Reconstruction of the Origin of a Neo-Y Sex Chromosome and Its Evolution in the Spotted Knifejaw, Oplegnathus punctatus

Assembly and analysis of Sinipercidae fish sex chromosomes reveals that a supergene drives sex chromosome origin and turnover

The sex chromosomes of fish are usually homomorphic and recently derived, making them an ideal model to understand the origin and evolution of sex chromosomes in vertebrates. Here, combined Pacbio, Hi-C, and Illumina sequencing of the male mandarin fish (Siniperca chuatsi) genome enabled the assembly of a high-quality chromosome-level genome, including highly resolved X and Y chromosome assemblies. Genome wide association study (GWAS) and coverage information analysis revealed a 2.0 Mbp sex determining region (SDR). A Y-specific duplication of the anti-Müllerian hormone (amh) gene, amhy, was identified that encoded a truncated AMH protein. Loss of function and overexpression experiments demonstrated that amhy may act as a male sex-determining gene (SDG). GWAS led to the identification of a common sex chromosome (Chr24) and SDG (amhy) in S. scherzeri, while another sex chromosome (Chr11) was identified in Coreoperca whiteheadi. Interestingly, completely conserved protein coding sequences of amhy were commonly identified in male S. chuatsi, S. scherzeri, and S. knerii. These results support a classic model for the origin and evolution of early sex chromosomes and suggest that amhy is a super SDG that can drive the origin and turnover of sex chromosome in vertebrates.

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

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

Developing a genome-wide long sequence-specific tag for sex identification in spotted knifejaw (Oplegnathus punctatus)

Spotted knifejaw (Oplegnathus punctatus), an economically important species in marine aquaculture, employs a unique sex determination mechanism based on a complex sex chromosome system (X1X1X2X2/X1X2Y). Males (2n = 47) possess one fewer chromosome than females (2n = 48), and their karyotype includes an unusually large neo-Y chromosome. Additionally, a pronounced sexual dimorphism in growth rate is observed, with males exhibiting a faster growth rate than females. In this study, we conducted a comprehensive whole-genome scan, which initially revealed structural variations in the anti-inflammatory itih4 gene between male and female O. punctatus. Additionally, we designed a pair of primers to detect DNA sequence variations within the itih4a/itih4b gene. These variations are located in the intergenic region of the fusion Y chromosome in male O. punctatus, compared to the homologous X chromosome in females. In females without DNA insertions in the itih4a/itih4b intergenic region, a single band of 351 bp is amplified. By contrast, in males with DNA insertions, two bands are amplified (755 bp and 351 bp). The 755 bp band specifically indicates the presence of a DNA insertion in the itih4a/itih4b intergenic region on the Y chromosome, associated with male-specific genetic traits. Our study will facilitate the rapid identification of the genetic sex of both male and female O. punctatus individuals.

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.

Rapid Sex Identification in Spotted Knifejaw (Oplegnathus punctatus) Using tmem88 Gene Structural Variation Markers

Spotted knifejaw (Oplegnathus punctatus) is an economically important marine cultured species exhibiting a unique complex sex chromosome system (X1X1X2X2 in females and X1X2Y in males), with males possessing one fewer chromosome (2n = 47) than females (2n = 48) and an abnormally large Y chromosome. Additionally, males demonstrate significant growth advantages over females. Rapid and accurate sex identification is essential for effective culture management, selective breeding, and population control. In this study, we identified a homologous region of the tmem88 gene containing large DNA insertion markers on the X and Y chromosomes through whole-genome sequencing of O. punctatus. The X1 chromosome harbors a 278 bp DNA fragment, whereas the Y chromosome contains a 1472 bp fragment, resulting in a 1194 bp size difference indicative of structural variation in the non-coding region of the tmem88 gene. We developed a rapid detection method based on this variation, utilizing a pair of primers that amplify two distinct bands (278 bp and 1472 bp) in male (X1X2Y) individuals and a single 278 bp band in female (X1X1X2X2) individuals when analyzed by agarose gel electrophoresis. This method enables efficient and accurate sex differentiation in O. punctatus, significantly reducing the time required for identification and enhancing detection efficiency. This study provides a valuable tool for the rapid identification of sex in O. punctatus, facilitating improved breeding strategies and supporting the large-scale production of high-quality fry.

