Genetics of sexual development: an evolutionary playground for fish

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.

A study on the functional role of the DHCR24 gene in gonadal differentiation and development of Macrobrachium nipponense

Sex differentiation in crustaceans is a complex process influenced by various factors, including the androgenic gland and sex-related genes. This study characterized the role of the Mn-DHCR24 gene in the oriental river prawn (Macrobrachium nipponense). We used bioinformatics to analyze sequence features and phylogenetic relationships of a single Mn-DHCR24 gene. The expression patterns of Mn-DHCR24 across different tissues and developmental stages were determined by real-time PCR, and its localization in testis was determined by in situ hybridization. RNA interference was used to knock down Mn-DHCR24 expression, followed by examining changes in sex ratio and gonadal development at the PL10 stage. Additionally, an enzyme-linked immunosorbent assay measured 17α-methyltestosterone levels, and tissue sections were used to characterize gonadal development. The results indicated that Mn-DHCR24 was high expression in testis, which was critical for sperm maturation and gonadal differentiation. RNAi experiments showed the role of Mn-DHCR24 during reproductive regulation rather than as a master gene for sex differentiation. This study further showed that Mn-DHCR24 regulated sex and hormone-related genes, influencing steroid biosynthesis pathways. Together, these findings provided valuable insights into the genetic and hormonal mechanisms of gonadal differentiation in M. nipponense, and supported the development of monosex culture technology.

CRISPR/Cas9 Technology for Enhancing Desirable Traits of Fish Species in Aquaculture

Aquaculture, the world's fastest-growing food production sector, is critical for addressing food security concerns because of its potential to deliver high-quality, nutrient-rich supplies by 2050. This review assesses the effectiveness of CRISPR/Cas9 genome editing technology in enhancing desirable traits in fish species, including growth rates, muscle quality, disease resistance, pigmentation, and more. It also focuses on the potential effectiveness of the technology in allowing precise and targeted modifications of fish DNA to improve desirable characteristics. Many studies have reported successful applications of CRISPR/Cas9, such as knocking out reproductive genes to control reproduction and sex determination, enhancing feed conversion efficiency, and reducing off-target effects. Additionally, this technology has contributed to environmental sustainability by reducing nitrogen-rich waste and improving the nutritional composition of fish. However, the acceptance of CRISPR/Cas9 modified fish by the public and consumers is hindered by concerns regarding public perception, potential ecological impacts, and regulatory frameworks. To gain public approval and consumer confidence, clear communication about the editing process, as well as data on the safety and environmental considerations of genetically modified fish, are essential. This review paper discusses these challenges, provides possible solutions, and recommends future research on the integration of CRISPR/Cas9 into sustainable aquaculture practices, focusing on the responsible management of genetically modified fish to enable the creation of growth and disease-resistant strains. In conclusion, this review highlights the transformative potential of CRISPR/Cas9 technology in improving fish traits, while also considering the challenges and ethical considerations associated with sustainable and responsible practices in aquaculture.

Genomic architecture and population structure of Boreogadus saida from Canadian waters

The polar cod, Boreogadus saida, is an abundant and ubiquitous forage fish and a crucial link in Arctic marine trophic dynamics. Our objective was to unravel layers of genomic structure in B. saida from Canadian waters, specifically screening for potential hybridization with the Arctic cod, Arctogadus glacialis, large chromosomal inversions, and sex-linked regions, prior to interpreting population structure. Our analysis of 53,384 SNPs in 522 individuals revealed hybridization and introgression between A. glacialis and B. saida. Subsequent population level analyses of B. saida using 12,305 SNPs in 511 individuals revealed three large (ca. 7.4-16.1 Mbp) chromosomal inversions, and a 2 Mbp region featuring sex-linked loci. We showcase population structuring across the Western and Eastern North American Arctic, and subarctic regions ranging from the Hudson Bay to the Canadian Atlantic maritime provinces. Genomic signal for the inferred population structure was highly aggregated into a handful of SNPs (13.8%), pointing to potentially important adaptive evolution across the Canadian range. Our study provides a high-resolution perspective on the genomic structure of B. saida, providing a foundation for work that could be expanded to the entire circumpolar range for the species.

Effects of exogenous steroid hormones on growth, body color, and gonadal development in the Opsariichthys bidens

To investigate the effects of exogenous steroid hormones on growth, body color, and gonadal development in the Opsariichthys bidens (O. bidens), synthetic methyltestosterone (MT) and 17β-estradiol (E2) were used for 28 days' treatment of 4-month-old O. bidens before the breeding season. Our results suggested that MT had a significant growth-promoting effect (P < 0.05), whereas E2 played an inhibitory role. On the body surface, the females in the MT group showed gray stripes, and the fish in other groups showed no obvious stripes. The males with MT treatment displayed brighter blue-green stripes compared to the CK and E2 groups. The histological analysis showed that the MT significantly promoted testes development in males, blocked oocyte development, and caused massive apoptosis in females, whereas the E2 group promoted ovarian development and inhibited testes development. Based on qRT-PCR analysis, in females, the expression of igf-1, dmrt1, and cyp19a1a genes revealed that E2 treatment resulted in down-regulation of igf-1 expression and up-regulation of cyp19a1a expression. In males, igf-1 and dmrt1 were significantly up-regulated after MT treatment, and E2 treatment led to down-regulation of igf-1. Therefore, this study demonstrates that MT and E2 play an important role in reversing the morphological sex characteristics of females and males.

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.

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

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

Breaking Through the Bottleneck: Krogh's Principle in Behavioral Neuroendocrinology and the Potential of Gene Editing

In 1929, August Krogh wrote that for every question in biology, there is a species or collection of species in which pursuing such questions is the most appropriate for achieving the deepest insights. Referred to as "Krogh's Principle," these words are a guiding force for many biologists. In practice, Krogh's principle might guide a biologist interested in studying bi-parental care to choose not to use lab mice, in which the female does most of the parenting, but instead study species in which bi-parental care is present and clearly observable, such as in certain poison dart frogs. This approach to pursuing biological questions has been fruitful, with more in-depth insights achievable with new technologies. However, up until recently, an important limitation of Krogh's principle for biologists interested in the functions of certain genes, was certain techniques were only available for a few traditional model organisms such as lab mice, fruit flies (Drosophila melanogaster), zebrafish (Danio rerio) and C. elegans (Caenorhabditis elegans), in which testing the functions of molecular systems on biological processes can be achieved using genetic knockout (KO) and transgenic technology. These methods are typically more precise than other approaches (e.g., pharmacology) commonly used in nontraditional model organisms to address similar questions. Therefore, some of the most in-depth insights into our understanding of the molecular control of these mechanisms have come from a small number of genetically tractable species. Recent advances in gene editing technology such as CRISPR (Clustered Regularly Interspersed Short Palindromic Repeats)/Cas9 gene editing as a laboratory tool has changed the insights achievable for biologists applying Krogh's principle. In this review, we will provide a brief summary on how some researchers of nontraditional model organisms have been able to achieve different levels of experimental precision with limited genetic tractability in their non-traditional model organism in the field of behavioral neuroendocrinology, a field in which understanding tissue and brain-region specific actions of molecules of interest has been a major goal. Then, we will highlight the exciting potential of Krogh's principle using discoveries made in a popular model species of social behavior, the African cichlid fish Astatotilapia burtoni. Specifically, we will focus on insights gained from studies of the control of social status by sex steroid hormones (androgens and estrogens) in A. burtoni that originated during field observations during the 1970s, and have recently culminated in novel insights from CRISPR/Cas9 gene editing in laboratory studies. Our review highlighting discoveries in A. burtoni may function as a roadmap for others using Krogh's principle aiming to incorporate gene editing into their research program. Gene editing is thus a powerful complimentary laboratory tool researchers can use to yield novel insights into understanding the molecular mechanisms of physiology and behavior in non-traditional model organisms.

