RNA sequencing of male and female plants at different developmental stages. Using a pipeline involving differential gene expression analysis and weighted gene co-expression network analysis, we identified genes important for male and female flower development. We also demonstrate that sex-biased expression is already established at very early vegetative stages, before the onset of reproductive development, and identify several genes encoding transcription factors of the REM, bZIP, and MADS families as candidate sex-determination genes in hemp. Our findings demonstrate that the gene regulatory networks governing male and female development in hemp diverge at a very early stage, leading to profound morphological differences between male and female hemp plants.

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.

X-inactive-specific transcript: a long noncoding RNA with a complex role in sex differences in human disease

In humans, the X and Y chromosomes determine the biological sex, XX specifying for females and XY for males. The long noncoding RNA X-inactive specific transcript (lncRNA XIST) plays a crucial role in the process of X chromosome inactivation (XCI) in cells of the female, a process that ensures the balanced expression of X-linked genes between sexes. Initially, it was believed that XIST can be expressed only from the inactive X chromosome (Xi) and is considered a typically female-specific transcript. However, accumulating evidence suggests that XIST can be detected in male cells as well, and it participates in the development of cancers and other human diseases by regulating gene expression at epigenetic, chromatin remodeling, transcriptional, and translational levels. XIST is abnormally expressed in many sexually dimorphic diseases, including autoimmune and neurological diseases, pulmonary arterial hypertension (PAH), and some types of cancers. However, the underlying mechanisms are not fully understood. Escape from XCI and skewed XCI also contributes to sex-biased diseases and their severity. Interestingly, in humans, similar to experimental animal models of human disease, the males with the XIST gene activated display the sex-biased disease condition at a rate close to females, and significantly greater than males who had not been genetically modified. For instance, the men with supernumerary X chromosomes, such as men with Klinefelter syndrome (47, XXY), are predisposed toward autoimmunity similar to females (46, XX), and have increased risk for strongly female biased diseases, compared to 46, XY males. Interestingly, chromosome X content has been linked to a longer life span, and the presence of two chromosome X contributes to increased longevity regardless of the hormonal status. In this review, we summarize recent knowledge about XIST structure/function correlation and involvement in human disease with focus on XIST abnormal expression in males. Many human diseases show differences between males and females in penetrance, presentation, progression, and survival. In humans, the X and Y sex chromosomes determine the biological sex, XX specifying for females and XY for males. This numeric imbalance, two X chromosomes in females and only one in males, known as sex chromosome dosage inequality, is corrected in the first days of embryonic development by inactivating one of the X chromosomes in females. While this "dosage compensation" should in theory solve the difference in the number of genes between sexes, the expressed doses of X genes are incompletely compensated by X chromosome inactivation in females. In this review we try to highlight how abnormal expression and function of XIST, a gene on the X chromosome responsible for this inactivation process, may explain the sex differences in human health and disease. A better understanding of the molecular mechanisms of XIST participation in the male-female differences in disease is highly relevant since it would allow for improving the personalization of diagnosis and sex-specific treatment of patients.

Evidence for a Novel X Chromosome in Termites

Termites, together with cockroaches, belong to the Blattodea. They possess an XX/XY sex determination system which has evolved from an XX/X0 system present in other Blattodean species, such as cockroaches and wood roaches. Little is currently known about the sex chromosomes of termites, their gene content, or their evolution. We here investigate the X chromosome of multiple termite species and compare them with the X chromosome of cockroaches using genomic and transcriptomic data. We find that the X chromosome of the termite Macrotermes natalensis is large and differentiated showing hall marks of sex chromosome evolution such as dosage compensation, while this does not seem to be the case in the other two termite species investigated here where sex chromosomes may be evolutionary younger. Furthermore, the X chromosome in M. natalensis is different from the X chromosome found in the cockroach Blattella germanica indicating that sex chromosome turn-over events may have happened during termite evolution.