Development of DNA Insertion-specific Markers Based on the Intron Region of Oplegnathus punctatus itih4b for Genetic Sex Identification

Spotted knifejaw (Oplegnathus punctatus) is a significant marine fish species that exhibits pronounced sexual dimorphism, with males generally exhibiting greater weight and growth rates than females. Therefore, the farming of O. punctatus with a high proportion of males is beneficial for improving the quality and efficiency of the O. punctatus aquaculture industry. Furthermore, the development of a rapid technique in sexing O. punctatus fry will facilitate the selection and breeding of superior male varieties of O. punctatus. In this study, genome-wide scanning, comparative genomics, and structural variation analysis methods were employed to identify and extract the homologous region of the inter-alpha-trypsin inhibitor heavy chain 4 (itih4b) gene on the X and Y chromosomes from the complete genome sequence of O. punctatus. This analysis revealed the presence of a large segment of DNA insertion markers on the Y chromosome in the region. Itih4b plays an important role in the mechanisms that regulate inflammatory and immune responses in multicellular organisms. The method described here involved the design of a pair of primers to amplify two bands of 532 bp and 333 bp in males (individuals with DNA insertion variants in the intron of the itih4b gene). In females (individuals without DNA insertion), only one band of 333 bp could be distinguished by agarose gel electrophoresis. This method shortened the time required to accurately characterize intronic DNA insertion variants and genetic sexes in O. punctatus, thereby improving detection efficiency. This study has significant value for the large-scale breeding of O. punctatus all-male seedlings and provides a reference point for the study of intron variation regulation and RNA shearing in the itih4b gene.

Exploitation and Application of a New Genetic Sex Marker Based on Intron Insertion Variation of erc2 Gene in Oplegnathus punctatus

Spotted knifejaw (Oplegnathus punctatus), one of the most valuable mariculture species, grows with significant sexual dimorphism, with males growing significantly faster than females. O. punctatus not only has excellent growth characteristics and high food value, but also shows high economic value in aquaculture, which has become a hotspot in the field of aquaculture. The current insufficiency of sex marker identification in O. punctatus restricts the process of its unisexual breeding. Rapid identification of sex will help to study the mechanisms of sex determination and accelerate the development of sex-controlled breeding. With the completion of the sequencing of the male and female genomes of O. punctatus, the efficient and precise development of genetic sex markers has been made possible. In this study, we used genome-wide information combined with molecular biology techniques from marker sequences to further establish a rapid method for DNA insertion variant detection in the intron of O. punctatus erc2 gene, which can be used to rapidly, accurately, and efficiently identify whether DNA insertion occurs in the intron of O. punctatus erc2 gene to be detected, and to identify the sex of O. punctatus to be detected. It could also be distinguished by agarose gel electrophoresis, which would shorten the time for accurate identification and improves the detection efficiency. Homozygous comparison of male and female individuals showed that the length of the DNA fragment of the erc2 gene was 239 bp on chromosome X1 and 1173 bp on chromosome Y. It can therefore be inferred that a 934 bp insertion fragment exists on the Y chromosome. The PCR amplification results showed that two DNA fragments of 1173 bp and 239 bp could be amplified in male O. punctatus, and the 1173 bp fragment was a marker fragment specific to the variant intron erc2 gene, while only a single DNA fragment of 239 bp was amplified in female O. punctatus. It has important significance and application value in the study of neurotransmitter transmission and environmental adaptability of female and male fish based on erc2 gene, as well as the identification of male and female sex, the preparation of high male fry, and family breeding.