Limited evidence for extensive genetic differentiation between X and Y chromosomes in Hybognathus amarus (Cypriniformes: Leuciscidae)

Sex determination systems and genetic sex differentiation across fishes are highly diverse but are unknown for most Cypriniformes, including Rio Grande silvery minnow (Hybognathus amarus). In this study, we aimed to detect and validate sex-linked markers to infer sex determination system and to demonstrate the utility of combining several methods for sex-linked marker detection in nonmodel organisms. To identify potential sex-linked markers, Nextera-tagmented reductively amplified DNA (nextRAD) libraries were generated from 66 females, 64 males, and 60 larvae of unknown sex. These data were combined with female and male de novo genomes from Nanopore long-read sequences. We identified five potential unique male nextRAD-tags and one potential unique male contig, suggesting an XY sex determination system. We also identified two single-nucleotide polymorphisms (SNPs) in the same contig with values of FST, allele frequencies, and heterozygosity conforming with expectations of an XY system. Through PCR we validated the marker containing the sex-linked SNPs and a single nextRAD-tag sex-associated marker but it was not male specific. Instead, more copies of this locus in the male genome were suggested by enhanced amplification in males. Results are consistent with an XY system with low differentiation between sex-determining regions. Further research is needed to confirm the level of differentiation between the sex chromosomes. Nonetheless, this study highlighted the power of combining reduced representation and whole-genome sequencing for identifying sex-linked markers, especially when reduced representation sequencing does not include extensive variation between sexes, either because such variation is not present or not captured.

De Novo Assembly, Characterization and Comparative Transcriptome Analysis of the Gonads of Jade Perch (Scortum barcoo)

Due to the high meat yield and rich nutritional content, jade perch (Scortum barcoo) has become an important commercial aquaculture species in China. Jade perch has a slow growth rate, taking 3-4 years to reach sexual maturity, and has almost no difference in body size between males and females. However, the study of its gonad development and reproduction regulation is still blank, which limited the yield increase. Herein, the gonad transcriptomes of juvenile males and females of S. barcoo were identified for the first time. A total of 107,060 unigenes were successfully annotated. By comparing male and female gonad transcriptomes, a total of 23,849 differentially expressed genes (DEGs) were identified, of which 9517 were downregulated, and 14,332 were upregulated in the testis. In addition, a large number of DEGs involved in sex differentiation, gonadal development and differentiation and gametogenesis were identified, and the differential expression patterns of some genes were further verified using real-time fluorescence quantitative PCR. The results of this study will provide a valuable resource for further studies on sex determination and gonadal development of S. barcoo.

Validation of a male-specific DNA marker confirms XX/XY-type sex determination in several Hungarian strains of African catfish (Clarias gariepinus)

African catfish (Clarias gariepinus) is a promising food fish species with significant potential and growing mass of production in freshwater aquaculture. Male African catfish possess improved production characteristics over females, therefore the use of monosex populations could be advantageous for aquaculture production. However, our knowledge about the sex determination mechanism of this species is still limited and controversial. A previously isolated male-specific DNA marker (CgaY1) was validated using offspring groups from targeted crosses (n = 630) and it was found to predict the sex of 608 individuals correctly (96.43% accuracy). Using the proportion of recombinants, we estimated the average genetic distance between the potential sex determination locus and the sex-specific marker to be 3.57 cM. As an earlier study suggested that both XX/XY and ZZ/ZW systems coexist in this species, we tested the applicability of their putative 'moderately sex-linked loci' and found that no sex-specific amplification could be detected for any of them. In addition, temperature-induced masculinization suggested by others was also tested, but no such effect was detected in our stocks when the published parameters were used for heat treatment. Altogether, our results support an exclusive XX/XY sex determination system in our African catfish stock and indicate a good potential for the future use of this male-specific DNA marker in research and commercial production.

Insights into Early Ontogenesis of Salmo salar: RNA Extraction, Housekeeping Gene Validation and Transcriptional Expression of Important Primordial Germ Cell and Sex-Determination Genes

The challenge in extracting high-quality RNA impedes the investigation of the transcriptome of developing salmonid embryos. Furthermore, the mRNA expression pattern of important PGC and SD genes during the initial embryonic development of Salmo salar is yet to be studied. So, in the present study, we aimed to isolate high-quality RNA from eggs and developing embryos to check vasa, dnd1, nanos3a, sdf1, gsdf, amh, cyp19a, dmrt1 and foxl2 expression by qPCR. Additionally, four HKGs (GAPDH, UB2L3, eEf1a and β-actin) were validated to select the best internal control for qPCR. High-quality RNA was extracted, which was confirmed by spectrophotometer, agarose gel electrophoresis and Agilent TapeStation analysis. UB2L3 was chosen as a reference gene because it exhibited lower intra- and inter-sample variation. vasa transcripts were expressed in all the developmental stages, while dnd1 was expressed only up to 40 d°C. Nanos3a was expressed in later stages and remained at its peak for a shorter period, while sdf1 showed an irregular pattern of mRNA expression. The mRNA expression levels of SD genes were observed to be upregulated during the later stages of development, prior to hatching. This study presents a straightforward methodology for isolating high-quality RNA from salmon eggs, and the resulting transcript profiles of significant PGC and SD genes in S. salar could aid in improving our comprehension of reproductive development in this commercially important species.

A high-quality chromosome-level genome assembly of rohu carp, Labeo rohita, and its utilization in SNP-based exploration of gene flow and sex determination

Labeo rohita (rohu) is a carp important to aquaculture in South Asia, with a production volume close to Atlantic salmon. While genetic improvements to rohu are ongoing, the genomic methods commonly used in other aquaculture improvement programs have historically been precluded in rohu, partially due to the lack of a high-quality reference genome. Here we present a high-quality de novo genome produced using a combination of next-generation sequencing technologies, resulting in a 946 Mb genome consisting of 25 chromosomes and 2,844 unplaced scaffolds. Notably, while approximately half the size of the existing genome sequence, our genome represents 97.9% of the genome size newly estimated here using flow cytometry. Sequencing from 120 individuals was used in conjunction with this genome to predict the population structure, diversity, and divergence in three major rivers (Jamuna, Padma, and Halda), in addition to infer a likely sex determination mechism in rohu. These results demonstrate the utility of the new rohu genome in modernizing some aspects of rohu genetic improvement programs.

Inactivation of the Anti-Müllerian Hormone Receptor Type 2 (amhrII) Gene in Northern Pike (Esox lucius) Results in Male-To-Female Sex Reversal

BACKGROUND

The anti-müllerian hormone (Amh) pathway is crucial for sexual development in teleosts. A male-specific duplicate of anti-müllerian hormone (amhby) was previously identified as the northern pike (Esox lucius) master sex determination gene. However, the role of its putative cognate receptor, i.e., the anti-müllerian hormone receptor type 2 (amhrII) was unclear in this species.

OBJECTIVE

Here, we investigated the role of amhrII during sexual development of northern pike.