Making sense of recent models of the "sheltering" hypothesis for recombination arrest between sex chromosomes

In their most extreme form, sex chromosomes exhibit a complete lack of genetic recombination along much of their length in the heterogametic sex. Some recent models explain the evolution of such suppressed recombination by the "sheltering" of deleterious mutations by chromosomal inversions that prevent recombination around a polymorphic locus controlling sex. This sheltering hypothesis is based on the following reasoning. An inversion that is associated with the male-determining allele (with male heterogamety) is present only in the heterozygous state. If such an inversion carries a lower-than-average number of deleterious mutations, it will accrue a selective advantage and will be sheltered from homozygosity for any mutations that it carries due to the enforced heterozygosity for the inversion itself. It can, therefore, become fixed among all carriers of the male-determining allele. Recent population genetics models of this process are discussed. It is shown that, except under the unlikely scenario of a high degree of recessivity of most deleterious mutations, inversions of this type that lack any other fitness effects will have, at best, a modest selective advantage; they will usually accumulate on proto-Y chromosomes at a rate close to, or less than, the neutral expectation. While the existence of deleterious mutations does not necessarily prevent the spread of Y-linked inversions, it is unlikely to provide a significant selective advantage to them.

Chromosome-level genome assembly of a stored-product psocid, Liposcelis tricolor (Psocodea: Liposcelididae)

Liposcelis tricolor (Psocoptera: Liposcelididae) is a significant pest affecting stored products globally. However, due to the lack of a detailed genomic reference, the mechanisms of sex determination, stress resistance, and potential control methods for this booklouse remain poorly understood. In this study, the chromosome-level genome of L. tricolor was assembled by employing Illumina, Nanopore, and Hi-C sequencing technologies. The final genome size was determined to be 229.33 Mb, anchored to 9 pseudo-chromosomes. BUSCO analysis showed that 99.2% of complete BUSCOs were identified, suggesting the high completeness of the genome. A total of 91.49 Mb of repetitive sequences, accounting for 38.84% of the total genome, were annotated, and 15,647 protein-coding genes were predicted, with 88.17% functionally annotated. Additionally, we identified 25 typical sex-determining genes based on the genomic data. This high-quality genome assembly provides a crucial foundation for advancing our comprehension of the molecular biology, genetics, and potential control strategies for psocid L. tricolor.

The interplay of local adaptation and gene flow may lead to the formation of supergenes

Supergenes are genetic architectures resulting in the segregation of alternative combinations of alleles underlying complex phenotypes. The co-segregation of alleles at linked loci is often facilitated by polymorphic chromosomal rearrangements suppressing recombination locally. Supergenes are involved in many complex polymorphisms, including sexual, colour or behavioural polymorphisms in numerous plants, fungi, mammals, fish, and insects. Despite a long history of empirical and theoretical research, the formation of supergenes remains poorly understood. Here, using a two-island population genetic model, we explore how gene flow and the evolution of overdominant chromosomal inversions may jointly lead to the formation of supergenes. We show that the evolution of inversions in differentiated populations, both under disruptive selection, leads to an increase in frequency of poorly adapted, immigrant haplotypes. Indeed, rare allelic combinations, such as immigrant haplotypes, are more frequently reshuffled by recombination than common allelic combinations, and therefore benefit from the recombination suppression generated by inversions. When an inversion capturing a locally adapted haplotype spreads but is associated with a fitness cost hampering its fixation (e.g. a recessive mutation load), the maintenance of a non-inverted haplotype in the population is enhanced; under certain conditions, the immigrant haplotype persists alongside the inverted local haplotype, while the standard local haplotype disappears. This establishes a stable, local polymorphism with two non-recombining haplotypes encoding alternative adaptive strategies, that is, a supergene. These results bring new light to the importance of local adaptation, overdominance, and gene flow in the formation of supergenes and inversion polymorphisms in general.

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.

Stochastic Epigenetic Modification and Evolution of Sex Determination in Vertebrates

In this report, we propose a novel mathematical model of the origin and evolution of sex determination in vertebrates that is based on the stochastic epigenetic modification (SEM) mechanism. We have previously shown that SEM, with rates consistent with experimental observation, can both increase the rate of gene fixation and decrease pseudogenization, thus dramatically improving the efficacy of evolution. Here, we present a conjectural model of the origin and evolution of sex determination wherein the SEM mechanism alone is sufficient to parsimoniously trigger and guide the evolution of heteromorphic sex chromosomes from the initial homomorphic chromosome configuration, without presupposing any allele frequency differences. Under this theoretical model, the SEM mechanism (i) predated vertebrate sex determination origins and evolution, (ii) has been conveniently and parsimoniously co-opted by the vertebrate sex determination systems during the evolutionary transitioning to the extant vertebrate sex determination, likely acting "on top" of these systems, and (iii) continues existing, alongside all known vertebrate sex determination systems, as a universal pan-vertebrate sex determination modulation mechanism.