Orthopteran Neo-Sex Chromosomes Reveal Dynamics of Recombination Suppression and Evolution of Supergenes

The early evolution of sex chromosomes has remained obscure for more than a century. The Vandiemenella viatica species group of morabine grasshoppers is highly suited for studying the early stages of sex chromosome divergence and degeneration of the Y chromosome. This stems from the fact that neo-XY sex chromosomes have independently evolved multiple times by X-autosome fusions with different autosomes. Here, we generated new chromosome-level assemblies for two chromosomal races representing karyotypes with and without neo-sex chromosomes (P24XY and P24X0), and sequence data of a third chromosomal race with a different neo-XY chromosome system (P25XY). Interestingly, these two neo-XY chromosomal races are formed by different X-autosome fusions (involving chr1 and chrB, respectively), and we found that both neo-Y chromosomes have partly ceased to recombine with their neo-X counterpart. We show that the neo-XY chromosomes have diverged through accumulation of SNPs and structural mutations, and that many neo-Y-linked genes have degenerated since recombination ceased. However, the non-recombining regions of neo-Y chromosomes host non-degenerated genes crucial for sex determination, such as sex-lethal and transformer, alongside genes associated with spermatogenesis, fertility, and reproduction, illustrating their integrative role as a masculinizing supergene. Contrary to expectations, the neo-Y chromosomes showed (slightly) lower density of transposable elements (TEs) compared to other genomic regions. The study reveals the unique dynamics of young sex chromosomes, with evolution of recombination suppression and pronounced decay of (some) neo-sex chromosome genes, and provides a compelling case illustrating how chromosomal fusions and post-fusion mutational processes contribute to the evolution of supergenes.

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.

Advances in biotechnology and breeding innovations in China's marine aquaculture

Biotechnology is the key driving force behind the sustainable development of aquaculture, as biological innovation would significantly improve the capabilities of aquatic breeding and achieve independent and controllable seeding sources to ensure food safety. In this article, we have analyzed the current status and existing problems of marine aquaculture in China. Based on these data, we have summarized the recent (especially the last 10 years) biotechnological innovation and breeding progress of marine aquaculture in China, including whole genome sequencing, sex-related marker screening, genomic selection, and genome editing, as well as progress of improved marine fish varieties in China. Finally, the perspectives in this field have been discussed, and three future countermeasures have been proposed.

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.

Decoding the fish genome opens a new era in important trait research and molecular breeding in China

Aquaculture represents the fastest-growing global food production sector, as it has become an essential component of the global food supply. China has the world's largest aquaculture industry in terms of production volume. However, the sustainable development of fish culture is hindered by several concerns, including germplasm degradation and disease outbreaks. The practice of genomic breeding, which relies heavily on genome information and genotypephenotype relationships, has significant potential for increasing the efficiency of aquaculture production. In 2014, the completion of the genome sequencing and annotation of the Chinese tongue sole signified the beginning of the fish genomics era in China. Since then, domestic researchers have made dramatic progress in functional genomic studies. To date, the genomes of more than 60 species of fish in China have been assembled and annotated. Based on these reference genomes, evolutionary, comparative, and functional genomic studies have revolutionized our understanding of a wide range of biologically and economically important traits of fishes, including growth and development, sex determination, disease resistance, metamorphosis, and pigmentation. Furthermore, genomic tools and breeding techniques such as SNP arrays, genomic selection, and genome editing have greatly accelerated genetic improvement through the incorporation of functional genomic information into breeding activities. This review aims to summarize the current status, advances, and perspectives of the genome resources, genomic study of important traits, and genomic breeding techniques of fish in China. The review will provide aquaculture researchers, fish breeders, and farmers with updated information concerning fish genomic research and breeding technology. The summary will help to promote the genetic improvement of production traits and thus will support the sustainable development of fish aquaculture.

Genome assemblies for Chromidotilapia guntheri (Teleostei: Cichlidae) identify a novel candidate gene for vertebrate sex determination, RIN3

Advances in genome sequencing have greatly accelerated the identification of sex chromosomes in a variety of species. Many of these species have experienced structural rearrangements that reduce recombination between the sex chromosomes, allowing the accumulation of sequence differences over many megabases. Identification of the genes that are responsible for sex determination within these sometimes large regions has proved difficult. Here, we identify an XY sex chromosome system on LG19 in the West African cichlid fish Chromidotilapia guntheri in which the region of differentiation extends over less than 400 kb. We develop high-quality male and female genome assemblies for this species, which confirm the absence of structural variants, and which facilitate the annotation of genes in the region. The peak of differentiation lies within rin3, which has experienced several debilitating mutations on the Y chromosome. We suggest two hypotheses about how these mutations might disrupt endocytosis, leading to Mendelian effects on sexual development.