METHOD

We generated stable mutants with deletions in exon 9 of amhrII, inactivating the AmhrII protein using a CRISPR-Cas9-mediated gene knockout strategy.

RESULT

The inactivation of amhrII in northern pike results in a high level of male-to-female sex reversal.

CONCLUSION

This result demonstrates that amhrII is necessary for male sexual development in northern pike and supports the idea that AmhrII is a conserved regulator of the teleosts sex differentiation network.

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

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

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.

A chromosome-level genome assembly of the potato grouper (Epinephelus tukula)

The potato grouper, Epinephelus tukula, is one of the largest coral reef teleost, and it is an important germplasm resource for selection and cross breeding. Here we report a potato grouper genome assembly generated using PacBio long-read sequencing, Illumina sequencing and high-throughput chromatin conformation capture (Hi-C) technology. The genome size was 1.13 Gb, with a total of 508 contigs anchored into 24 chromosomes. The scaffold N50 was 42.65 Mb. For the genome models, our assembled genome contained 98.11% complete BUSCO with the vertebrata_odb9 database. One more copies of Gh and Hsp90b1 were identified in the E. tukula genome, which might contribute to its fast growth and high resistance to stress. In addition, 435 putative antimicrobial peptide (AMP) genes were identified in the potato grouper. This study provides a good reference for whole genome selective breeding of the potato grouper and for future development of novel marine drugs.

Whole-Genome Inter-Sex Variation in Russian Sturgeon (Acipenser gueldenstaedtii)

The Russian sturgeon (Acipenser gueldenstaedtii, AG) is an endangered fish species increasingly raised on fish farms for black caviar. Understanding the process of sex determination in AG is, therefore, of scientific and commercial importance. AG lacks sexual dimorphism until sexual maturation and has a predominantly octoploid genome without a definite sex chromosome. A conserved short female-specific genomic sequence was recently described, leading to the development of a genetic sex marker. However, no biological function has been reported for this sequence. Thus, the mechanism of sex determination and the overall inter-sex genomic variation in AG are still unknown. To comprehensively analyze the inter-sex genomic variation and assess the overall inter-species variation between AG and A. ruthenus (AR, sterlet), a related tetraploid sturgeon species, we performed whole-genome sequencing on DNA from 10 fish-farm-raised adult AG (5 males and 5 females). We produced a partially assembled, ~2390 MBp draft genome for AG. We validated in AG the female-specific region previously described in AR. We identified ~2.8 million loci (SNP/indels) varying between the species, but only ~7400 sex-associated loci in AG. We mapped the sex-associated AG loci to the AR genome and identified 15 peaks of sex-associated variation (10 kb segments with 30 or more sex-associated variants), 1 of which matched the previously reported sex-variable region. Finally, we identified 14 known and predicted genes in proximity to these peaks. Our analysis suggests that one or more of these genes may have functional roles in sex determination and/or sexual differentiation in sturgeons. Further functional studies are required to elucidate these roles.

Identification of sex chromosome and sex-determining gene of southern catfish (Silurus meridionalis) based on XX, XY and YY genome sequencing

Teleosts are important models to study sex chromosomes and sex-determining (SD) genes because they present a variety of sex determination systems. Here, we used Nanopore and Hi-C technologies to generate a high-contiguity chromosome-level genome assembly of a YY southern catfish (Silurus meridionalis). The assembly is 750.0 Mb long, with contig N50 of 15.96 Mb and scaffold N50 of 27.22 Mb. We also sequenced and assembled an XY male genome with a size of 727.2 Mb and contig N50 of 13.69 Mb. We identified a candidate SD gene through comparisons to our previous assembly of an XX individual. By resequencing male and female pools, we characterized a 2.38 Mb sex-determining region (SDR) on Chr24. Analysis of read coverage and comparison of the X and Y chromosome sequences showed a Y specific insertion (approx. 500 kb) in the SDR which contained a male-specific duplicate of amhr2 (named amhr2y). amhr2y and amhr2 shared high-nucleotide identity (81.0%) in the coding region but extremely low identity in the promotor and intron regions. The exclusive expression in the male gonadal primordium and loss-of-function inducing male to female sex reversal confirmed the role of amhr2y in male sex determination. Our study provides a new example of amhr2 as the SD gene in fish and sheds light on the convergent evolution of the duplication of AMH/AMHR2 pathway members underlying the evolution of sex determination in different fish lineages.

Sexual development dysgenesis in interspecific hybrids of Medaka fish

Fish are amongst vertebrates the group with the highest diversity of known sex-determining genes. Particularly, the genus Oryzias is a suitable taxon to understand how different sex determination genetic networks evolved in closely related species. Two closely related species, O. latipes and O. curvinotus, do not only share the same XX/XY sex chromosome system, but also the same male sex-determining gene, dmrt1bY. We performed whole mRNA transcriptomes and morphology analyses of the gonads of hybrids resulting from reciprocal crosses between O. latipes and O. curvinotus. XY male hybrids, presenting meiotic arrest and no production of sperm were sterile, and about 30% of the XY hybrids underwent male-to-female sex reversal. Both XX and XY hybrid females exhibited reduced fertility and developed ovotestis while aging. Transcriptome data showed that male-related genes are upregulated in the XX and XY female hybrids. The transcriptomes of both types of female and of the male gonads are characterized by upregulation of meiosis and germ cell differentiation genes. Differences in the parental species in the downstream pathways of sexual development could explain sex reversal, sterility, and the development of intersex gonads in the hybrids. We hypothesize that male-to-female sex reversal may be connected to a different development time between species at which dmrt1bY expression starts. Our results provide molecular clues for the proximate mechanisms of hybrid incompatibility and Haldane’s rule.

Heterochiasmy and the establishment of gsdf as a novel sex determining gene in Atlantic halibut

Atlantic Halibut (Hippoglossus hippoglossus) has a X/Y genetic sex determination system, but the sex determining factor is not known. We produced a high-quality genome assembly from a male and identified parts of chromosome 13 as the Y chromosome due to sequence divergence between sexes and segregation of sex genotypes in pedigrees. Linkage analysis revealed that all chromosomes exhibit heterochiasmy, i.e. male-only and female-only meiotic recombination regions (MRR/FRR). We show that FRR/MRR intervals differ in nucleotide diversity and repeat class content and that this is true also for other Pleuronectidae species. We further show that remnants of a Gypsy-like transposable element insertion on chr13 promotes early male specific expression of gonadal somatic cell derived factor (gsdf). Less than 4.5 MYA, this male-determining element evolved on an autosomal FRR segment featuring pre-existing male meiotic recombination barriers, thereby creating a Y chromosome. Our findings indicate that heterochiasmy may facilitate the evolution of genetic sex determination systems relying on linkage of sexually antagonistic loci to a sex-determining factor.

Even closely related fish species can have different sex chromosomes, but this turn-over of sex determination systems is poorly understood. Here, we used large-scale genome sequencing to determine the DNA sequence of the Atlantic halibut chromosomes and compared sequencing data from males and females to identify the sex chromosomes. We show that males have much higher gene activity of the gene gonadal somatic cell derived factor (gsdf), which is located on the sex chromosomes and has a role in testicular development. The genome contains many mobile DNA sequences, transposable elements (TEs), one placed in front of gsdf, enhancing its activity. This made gsdf the sex determining factor, thereby creating a new Y-chromosome. We further describe how all Atlantic halibut chromosomes behave similar to sex chromosomes in that most regions only recombine in one sex. This phenomenon may contribute to the rapid turn-over of genetic sex determination systems in fish. Our results highlight the molecular events creating a new Y-chromosome and show that the new Atlantic halibut Y was formed less than 4.5 million years ago. Future studies in Atlantic halibut and closely related species can shed light on mechanisms contributing to sex chromosome evolution in fish.