Sex chromosome turnover and biodiversity in fishes

The impact of sex chromosomes and their turnover in speciation remains a subject of ongoing debate in the field of evolutionary biology. Fishes are the largest group of vertebrates, and they exhibit unparalleled sexual plasticity, as well as diverse sex-determining (SD) genes, sex chromosomes, and sex-determination mechanisms. This diversity is hypothesized to be associated with the frequent turnover of sex chromosomes in fishes. Although it is evident that amh and amhr2 are repeatedly and independently recruited as SD genes, their relationship with the rapid turnover of sex chromosomes and the biodiversity of fishes remains unknown. We summarize the canonical models of sex chromosome turnover and highlight the vital roles of gene mutation and hybridization with empirical evidence. We revisit Haldane's rule and the large X-effect and propose the hypothesis that sex chromosomes accelerate speciation by multiplying genotypes via hybridization. By integrating recent findings on the turnover of SD genes, sex chromosomes, and sex-determination systems in fish species, this review provides insights into the relationship between sex chromosome evolution and biodiversity in fishes.

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.

Sex Chromosome Evolution: Hallmarks and Question Marks

Sex chromosomes are widespread in species with separate sexes. They have evolved many times independently and display a truly remarkable diversity. New sequencing technologies and methodological developments have allowed the field of molecular evolution to explore this diversity in a large number of model and nonmodel organisms, broadening our vision on the mechanisms involved in their evolution. Diverse studies have allowed us to better capture the common evolutionary routes that shape sex chromosomes; however, we still mostly fail to explain why sex chromosomes are so diverse. We review over half a century of theoretical and empirical work on sex chromosome evolution and highlight pending questions on their origins, turnovers, rearrangements, degeneration, dosage compensation, gene content, and rates of evolution. We also report recent theoretical progress on our understanding of the ultimate reasons for sex chromosomes' existence.

Out with the old, in with the new: Meiotic driving of sex chromosome evolution

Chromosomal regions with meiotic drivers exhibit biased transmission (> 50 %) over their competing homologous chromosomal region. These regions often have two prominent genetic features: suppressed meiotic crossing over and rapidly evolving multicopy gene families. Heteromorphic sex chromosomes (e.g., XY) often share these two genetic features with chromosomal regions exhibiting meiotic drive. Here, we discuss parallels between meiotic drive and sex chromosome evolution, how the divergence of heteromorphic sex chromosomes can be influenced by meiotic drive, experimental approaches to study meiotic drive on sex chromosomes, and meiotic drive in traditional and non-traditional model organisms with high-quality genome assemblies. The newly available diversity of high-quality sex chromosome sequences allows us to revisit conventional models of sex chromosome evolution through the lens of meiotic drive.

Unveiling potential sex-determining genes and sex-specific markers in autotetraploid Carassius auratus

Autotetraploid Carassius auratus is a stable hereditary autotetraploid fish resulting from the hybridization of Carassius auratus red var. (RCC, ♀) × Megalobrama amblycephala (BSB, ♂), containing four sets of RCC chromosomes. However, the molecular mechanism underlying the determination of sex in this species remains largely unknown. Currently, there lacks a full understanding of the molecular mechanisms governing sex determination and specific molecular markers to differentiate sex in this species. In this study, 25,801,677 SNPs (Single-nucleotide polymorphism) and 6,210,306 Indels (insertion-deletion) were obtained from whole-genome resequencing of 100 individuals (including 50 female and 50 male). Further identification confirmed the candidate chromosomes as Chr46B, with the sex-determining region located at Chr46B: 22,500,000-22,800,000 bp. Based on the male-specific insertion (26 bp) within the candidate sex-determining region, a pair of sex-specific molecular markers has been identified. In addition, based on the screening of candidate sex-determining region genes and RT-qPCR validation analysis, ADAM10, AQP9 and tc1a were identified as candidate sex-determining genes. These findings provide a robust foundation for investigating sex determination mechanisms in fish, the evolution of sex chromosomes, and the development of monosex populations.

Delineating the W Sex Chromosome in the Clam Shrimp, Eulimnadia texana

INTRODUCTION

Sex chromosomes have evolved independently across various lineages, often showing convergent degradation of the sex-limited chromosome. While extensively studied in model organisms with ancient sex chromosomal systems, the evolution of early-stage sex chromosomes remains poorly understood. Eulimnadia texana, a freshwater crustacean with a unique androdioecious breeding system (ZZ, ZW, and viable WW genotypes), provides a rare opportunity to study early sex chromosome evolution. This study examines E. texana's W chromosome for evidence of a small localized non-recombining region, characterized by a transposable element (TE) "hotspot," low gene density, and low GC content.