Development of DNA Insertion-specific Markers Based on the Intergenic Region of Oplegnathus punctatus Cdkn1/srsf3 for Sex Identification

Spotted knifejaw (Oplegnathus punctatus) is a marine economic fish with high food and ecological value, and its growth process has obvious male and female sexual dimorphism, with males growing significantly faster than females. However, the current sex identification technology is not yet mature, which will limit the growth rate of O. punctatus aquaculture and the efficiency of separate sex breeding, so the development of efficient sex molecular markers is imperative. This study identified a 926 bp DNA insertion fragment in the cdkn1/srsf3 intergenic region of O. punctatus males through whole-genome scanning, comparative genomics, and structural variant analysis. A pair of primers was designed based on the insertion information of the Y chromosome intergenic region in male individuals. Agarose gel electrophoresis revealed the amplification of two DNA fragments, 1118 bp and 192 bp, in male O. punctatus individuals. The 926 bp fragment was identified as the insertion in the intergenic region of cdkn1/srsf3 in males, while only a single 192 bp DNA fragment was amplified in females. The biological sex of the individuals identified in this manner was consistent with their known phenotypic sex. In this study, we developed a method to detect DNA insertion variants in the intergenic region of O. punctatus. Additionally, we introduced a new DNA marker for the rapid identification of the sex of O. punctatus, which enhances detection efficiency. The text has important reference significance and application value in sex identification, all-male breeding, and lineage selection. It provides new insights into the regulation of variation in the intergenic region of cdkn1/srsf3 genes and the study of RNA shearing.

De novo assembly and characterization of a highly degenerated ZW sex chromosome in the fish Megaleporinus macrocephalus

BACKGROUND

Megaleporinus macrocephalus (piauçu) is a Neotropical fish within Characoidei that presents a well-established heteromorphic ZZ/ZW sex determination system and thus constitutes a good model for studying W and Z chromosomes in fishes. We used PacBio reads and Hi-C to assemble a chromosome-level reference genome for M. macrocephalus. We generated family segregation information to construct a genetic map, pool sequencing of males and females to characterize its sex system, and RNA sequencing to highlight candidate genes of M. macrocephalus sex determination.

RESULTS

The reference genome of M. macrocephalus is 1,282,030,339 bp in length and has a contig and scaffold N50 of 5.0 Mb and 45.03 Mb, respectively. In the sex chromosome, based on patterns of recombination suppression, coverage, FST, and sex-specific SNPs, we distinguished a putative W-specific region that is highly differentiated, a region where Z and W still share some similarities and is undergoing degeneration, and the PAR. The sex chromosome gene repertoire includes genes from the TGF-β family (amhr2, bmp7) and the Wnt/β-catenin pathway (wnt4, wnt7a), some of which are differentially expressed.

CONCLUSIONS

The chromosome-level genome of piauçu exhibits high quality, establishing a valuable resource for advancing research within the group. Our discoveries offer insights into the evolutionary dynamics of Z and W sex chromosomes in fish, emphasizing ongoing degenerative processes and indicating complex interactions between Z and W sequences in specific genomic regions. Notably, amhr2 and bmp7 are potential candidate genes for sex determination in M. macrocephalus.