Labile sex chromosomes in the Australian freshwater fish family Percichthyidae

Sex-specific ecology has management implications, but rapid sex-chromosome turnover in fishes hinders sex-marker development for monomorphic species. We used annotated genomes and reduced-representation sequencing data for two Australian percichthyids, Macquarie perch Macquaria australasica and golden perch M. ambigua, and whole genome resequencing for 50 Macquarie perch of each sex, to identify sex-linked loci and develop an affordable sexing assay. In silico pool-seq tests of 1,492,004 Macquarie perch SNPs revealed that a 275-kb scaffold was enriched for gametologous loci. Within this scaffold, 22 loci were sex-linked in a predominantly XY system, with females being homozygous for the X-linked allele at all 22, and males having the Y-linked allele at >7. Seven XY-gametologous loci (all males, but no females, are heterozygous or homozygous for the male-specific allele) were within a 146-bp region. A PCR-RFLP sexing assay targeting one Y-linked SNP, tested in 66 known-sex Macquarie perch and two of each sex of three confamilial species, plus amplicon sequencing of 400 bp encompassing the 146-bp region, revealed that the few sex-linked positions differ between species and between Macquarie perch populations. This indicates sex-chromosome lability in Percichthyidae, supported by nonhomologous scaffolds containing sex-linked loci for Macquarie- and golden perches. The present resources facilitate genomic research in Percichthyidae, including formulation of hypotheses about candidate genes of interest such as transcription factor SOX1b that occurs in the 275-kb scaffold ~38 kb downstream of the 146-bp region containing seven XY-gametologous loci. Sex-linked markers will be useful for determining genetic sex in some populations and studying sex chromosome turnover.

Reference genome of Lumpfish Cyclopterus lumpus Linnaeus provides evidence of male heterogametic sex determination through the AMH pathway

Teleosts exhibit extensive diversity of sex determination (SD) systems and mechanisms, providing the opportunity to study the evolution of sex determination and sex chromosomes. Here we sequenced the genome of the Common Lumpfish (Cyclopterus lumpus Linnaeus), a species of increasing importance to aquaculture, and identified the SD region and master SD locus using a 70K SNP array and tissue-specific expression data. The chromosome-level assembly identified 25 diploid chromosomes with a total size of 572.89 Mb, a scaffold N50 of 23.86 Mb, and genome annotation predicted 21,480 protein-coding genes. Genome wide association analysis located a highly sex-associated region on chromosome 13, suggesting that anti-Müllerian hormone (AMH) is the putative SD factor. Linkage disequilibrium and heterozygosity across chromosome 13 support a proto-XX/XY system, with an absence of widespread chromosome divergence between sexes. We identified three copies of AMH in the Lumpfish primary and alternate haplotype assemblies localized in the SD region. Comparison to sequences from other teleosts suggested a monophyletic relationship and conservation within the Cottioidei. One AMH copy showed similarity to AMH/AMHY in a related species and was also the only copy with expression in testis tissue, suggesting this copy may be the functional copy of AMH in Lumpfish. The two other copies arranged in tandem inverted duplication were highly similar, suggesting a recent duplication event. This study provides a resource for the study of early sex chromosome evolution and novel genomic resources that benefits Lumpfish conservation management and aquaculture.

The genome of New Zealand trevally (Carangidae: Pseudocaranx georgianus) uncovers a XY sex determination locus

BACKGROUND

The genetic control of sex determination in teleost species is poorly understood. This is partly because of the diversity of mechanisms that determine sex in this large group of vertebrates, including constitutive genes linked to sex chromosomes, polygenic constitutive mechanisms, environmental factors, hermaphroditism, and unisexuality. Here we use a de novo genome assembly of New Zealand silver trevally (Pseudocaranx georgianus) together with sex-specific whole genome sequencing data to detect sexually divergent genomic regions, identify candidate genes and develop molecular makers.

RESULTS

The de novo assembly of an unsexed trevally (Trevally_v1) resulted in a final assembly of 579.4 Mb in length, with a N50 of 25.2 Mb. Of the assembled scaffolds, 24 were of chromosome scale, ranging from 11 to 31 Mb in length. A total of 28,416 genes were annotated after 12.8 % of the assembly was masked with repetitive elements. Whole genome re-sequencing of 13 wild sexed trevally (seven males and six females) identified two sexually divergent regions located on two scaffolds, including a 6 kb region at the proximal end of chromosome 21. Blast analyses revealed similarity between one region and the aromatase genes cyp19 (a1a/b) (E-value < 1.00E-25, identity > 78.8 %). Males contained higher numbers of heterozygous variants in both regions, while females showed regions of very low read-depth, indicative of male-specificity of this genomic region. Molecular markers were developed and subsequently tested on 96 histologically-sexed fish (42 males and 54 females). Three markers amplified in absolute correspondence with sex (positive in males, negative in females).

CONCLUSIONS

The higher number of heterozygous variants in males combined with the absence of these regions in females support a XY sex-determination model, indicating that the trevally_v1 genome assembly was developed from a male specimen. This sex system contrasts with the ZW sex-determination model documented in closely related carangid species. Our results indicate a sex-determining function of a cyp19a1a-like gene, suggesting the molecular pathway of sex determination is somewhat conserved in this family. The genomic resources developed here will facilitate future comparative work, and enable improved insights into the varied sex determination pathways in teleosts. The sex marker developed in this study will be a valuable resource for aquaculture selective breeding programmes, and for determining sex ratios in wild populations.

Against the mainstream: exceptional evolutionary stability of ZW sex chromosomes across the fish families Triportheidae and Gasteropelecidae (Teleostei: Characiformes)

Teleost fishes exhibit a breath-taking diversity of sex determination and differentiation mechanisms. They encompass at least nine sex chromosome systems with often low degree of differentiation, high rate of inter- and intra-specific variability, and frequent turnovers. Nevertheless, several mainly female heterogametic systems at an advanced stage of genetic differentiation and high evolutionary stability have been also found across teleosts, especially among Neotropical characiforms. In this study, we aim to characterize the ZZ/ZW sex chromosome system in representatives of the Triportheidae family (Triportheus auritus, Agoniates halecinus, and the basal-most species Lignobrycon myersi) and its sister clade Gasteropelecidae (Carnegiella strigata, Gasteropelecus levis, and Thoracocharax stellatus). We applied both conventional and molecular cytogenetic approaches including chromosomal mapping of 5S and 18S ribosomal DNA clusters, cross-species chromosome painting (Zoo-FISH) with sex chromosome-derived probes and comparative genomic hybridization (CGH). We identified the ZW sex chromosome system for the first time in A. halecinus and G. levis and also in C. strigata formerly reported to lack sex chromosomes. We also brought evidence for possible mechanisms underlying the sex chromosome differentiation, including inversions, repetitive DNA accumulation, and exchange of genetic material. Our Zoo-FISH experiments further strongly indicated that the ZW sex chromosomes of Triportheidae and Gasteropelecidae are homeologous, suggesting their origin before the split of these lineages (approx. 40-70 million years ago). Such extent of sex chromosome stability is almost exceptional in teleosts, and hence, these lineages afford a special opportunity to scrutinize unique evolutionary forces and pressures shaping sex chromosome evolution in fishes and vertebrates in general.