METHODS

Sex-linked markers were mapped onto the W chromosome (scaffold 1). TEs in the WW genome were identified using RepeatModeler and RepeatMasker. Statistical analyses compared TE distribution between the genome and scaffold 1, which was then divided into 20 equal-sized "bins" for finer-scale statistical analyses. Gene density and GC content were analyzed across these bins.

RESULTS

While no significant TE accumulation was found across the entire W chromosome compared to the remaining genome, a specific region (6.6-8.8 Mb, fourth bin) showed significantly higher TE accumulation. This region also exhibited low gene density and low GC content, indicative of reduced recombination.

CONCLUSION

Our findings suggest that E. texana's W chromosome contains a smaller region of crossover suppression, supporting the hypothesis that it is a proto-sex chromosome in early evolutionary development. This study provides valuable insights into early sex chromosome evolution and establishes E. texana as an ideal model for further investigation of evolutionary processes driving proto-sex chromosome differentiation.

Trans regulation of an odorant binding protein by a proto-Y chromosome affects male courtship in house fly

The male-limited inheritance of Y chromosomes favors alleles that increase male fitness, often at the expense of female fitness. Determining the mechanisms underlying these sexually antagonistic effects is challenging because it can require studying Y-linked alleles while they still segregate as polymorphisms. We used a Y chromosome polymorphism in the house fly, Musca domestica, to address this challenge. Two male determining Y chromosomes (YM and IIIM) segregate as stable polymorphisms in natural populations, and they differentially affect multiple traits, including male courtship performance. We identified differentially expressed genes encoding odorant binding proteins (in the Obp56h family) as candidate agents for the courtship differences. Through network analysis and allele-specific expression measurements, we identified multiple genes on the house fly IIIM chromosome that could serve as trans regulators of Obp56h gene expression. One of those genes is homologous to Drosophila melanogaster CG2120, which encodes a transcription factor that binds near Obp56h. Upregulation of CG2120 in D. melanogaster nervous tissues reduces copulation latency, consistent with this transcription factor acting as a negative regulator of Obp56h expression. The transcription factor gene, which we name speed date, demonstrates a molecular mechanism by which a Y-linked gene can evolve male-beneficial effects.

Population genomic analysis reveals a polygenic sex determination system in Apostichopus japonicus

The sea cucumber Apostichopus japonicus, a key species in Chinese aquaculture, plays a significant evolutionary role within the Echinodermata phylum. However, the sex determination mechanism in this species remains poorly understood. Here, we conducted extensive sex surveys and sampling of eight wild populations, investigating the sex-related SNPs and insertion or deletions (indels) through bulk segregation analysis (BSA) and genome-wide association study (GWAS) analysis. Our findings suggest that A. japonicus employs a polygenic sex determination (PSD) system, with solute carrier family 8 (SLC8A) being the candidate gene for sex determination, encoding sodium-calcium exchanger (NCX1). The analysis of normalized sequencing depth reveals variations across chromosomes 6, 13, 14, 16, and 18, supporting the PSD system. We also identified 541.656 kb of male-specific sequences and screened five markers (C77185, C98086, C64977, C125, and C876) for molecular sex identification. Overall, this study provides new insights into A. japonicus sex determination, highlighting a complex multi-gene mechanism rather than a simple XX/XY system.

Insights into the molecular bases of multicellular development from brown algae

The transition from simple to complex multicellularity represents a major evolutionary step that occurred in only a few eukaryotic lineages. Comparative analyses of these lineages provide insights into the molecular and cellular mechanisms driving this transition, but limited understanding of the biology of some complex multicellular lineages, such as brown algae, has hampered progress. This Review explores how recent advances in genetic and genomic technologies now allow detailed investigations into the molecular bases of brown algae development. We highlight how forward genetic techniques have identified mutants that enhance our understanding of pattern formation and sexual differentiation in these organisms. Additionally, the existence and nature of morphogens in brown algae and the potential influence of the microbiome in key developmental processes are examined. Outstanding questions, such as the identity of master regulators, the definition and characterization of cell types, and the molecular bases of developmental plasticity are discussed, with insights into how recent technical advances could provide answers. Overall, this Review highlights how brown algae are emerging as alternative model organisms, contributing to our understanding of the evolution of multicellular life and the diversity of body plans.