Characterization of Early Gonadal Differentiation and Induction of Sex Reversal in the Rock Bream Oplegnathus fasciatus

Rock bream (Oplegnathus fasciatus) is a typical fish that has a unique multiple sex chromosome system (♀X1X1X2X2/♂X1X2Y). We examined the early gonadal development in rock bream via continuous histological observations of the gonads at 40-120 days post hatching (dph). The fish was identified as a typical gonochorist, and female gonads were found to differentiate earlier than male gonads. The ovarian cavity of the female was initially observed at 80 dph, whereas the efferent duct of the male was not observed until 100 dph. Immunofluorescence with the vasa-antibody revealed that germ cells were predominantly distributed around the ovarian cavity in females and on the edge of the gonad in males during the early stages of sex differentiation. Sex reversal was induced via the oral administration of letrozole (LTZ), 17α-methyltestosterone (MT), and 17β-estradiol (E2), respectively, during the labile period of gonadal development. LTZ and MT induced 100% masculinization of genotype-females, whereas E2 induced only 50-60% feminization of genotype-males. Such findings suggest that the fish retained high sexual plasticity despite the existence of the neo-Y chromosome. MT and E2 had negative effect on fish growth, whereas LTZ did not exert such side effect. LTZ and MT could accelerate gonadal development in sex-reversed genotype-males, whereas E2 inhibited gonadal development in genotype-females of rock bream. These findings provide a basis for further research on the mechanisms of sex determination and differentiation in fishes with X1X2Y sex chromosome system and provide a sex reversal protocol for rock bream.

Massive expansion of sex-specific SNPs, transposon-related elements, and neocentromere formation shape the young W-chromosome from the mosquitofish Gambusia affinis

BACKGROUND

The Western mosquitofish, Gambusia affinis, is a model for sex chromosome organization and evolution of female heterogamety. We previously identified a G. affinis female-specific marker, orthologous to the aminomethyl transferase (amt) gene of the related platyfish (Xiphophorus maculatus). Here, we have analyzed the structure and differentiation of the G. affinis W-chromosome, using a cytogenomics and bioinformatics approach.

RESULTS

The long arm of the G. affinis W-chromosome (Wq) is highly enriched in dispersed repetitive sequences, but neither heterochromatic nor epigenetically silenced by hypermethylation. In line with this, Wq sequences are highly transcribed, including an active nucleolus organizing region (NOR). Female-specific SNPs and evolutionary young transposable elements were highly enriched and dispersed along the W-chromosome long arm, suggesting constrained recombination. Wq copy number expanded elements also include female-specific transcribed sequences from the amt locus with homology to TE. Collectively, the G. affinis W-chromosome is actively differentiating by sex-specific copy number expansion of transcribed TE-related elements, but not (yet) by extensive sequence divergence or gene decay.

CONCLUSIONS

The G. affinis W-chromosome exhibits characteristic genomic properties of an evolutionary young sex chromosome. Strikingly, the observed sex-specific changes in the genomic landscape are confined to the W long arm, which is separated from the rest of the W-chromosome by a neocentromere acquired during sex chromosome evolution and may thus have become functionally insulated. In contrast, W short arm sequences were apparently shielded from repeat-driven differentiation, retained Z-chromosome like genomic features, and may have preserved pseudo-autosomal properties.

Slower-X: reduced efficiency of selection in the early stages of X chromosome evolution

Differentiated X chromosomes are expected to have higher rates of adaptive divergence than autosomes, if new beneficial mutations are recessive (the “faster-X effect”), largely because these mutations are immediately exposed to selection in males. The evolution of X chromosomes after they stop recombining in males, but before they become hemizygous, has not been well explored theoretically. We use the diffusion approximation to infer substitution rates of beneficial and deleterious mutations under such a scenario. Our results show that selection is less efficient on diploid X loci than on autosomal and hemizygous X loci under a wide range of parameters. This “slower-X” effect is stronger for genes affecting primarily (or only) male fitness, and for sexually antagonistic genes. These unusual dynamics suggest that some of the peculiar features of X chromosomes, such as the differential accumulation of genes with sex-specific functions, may start arising earlier than previously appreciated.