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

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

Dynamics of sex chromosome evolution in a rapid radiation of cichlid fishes

Sex is a fundamental trait determined by environmental and/or genetic factors, including sex chromosomes. Sex chromosomes are studied in species scattered across the tree of life, yet little is known about tempo and mode of sex chromosome evolution among closely related species. Here, we examine sex chromosome evolution in the adaptive radiation of cichlid fishes in Lake Tanganyika. Through the analysis of male and female genomes from 244 cichlid taxa (189 described species with 5 represented with two local variants/populations; 50 undescribed species) and of 396 multitissue transcriptomes from 66 taxa, we identify signatures of sex chromosomes in 79 taxa, involving 12 linkage groups. We find that Tanganyikan cichlids have the highest rates of sex chromosome turnover and heterogamety transitions known to date. We show that sex chromosome recruitment is not at random. Moreover convergently emerged sex chromosomes in cichlids support the “limited options” hypothesis of sex chromosome evolution.

Might Gene Duplication and Neofunctionalization Contribute to the Sexual Lability Observed in Fish?

Sex determination and differentiation varies widely across vertebrates, but is most dramatically diverse in fishes. Among fishes sex reversal and sex change are observed in 41 teleost families spanning 7 orders. These sex-changing fish perhaps highlight better than any other system that sex determination is not the narrow and fixed construct we once thought, but a plastic trait that is better viewed as a reaction norm. However, while this stunning transformation is increasingly understood, a fundamental question arises, which is why some fish species have retained this inherent plasticity in sexual fate, while others have not? Here, we explore our current understanding of sex change in fish, some of the factors that permit and constrain sex reversal, and posit that gene duplication and neofunctionalization contribute to the sexual lability observed in fish.

Oryzias curvinotus in Sanya Does Not Contain the Male Sex-Determining Gene dmy

Hainan medaka (Oryzias curvinotus) is distributed in the coastal waters of the South China Sea and is able to adapt to a wide range of salinities. In this study, we characterized O. curvinotus in Sanya River (SY-medaka), which lacks dmy (a male sex-determining gene in O. latipes and O. curvinotus). In a comparison of SY-medaka and Gaoqiao medaka (GQ-medaka), the morphological difference between the two populations does not reach the subspecies level and they can be considered two geographic populations of O. curvinotus. A mitochondrial cytochrome oxidase subunit I (CoI) sequence alignment showed that the sequence identities between SY-medaka and other geographic populations of O. curvinotus are as high as 95%. A phylogenetic analysis of the mitochondrial genome also indicated that SY-medaka belongs to O. curvinotus. Molecular marker-based genetic sex assays and whole genome re-sequencing showed that SY-medaka does not contain dmy. Further, in RNA-Seq analyses of the testis and ovaries of sexually mature SY-medaka, dmy expression was not detected. We speculate that high temperatures resulted in the loss of dmy in SY-medaka during evolution, or the lineage has another sex-determining gene. This study provides a valuable dataset for elucidating the mechanism underlying sex determination in Oryzias genus and advances research on functional genomics or reproduction biology in O. curvinotus.

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

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

RADSex: A computational workflow to study sex determination using restriction site-associated DNA sequencing data

The study of sex determination and sex chromosome organization in nonmodel species has long been technically challenging, but new sequencing methodologies now enable precise and high-throughput identification of sex-specific genomic sequences. In particular, restriction site-associated DNA sequencing (RAD-Seq) is being extensively applied to explore sex determination systems in many plant and animal species. However, software specifically designed to search for and visualize sex-biased markers using RAD-Seq data is lacking. Here, we present RADSex, a computational analysis workflow designed to study the genetic basis of sex determination using RAD-Seq data. RADSex is simple to use, requires few computational resources, makes no prior assumptions about the type of sex-determination system or structure of the sex locus, and offers convenient visualization through a dedicated R package. To demonstrate the functionality of RADSex, we re-analysed a published data set of Japanese medaka, Oryzias latipes, where we uncovered a previously unknown Y chromosome polymorphism. We then used RADSex to analyse new RAD-Seq data sets from 15 fish species spanning multiple taxonomic orders. We identified the sex determination system and sex-specific markers in six of these species, five of which had no known sex-markers prior to this study. We show that RADSex greatly facilitates the study of sex determination systems in nonmodel species thanks to its speed of analyses, low resource usage, ease of application and visualization options. Furthermore, our analysis of new data sets from 15 species provides new insights on sex determination in fish.

fshr: a fish sex-determining locus shows variable incomplete penetrance across flathead grey mullet populations

Whole-genome sequencing data were produced from a single flathead grey mullet female and assembled into a draft genome sequence, whereas publicly available sequence data were used to obtain a male draft sequence. Two pools, each consisting of 60 unrelated individuals, respectively, of male and female fish were analyzed using Pool-Sequencing. Mapping and analysis of Pool-Seq data against the draft genome(s) revealed >30 loci potentially associated with sex, the most promising locus of which, encoding the follicle-stimulating hormone receptor (fshr) and harboring two missense variants, was genotyped on 245 fish from four Mediterranean populations. Genotype data showed that fshr represents a previously unknown sex-determining locus, although the incomplete association pattern between fshr genotype and sex-phenotype, the variability of such pattern across different populations, and the presence of other candidate loci reveal that a greater complexity underlies sex determination in the flathead grey mullet.

Autosomal sdY Pseudogenes Explain Discordances Between Phenotypic Sex and DNA Marker for Sex Identification in Atlantic Salmon

Despite the key role that sex-determination plays in evolutionary processes, it is still poorly understood in many species. In salmonids, which are among the best studied fishes, the master sex-determining gene sexually dimorphic on the Y-chromosome (sdY) has been identified. However, sdY displays unexplained discordance to the phenotypic sex, with a variable frequency of phenotypic females being reported as genetic males. Multiple sex determining loci in Atlantic salmon have also been reported, possibly as a result of recent transposition events in this species. We hypothesized the existence of an autosomal copy of sdY, causing apparent discordance between phenotypic and genetic sex, that is transmitted in accordance with autosomal inheritance. To test this, we developed a qPCR methodology to detect the total number of sdY copies present in the genome. Based on the observed phenotype/genotype frequencies and linkage analysis among 2,025 offspring from 64 pedigree-controlled families of accurately phenotyped Atlantic salmon, we identified both males and females carrying one or two autosomal copies of sdY in addition to the Y-specific copy present in males. Patterns across families were highly consistent with autosomal inheritance. These autosomal sdY copies appear to have lost the ability to function as a sex determining gene and were only occasionally assigned to the actual sex chromosome in any of the affected families.

Epigenetic regulation of gonadal and brain aromatase expression in a cichlid fish with environmental sex determination

A fit animal must develop testes or ovaries, with brain and physiology to match. In species with alternative male morphs this coordination of development across tissues operates within sexes as well as between. For Pelvicachromis pulcher, an African cichlid in which early pH exposure influences both sex and alternative male morph, we sequence both copies of aromatase (cyp19a1), a key gene for sex determination. We analyze gene expression and epigenetic state, comparing gonad and brain tissue from females, alternative male morphs, and fry. Relative to brain, we find elevated expression of the A-copy in the ovaries but not testes. Methylation analysis suggests strong epigenetic regulation, with one region specifying sex and another specifying tissue. We find elevated brain expression of the B-copy with no sex or male morph differences. B-copy methylation follows that of the A-copy rather than corresponding to B-copy expression. In 30-day old fry, we see elevated B-copy expression in the head, but we do not see the expected elevated A-copy expression in the trunk that would reflect ovarian development. Interestingly, the A-copy epialleles that distinguish ovaries from testes are among the most explanatory patterns for variation among fry, suggesting epigenetic marking of sex prior to differentiation and thus laying the groundwork for mechanistic studies of epigenetic regulation of sex and morph differentiation.