Genome-Wide Association Studies (GWAS) and Transcriptome Analysis Reveal Male Heterogametic Sex-Determining Regions and Candidate Genes in Northern Snakeheads (Channa argus)

The Northern snakehead (Channa argus) is a significant economic aquaculture species in China. Exhibiting sexual dimorphism in the growth rate between females and males, mono-sex breeding holds substantial value for aquaculture. This study employed GWAS and transcriptome analysis were applied to identify sex determination genomic regions and develop sex-specific markers. A total of 270 single-nucleotide polymorphisms (SNPs) and 31 insertion-deletions (InDels) were identified as being sexually dimorphic through GWAS and fixation index (Fst) scanning. Based on GWAS results, two sex-specific InDel markers were developed, effectively distinguishing genetic sex for XX females, XY males, and YY super-males via (polymerase chain reaction) PCR amplification. A major genomic segment of approximately 115 kb on chromosome 3 (Chr 03) was identified as the sex-determination region. A comparative transcriptome analysis of gonads for three sexes identified 158 overlapping differentially expressed genes (DEGs). Additionally, three sex-related candidate genes were identified near the sex determination region, including id2, sox11, and rnf144a. Further studies are required to elucidate the functions of these genes. Overall, two sex-specific InDel markers support a male heterogametic XX/XY sex-determination system in Northern snakeheads and three candidate genes offer new insights into sex determination and the evolution of sex chromosomes in teleost fish.

The Hypolimnas misippus Genome Supports a Common Origin of the W Chromosome in Lepidoptera

Moths and butterflies (Lepidoptera) have a heterogametic sex chromosome system with females carrying ZW chromosomes and males ZZ. The lack of W chromosomes in early-diverging lepidopteran lineages has led to the suggestion of an ancestral Z0 system in this clade and a B chromosome origin of the W. This contrasts with the canonical model of W chromosome evolution in which the W would have originated from the same homologous autosomal pair as the Z chromosome. Despite the distinct models proposed, the rapid evolution of the W chromosome has hindered the elucidation of its origin. Here, we present high-quality, chromosome-level genome assemblies of 2 Hypolimnas species (Hypolimnas misippus and Hypolimnas bolina) and use the H. misippus assembly to explore the evolution of W chromosomes in butterflies and moths. We show that in H. misippus, the W chromosome has higher similarity to the Z chromosome than any other chromosome, which could suggest a possible origin from the same homologous autosome pair as the Z chromosome. However, using genome assemblies of closely related species (ditrysian lineages) containing assembled W chromosomes, we present contrasting evidence suggesting that the W chromosome might have evolved from a B chromosome instead. Crucially, by using a synteny analysis to infer homology, we show that W chromosomes are likely to share a common evolutionary origin in Lepidoptera. This study highlights the difficulty of studying the evolution of W chromosomes and contributes to better understanding its evolutionary origins.

An explanation for the prevalence of XY over ZW sex determination in species derived from hermaphroditism

The many independent transitions from hermaphroditism to separate sexes (dioecy) in flowering plants and some animal clades must often have involved the emergence of a heterogametic sex-determining locus, the basis of XY and ZW sex determination (i.e., male and female heterogamety). Current estimates indicate that XY sex determination is much more frequent than ZW, but the reasons for this asymmetry are unclear. One proposition is that separate sexes evolve through the invasion of sterility mutations at closely linked loci, in which case XY sex determination evolves if the initial male sterility mutation is fully recessive. Alternatively, dioecy may evolve via the gradual divergence of male and female phenotypes, but the genetic basis of such divergence and its connection to XY and ZW systems remain poorly understood. Using mathematical modeling, we show how dioecy with XY or ZW sex determination can emerge from the joint evolution of resource allocation to male and female function with its genetic architecture. Our model reveals that whether XY or ZW sex determination evolves depends on the trade-off between allocation to male and female function, and on the mating system of the ancestral hermaphrodites, with selection for female specialization or inbreeding avoidance both favoring XY sex determination. Together, our results cast light on an important but poorly understood path from hermaphroditism to dioecy, and provide an adaptive hypothesis for the preponderance of XY systems. Beyond sex and sex determination, our model shows how ecology can influence the way selection shapes the genetic architecture of polymorphic traits.