Origin and chromatin remodeling of young X/Y sex chromosomes in catfish with sexual plasticity

Assembly of a complete Y chromosome is a significant challenge in animals with an XX/XY sex-determination system. Recently, we created YY-supermale yellow catfish by crossing XY males with sex-reversed XY females, providing a valuable model for Y-chromosome assembly and evolution. Here, we assembled highly homomorphic Y and X chromosomes by sequencing genomes of the YY supermale and XX female in yellow catfish, revealing their nucleotide divergences with only less than 1% and with the same gene compositions. The sex-determining region (SDR) was identified to locate within a physical distance of 0.3 Mb by F_ST scanning. Strikingly, the incipient sex chromosomes were revealed to originate via autosome-autosome fusion and were characterized by a highly rearranged region with an SDR downstream of the fusion site. We found that the Y chromosome was at a very early stage of differentiation, as no clear evidence of evolutionary strata and classical structure features of recombination suppression for a rather late stage of Y-chromosome evolution were observed. Significantly, a number of sex-antagonistic mutations and the accumulation of repetitive elements were discovered in the SDR, which might be the main driver of the initial establishment of recombination suppression between young X and Y chromosomes. Moreover, distinct three-dimensional chromatin organizations of the Y and X chromosomes were identified in the YY supermales and XX females, as the X chromosome exhibited denser chromatin structure than the Y chromosome, while they respectively have significantly spatial interactions with female- and male-related genes compared with other autosomes. The chromatin configuration of the sex chromosomes as well as the nucleus spatial organization of the XX neomale were remodeled after sex reversal and similar to those in YY supermales, and a male-specific loop containing the SDR was found in the open chromatin region. Our results elucidate the origin of young sex chromosomes and the chromatin remodeling configuration in the catfish sexual plasticity.

Identification of Male-Specific Molecular Marker and Development of PCR-Based Genetic Sex Identification Technique in Spotted Knifejaw (Oplegnathus punctatus)

Spotted knifejaw (Oplegnathus punctatus) is a marine teleost species that is economically important for aquaculture and marine pasture proliferation and shows obvious bisexual growth dimorphism, but molecular sex markers are currently lacking. A 290 bp (base pair) insertion with two fragments (230 bp and 60 bp) was identified in male individuals of O. punctatus based on whole-genome sequencing scanning and structural variation analyses. The gene annotation results showed that the insertion event occurred in the Igfn1 gene of male O. punctatus. The results of amino acid analysis further showed that the insertion event resulted in the functional variation of Igfn1 in male O. punctatus, and recombination caused the inactivation of Igfn1. According to the male-specific insertion information, we designed a PCR-based genetic amplification technique for rapid sex identification in O. punctatus. The results of agarose gel electrophoresis showed that two DNA fragments of 635 bp and 925 bp were amplified in male O. punctatus, while only a single DNA fragment of 635 bp was amplified in female individuals. The sex of individuals identified by this method was consistent with their known phenotypic sex, which will improve sex identification efficiency. This method provides a new DNA marker for rapid sex identification in O. punctatus, which has great significance and application value in monosex breeding and provides new insights for the study of Igfn1 gene recombination and inactivation in male O. punctatus.

Transcriptomic analysis reveals the gene expression profiles in the spleen of spotted knifejaw (Oplegnathus punctatus) infected by Vibrio harveyi

As one of the most valuable maricultured species, spotted knifejaw (Oplegnathus punctatus) has high popularity in eastern Asia. In recent years, diseases caused by Vibrio harveyi have brought huge economic losses in spotted knifejaw industry. To better understand the molecular mechanisms of immune response about V. harveyi resistance in spotted knifejaw, a comparative transcriptome analysis was performed on spleen tissues at five different time points post-infection (0, 12, 24, 48 and 72 hpi). A total of 4279 differentially expressed genes (DEGs) were identified. KEGG pathways analysis showed that multiple immune-related pathways were significant regulated, including Toll-like receptor signaling pathway, ECM-receptor interaction pathway, cytokine-cytokine receptor interaction pathway and hematopoietic cell lineage pathway. Weighted gene co-expression network analysis showed that several immune-related pathways of the highest correlation with 12 hpi (cor = 0.89, P = 7e-06) were significantly enriched. In addition, 12 hpi was a turning point for 7 gene clusters out of 9 that were divided according to gene expression patterns. Therefore, we speculated that 12 hpi might be a very critical time point for spotted knifejaw against V. harveyi infection. Additionally, qRT-PCR was carried out to validate the expressions of 12 DEGs. This study provided the first systematical transcriptome analysis of spotted knifejaw against V. harveyi. The results could help us better understand the dynamic immune responses of spotted knifejaw against bacterial infection, and provide useful information for antibacterial defense in spotted knifejaw industry as well.