Molecular and morphological sex differentiation in sablefish (Anoplopoma fimbria), a marine teleost with XX/XY sex determination

Phenotypic sex of an organism is determined by molecular changes in the gonads, so-called molecular sex differentiation, which should precede the rise of cellular or anatomical sex-distinguishing features. This study characterized molecular and morphological sex differentiation in sablefish (Anoplopoma fimbria), a marine teleost with established XX/XY genotypic sex determination. Next generation sequencing was conducted on sablefish ovarian and testicular mRNAs to obtain sequences for transcripts associated with vertebrate sex determination and differentiation and early reproductive development. Gene-specific PCRs were developed to determine the distribution and ontogenetic gonadal expression of transcription, growth, steroidogenic and germline factors, as well as gonadotropin and steroid receptors. Molecular changes associated with sex differentiation were first apparent in both XY- and XX-genotype sablefish at ~ 60 mm in body length and prior to histological signs of sex differentiation. The earliest and most robust markers of testicular differentiation were gsdf, amh, dmrt1, cyp11b, star, sox9a, and fshr. Markedly elevated mRNA levels of several steroidogenesis-related genes and ar2 in differentiating testes suggested that androgens play a role in sablefish testicular differentiation. The earliest markers of ovarian differentiation were cyp19a1a, lhcgr, foxl2, nr0b1, and igf3. Other transcripts such as figla, zp3, and pou5f3 were expressed predominantly in XX-genotype fish and significantly increased with the first appearance and subsequent development of primary oocytes. This study provides valuable insight to the developmental sequence of events associated with gonadal sex differentiation in marine teleosts with XX/XY sex determination. It also implicates particular genes in processes of male and female development and establishes robust molecular markers for phenotypic sex in sablefish, useful for ongoing work related to sex control and reproductive sterilization.

Methods for identifying and interpreting sex-linked SNP markers and carrying out sex assignment: application to thornback ray (Raja clavata)

Sex-determining modes remain unknown in numerous species, notably in fishes, in which a variety of modalities have been reported. Additionally, noninvasive individual sexing is problematic for species without external sex attributes or for early life stages, requiring cytogenetic or molecular analyses when sex chromosomes or sex-linked markers have been characterized. Genomics now provide a means to achieve this. Here, we review common sex-determination systems and corresponding statistical methods for identifying sex-linked genetic markers and their use for sex assignment, focusing on single nucleotide polymorphism (SNP) markers derived from reduced representation sequencing methods. We demonstrate the dependence of expected sex assignment error on the number of sex-linked SNPs and minor allele frequency. The application of three methods was made here: (a) identification of heterozygote excess in one sex, (b) F_ST outlier analysis between the two sexes and (c) neuronal net modelling. These methods were applied to a large SNP data set (4604 SNPs) for 1680 thornback rays (Raja clavata). Using method (a), nineteen putative sex-linked SNPs were identified. Comparison with the reference genome of a related species (Amblyraja radiata) indicated that all 19 SNPs are probably located on the same chromosome. These results suggest that thornback ray has a XX/XY sex-determination system. Method (b) identified eight SNPs probably located on different chromosomes. Method (a) led to the lowest sex assignment error among the three methods (4.2% error for females and 3.7% for males).

Exposure of zebrafish to elevated temperature induces sex ratio shifts and alterations in the testicular epigenome of unexposed offspring

Accumulating evidence shows that environmental changes can affect population sex ratios through epigenetic regulation of gene expression in species where sex depends on both genetic and environmental cues. Sometimes, altered sex ratios persist in the next generation even when the environmental cue is no longer present (a multigenerational effect). However, evidence of transgenerational effects (i.e., beyond the first non-exposed generation), which tend to be paternally transmitted, is scarce and a matter of debate. Here, we used the AB strain of zebrafish, where sex depends on both genetic and environmental influences, to study possible multi- (to the F₁) and transgenerational (to the F₂) effects of elevated temperature during the critical period of sex differentiation. From eight initial different families, five were selected in order to capture sufficient variation between the sex ratio of the control group (28 °C) and the group exposed to elevated (35 °C) temperature only at the parental (P) generation. Results showed a consistent increase in the proportion of males in the P generation in all five families as a result of heat treatment. Sex ratios were then determined in the F₁ and F₂ offspring derived from both above groups, which were all raised at 28 °C. A persisting male-skewed sex ratio in the 35°C-derived, unexposed offspring of the F₁ generation was observed in three families, denoting family-dependent multigenerational effects. However, no transgenerational effects were observed in the F₂ generation of any family. DNA methylation was also assessed in the testis of P, F₁ and F₂ males derived from exposed and non-exposed fathers and grandfathers. DNA methylation was significantly decreased only in the testis of the 35°C-derived males in the F₁ generation but not of the F₂ generation and, surprisingly, neither in the 35°C-exposed males of the P generation. Taken together, our results show great interfamily variation, not only in sex ratio response to elevated temperature, but also on its multigenerational effects, denoting a strong influence of genetics. Alterations in the testicular epigenome in F₁ males calls for attention to possible, previously unnoticed, effects of temperature in the unexposed offspring of heat-exposed parents in a global warming scenario.

Genome-wide association analyses based on whole-genome sequencing of Protosalanx hyalocranius provide insights into sex determination of Salangid fishes

Identification of sex determination system and sex-determining genes have important implications in conservation, ecology and evolution. However, much remains to be discovered about the evolution of different sexual determination systems in teleost fishes, of which the mechanisms of sex determination are remarkably variable. In the present study, the whole genomes of 20 males and 20 females of a Salangid fish, Protosalanx hyalocranius, were sequenced and genome wide association analyses were conducted to uncover its sex determination system and putative sex-determining genes. A total of 150 SNPs were significantly associated with sex, which showed high differentiation between sexes (F_ST ranged from 0.245 to 0.556). Of the 150 sex-associated SNPs, 76 SNPs displayed sex specificity with even coverage of depth and were female heterogametic, which suggested a ZZ/ZW sex determination system. Interestingly, one scaffold containing sex-specific SNPs displayed synteny to the sex chromosome of medaka. Annotations of sex-associated loci suggested that both transcriptional regulators (e.g., FOX genes) and secreted hormones and their receptors might be involved in the sex determination/differentiation of P. hyalocranius. More strikingly, we found a nonsense mutation in one copy of GALNT homology gene of all females, which suggested that "Z dosage" effect might play a vital role in the processes of sex determination/differentiation. These sex-specific loci could be a valuable resource for further research on sex determination of Salangid fishes and the results could contribute to the understanding of sex determination mechanisms and the evolution of sex chromosome in teleost fishes.

Characteristics and sex dimorphism of 17β-hydroxysteroid dehydrogenase family genes in the olive flounder Paralichthys olivaceus

Sex steroid hormones play important roles in fish sex differentiation, gonadal development and secondary sexual characteristics. Olive flounder Paralichthys olivaceus is a valuable commercial marine fish species and has marked sexual dimorphism. However, the mechanisms of action of sex hormones in flounder sex are still unclear. In this study, a total of ten Hsd17b family genes, including Hsd17b3, -4, -7, -8, -9, -10, -12a, -12b, -14 and -15, were identified in the flounder, which encoded critical enzymes acting on sex steroid synthesis and metabolism. Hsd17b genes were distributed on eight chromosomes. Hsd17b12a and -12b were located on chromosomes 19 and 7, respectively. It was speculated that these two genes were just highly similar rather than different transcripts derived from the same gene. According to the results of domain and motif analyses, they all belonged to the SDR superfamily and contained conserved Hsd17b motifs TGxxxGxG, PGxxxT, NNAG and YxxxK. Analysis of amino acid sequences predicted that Hsd17b1, -4, -7, -12a and -14 were hydrophilic proteins. The stability of Hsd17b1, -3 and -12b proteins was predicted to be low. The various Hsd17b family genes differed in tissue expression pattern, and Hsd17b10, -12a and -12b were highly expressed in the flounder ovary. Moreover, throughout gonadal development, Hsd17b3 was highly expressed in the testis, and Hsd17b1, -12a and -12b were highly expressed in the ovary, suggesting that they might play an important role in testosterone synthesis in the testis or estrogen synthesis in the ovary. Activities of Hsd17b3 at stages I-V were all significantly higher in the testis than in the ovary (P < 0.05, P < 0.01). Transfection analysis in HEK293T cells showed that Hsd17b1 and -3 were located in both the cytoplasm and nucleus. Additionally, after challenging fish with tamoxifen, Hsd17b3 expression level in the testis decreased significantly (P < 0.01), and in the ovary no significant change was observed. Moreover, the expression of Hsd17b1 in the ovary was significantly upregulated after injection with flutamide (P < 0.05). These findings introduce the characteristics of the flounder Hsd17b in subfamily, which contribute to our understanding of the regulation of sex steroid hormone synthesis in fish gonadal development.

A newly developed genetic sex marker and its application to understanding chemically induced feminisation in roach (Rutilus rutilus)

Oestrogenic wastewater treatment works (WwTW) effluents discharged into UK rivers have been shown to affect sexual development, including inducing intersex, in wild roach (Rutilus rutilus). This can result in a reduced breeding capability with potential population level impacts. In the absence of a sex probe for roach it has not been possible to confirm whether intersex fish in the wild arise from genetic males or females, or whether sex reversal occurs in the wild, as this condition can be induced experimentally in controlled exposures to WwTW effluents and a steroidal oestrogen. Using restriction site-associated DNA sequencing (RAD-seq), we identified a candidate for a genetic sex marker and validated this marker as a sex probe through PCR analyses of samples from wild roach populations from nonpolluted rivers. We also applied the sex marker to samples from roach exposed experimentally to oestrogen and oestrogenic effluents to confirm suspected phenotypic sex reversal from males to females in some treatments, and also that sex-reversed males are able to breed as females. We then show, unequivocally, that intersex in wild roach populations results from feminisation of males, but find no strong evidence for complete sex reversal in wild roach at river sites contaminated with oestrogens. The discovered marker has utility for studies in roach on chemical effects, wild stock assessments, and reducing the number of fish used where only one sex is required for experimentation. Furthermore, we show that the marker can be applied nondestructively using a fin clip or skin swab, with animal welfare benefits.

Spatial and temporal expression pattern of sex-related genes in ovo-testis of the self-fertilizing mangrove killifish (Kryptolebias marmoratus)

In vertebrates, sex determination and differentiation comprehend a fine balance between female and male factors, leading the bipotential anlage to develop towards ovary or testis, respectively. Nevertheless, the mangrove killifish, (Kryptolebias marmoratus) a simultaneous hermaphroditic species, could overcome those antagonistic pathways and evolved to develop and maintain reproductively active ovarian and testicular tissues in the same organ. Morphological and mRNA localization analyzes of developing and adult gonads demonstrate that genes related to testis (dmrt1 and amh) and ovary differentiation (foxl2 and sox9a) follow the same expression pattern observed in gonochoristic species, thus functioning as two independent organs. In addition, Amh expression patterns make it a strong candidate for initiation of the formation and maintenance of the testicular tissue in the hermaphroditic gonad. Differently from described so far, foxl3 seems to have an important role in oogenesis as well as spermatogenesis and gonadal structure.

Disruption of dmrt1 rescues the all-male phenotype of the cyp19a1a mutant in zebrafish - a novel insight into the roles of aromatase/estrogens in gonadal differentiation and early folliculogenesis

Sex determination and differentiation are complex processes controlled by many different factors; however, the relationships among these factors are poorly understood. Zebrafish gonadal differentiation exhibits high plasticity involving multiple factors and pathways, which provides an excellent model for investigating the interactions between them. Ovarian aromatase (cyp19a1a) and dmrt1 are key factors in directing vertebrate ovary and testis differentiation, respectively. Knockout of zebrafish cyp19a1a leads to all-male offspring, whereas the loss of dmrt1 results in a female-biased sex ratio. In the present study, we established dmrt1^-/- ;cyp19a1a^-/- double mutant zebrafish and discovered that the introduction of the dmrt1 mutation into the cyp19a1a mutant could rescue the all-male phenotype of the latter. Interestingly, despite the lack of aromatase/estrogens, the follicles in the ovary of the rescued cyp19a1a mutant could develop normally up to the previtellogenic stage. Further evidence suggested the ovarian aromatase directed ovarian differentiation by suppressing dmrt1 expression via nuclear estrogen receptors (nERs). Our results provide solid evidence for an interaction between cyp19a1a and dmrt1 in zebrafish gonadal differentiation, and for the dispensability of estrogens in controlling early folliculogenesis.

Transcriptome of tambaqui Colossoma macropomum during gonad differentiation: Different molecular signals leading to sex identity

Tambaqui (Colossoma macropomum) is the major native species in Brazilian aquaculture, and we have shown that females exhibit a higher growth compared to males, opening up the possibility for the production of all-female population. To date, there is no information on the sex determination and differentiation molecular mechanisms of tambaqui. In the present study, transcriptome sequencing of juvenile trunks was performed to understand the molecular network involved in the gonadal sex differentiation. The results showed that before differentiation, components of the Wnt/β-catenin pathway, fox and fst genes imprint female sex development, whereas antagonistic pathways (gsk3b, wt1 and fgfr2), sox9 and genes for androgen synthesis indicate male differentiation. Hence, in undifferentiated tambaqui, the Wnt/β-catenin exerts a role on sex differentiation, either upregulated in female-like individuals, or antagonized in male-like individuals.

Sex-specific floral attraction traits in a sequentially hermaphroditic species

●Many angiosperms are hermaphroditic and produce bisexual flowers in which male (pollen export) and female (stigma receptivity) functions are separated temporally. This sequential hermaphroditism may be associated with variation in flower size, color, or pattern, all of which may influence pollinator attraction. In this study, we describe variation in these traits across discrete functional sex stages within and between 225 greenhouse-grown individuals of Clarkia unguiculata (Onagraceae). In addition, to identify the effects of floral phenotype on pollinator attraction in this species, we examine the effects of these floral traits on pollen receipt in ~180 individuals in an experimental field array.●Petal area, ultraviolet (UV)-absorbing nectar guide area, and blue and green mean petal reflectance differ significantly across the functional sex stages of C. unguiculata. Male- and female-phase flowers display significantly different pollinator attraction traits. Petal and UV nectar guide area increase as flowers progress from male phase to female phase, while blue reflectance and green reflectance peak during anther maturation.●In field arrays of C. unguiculata, female-phase flowers with large UV nectar guides receive more pollen than those with small nectar guides, and female-phase flowers with high mean blue reflectance values are more likely to receive pollen than those with low blue reflectance. Female-phase flowers with green mean reflectance values that differ most from background foliage also receive more pollen than those that are more similar to foliage. These findings indicate that components of flower color and pattern influence pollen receipt, independent of other plant attributes that may covary with floral traits. We discuss these results in the context of hypotheses that have been proposed to explain sex-specific floral attraction traits, and we suggest future research that could improve our understanding of sexual dimorphism in sequentially hermaphroditic species and the evolution of features that promote outcrossing.

Evolution of the Proto Sex-Chromosome in Solea senegalensis

Solea senegalensis is a flatfish belonging to the Soleidae family within the Pleuronectiformes order. It has a karyotype of 2n = 42 (FN = 60; 6M + 4 SM + 8 St + 24 T) and a XX/XY system. The first pair of metacentric chromosomes has been proposed as a proto sex-chromosome originated by a Robertsonian fusion between acrocentric chromosomes. In order to elucidate a possible evolutionary origin of this chromosome 1, studies of genomic synteny were carried out with eight fish species. A total of 88 genes annotated within of 14 BACs located in the chromosome 1 of S. senegalensis were used to elaborate syntenic maps. Six BACs (BAC5K5, BAC52C17, BAC53B20, BAC84K7, BAC56H24, and BAC48P7) were distributed in, at least, 5 chromosomes in the species studied, and a group of four genes from BAC53B20 (grsf1, rufy3, slc4a4 and npffr2) and genes from BAC48K7 (dmrt2, dmrt3, dmrt1, c9orf117, kank1 and fbp1) formed a conserved cluster in all species. The analysis of repetitive sequences showed that the number of retroelements and simple repeat per BAC showed its highest value in the subcentromeric region where 53B20, 16E16 and 48K7 BACs were localized. This region contains all the dmrt genes, which are associated with sex determination in some species. In addition, the presence of a satellite “chromosome Y” (motif length: 860 bp) was detected in this region. These findings allowed to trace an evolutionary trend for the large metacentric chromosome of S. senegalensis, throughout different rearrangements, which could be at an initial phase of differentiation as sex chromosome.

Mismatches between the genetic and phenotypic sex in the wild Kou population of Nile tilapia Oreochromis niloticus

Sex determination and sex chromosomes can be very diverse between teleost species. The group of tilapias shows a polymorphism in sex determination not only between closely related species but also between domestic strains within a species. In the Nile tilapia, the major effect genes and therefore the Y chromosome have been located on either linkage group 1 (LG1) or LG23 depending on the strains. In a Japanese strain, the sex determinant of LG23 (the amhY gene) has been identified as a duplicated amh (anti-Müllerian hormone) gene, with its gametolog found on the X chromosome (amhX). AmhY is located in tandem with the amhΔY gene (a truncated form) on the Y chromosome. X and Y chromosome markers based on the amh genes have been validated only on a few domestic strains but not in wild populations. Here, we used four of these markers in order to examine (1) the possible variation in sex determination of a wild population of Nile tilapia living in Lake Kou (Burkina Faso), (2) putative polymorphisms for these amh copies and (3) the existence of sex reversed individuals in the wild. Our genotyping of 91 wild Kou individuals with the amh sex-diagnostic markers of LG23 showed that while phenotypic females were all XX, phenotypic males were either XY or XX. Progeny testing of eight of these XX males revealed that one of these males consistently sired all-female progenies, suggesting that it is a wild sex reversed male (which could result from high temperature effects). The other XX males gave balanced sex ratios, suggesting that sex is controlled by another locus (possibly on another LG) which may be epistatically dominant over the LG23 locus. Finally, identification of unexpected amh genotypes was found for two individuals. They produced either balanced or female-biased sex ratios, depending on the breeder with whom they were crossed, suggesting possible recombination between the X and the Y chromosomes.

The Genetics and Epigenetics of Sex Change in Fish

Fish show extraordinary sexual plasticity, changing sex naturally as part of their life cycle or reversing sex because of environmental stressors. This plasticity shows that sexual fate is not an irreversible process but the result of an ongoing tug-of-war for supremacy between male and female signaling networks. The behavioral, gonadal, and morphological changes involved in this process are well described, yet the molecular events that underpin those changes remain poorly understood. Epigenetic modifications emerge as a critical link between environmental stimuli, the onset of sex change, and subsequent maintenance of sexual phenotype. Here we synthesize current knowledge of sex change, focusing on the genetic and epigenetic processes that are likely involved in the initiation and regulation of sex change. We anticipate that better understanding of sex change in fish will shed new light on sex determination and development in vertebrates and on how environmental perturbations affect sexual fate.

Identification of the master sex determining gene in Northern pike (Esox lucius) reveals restricted sex chromosome differentiation

Teleost fishes, thanks to their rapid evolution of sex determination mechanisms, provide remarkable opportunities to study the formation of sex chromosomes and the mechanisms driving the birth of new master sex determining (MSD) genes. However, the evolutionary interplay between the sex chromosomes and the MSD genes they harbor is rather unexplored. We characterized a male-specific duplicate of the anti-Müllerian hormone (amh) as the MSD gene in Northern Pike (Esox lucius), using genomic and expression evidence as well as by loss-of-function and gain-of-function experiments. Using RAD-Sequencing from a family panel, we identified Linkage Group (LG) 24 as the sex chromosome and positioned the sex locus in its sub-telomeric region. Furthermore, we demonstrated that this MSD originated from an ancient duplication of the autosomal amh gene, which was subsequently translocated to LG24. Using sex-specific pooled genome sequencing and a new male genome sequence assembled using Nanopore long reads, we also characterized the differentiation of the X and Y chromosomes, revealing a small male-specific insertion containing the MSD gene and a limited region with reduced recombination. Our study reveals an unexpectedly low level of differentiation between a pair of sex chromosomes harboring an old MSD gene in a wild teleost fish population, and highlights both the pivotal role of genes from the amh pathway in sex determination, as well as the importance of gene duplication as a mechanism driving the turnover of sex chromosomes in this clade.

In stark contrast to mammals and birds, a high proportion of teleosts have homomorphic sex chromosomes and display a high diversity of sex determining genes. Yet, population level knowledge of both the sex chromosome and the master sex determining gene is only available for the Japanese medaka, a model species. Here we identified and provided functional proofs of an old duplicate of anti-Müllerian hormone (Amh), a member of the Tgf- β family, as the male master sex determining gene in the Northern pike, Esox lucius. We found that this duplicate, named amhby (Y-chromosome-specific anti-Müllerian hormone paralog b), was translocated to the sub-telomeric region of the new sex chromosome, and now amhby shows strong sequence divergence as well as substantial expression pattern differences from its autosomal paralog, amha. We assembled a male genome sequence using Nanopore long reads and identified a restricted region of differentiation within the sex chromosome pair in a wild population. Our results provide insight on the conserved players in sex determination pathways, the mechanisms of sex chromosome turnover, and the diversity of levels of differentiation between homomorphic sex chromosomes in teleosts.