Genome-wide identification, characterization and expression analysis of the BMP family associated with beak-like teeth in Oplegnathus

Bone morphogenetic proteins (BMPs), which belong to the transforming growth factor beta (TGF-β) family, are critical for the control of developmental processes such as dorsal-ventral axis formation, somite and tooth formation, skeletal development, and limb formation. Despite Oplegnathus having typical healing beak-like teeth and tooth development showing a trend from discrete to healing, the potential role of BMPs in the development of the beak-like teeth is incompletely understood. In the present study, 19 and 16 BMP genes were found in O. fasciatus and O. punctatus, respectively, and divided into the BMP2/4/16, BMP5/6/7/8, BMP9/10, BMP12/13/14, BMP3/15 and BMP11 subfamilies. Similar TGFb and TGF_β gene domains and conserved protein motifs were found in the same subfamily; furthermore, two common tandem repeat genes (BMP9 and BMP3a-1) were identified in both Oplegnathus fasciatus and Oplegnathus punctatus. Selection pressure analysis revealed 13 amino acid sites in the transmembrane region of BMP3, BMP7, and BMP9 proteins of O. fasciatus and O. punctatus, which may be related to the diversity and functional differentiation of genes within the BMP family. The qPCR-based developmental/temporal expression patterns of BMPs showed a trend of high expression at 30 days past hatching (dph), which exactly corresponds to the ossification period of the bones and beak-like teeth in Oplegnathus. Tissue-specific expression was found for the BMP4 gene, which was upregulated in the epithelial and mesenchymal tissues of the beak-like teeth, suggesting that it also plays a regulatory role in the development of the beak-like teeth in O. punctatus. Our investigation not only provides a scientific basis for comprehensively understanding the BMP gene family but also helps screen the key genes responsible for beak-like tooth healing in O. punctatus and sheds light on the developmental regulatory mechanism.

Identification of Male-Specific Molecular Markers by Recombination of RhoGEF10 Gene in Spotted Knifejaw (Oplegnathus punctatus)

The spotted knifejaw (Oplegnathus punctatus) is a marine economic fish with high ecological value, food value, and fishing value, and its growth has obvious sex dimorphism. The rapid identification of its sex is beneficial to the development of sex determination and breeding. In this study, the method of comparative genomics and PCR amplification was used to further establish a rapid detection method for the recombinant RhoGEF10 gene in O. punctatus, which can quickly, accurately, and efficiently identify the sex of the O. punctatus to be tested. The homologous comparison results of male and female individuals showed that the DNA fragment length of the RhoGEF10 gene on the X1 chromosome was 326 bp, and the DNA fragment length on the Y chromosome was 879 bp. Therefore, it can be concluded that there is an insert fragment of 553 bp on the Y chromosome. PCR amplification results showed that the two DNA fragments of 879 bp and 326 bp were amplified in the Y chromosome and X1 chromosome of the male O. punctatus (X1X2Y), respectively, and the 879 bp fragment was a unique marker fragment of the recombinant RhoGEF10 gene; The female O. punctatus (X1X1X2X2) only a single DNA fragment of 326 bp was amplified. At the same time, the inserted fragment of the male individual resulted in partial inactivation of the RhoGEF10 protein, which in turn resulted in a slowing of peripheral nerve conduction velocity and thinning of the myelin sheath in male O. punctatus. The method shortens the time for accurate identification of the O. punctatus RhoGEF10 gene recombination and improves the detection efficiency. It is of great significance and application value in the research of nerve conduction and myelin development, male and female sex identification, the preparation of high male seedlings, and family selection based on the RhoGEF10 gene in the O. punctatus.

Insights into chromosomal evolution and sex determination of Pseudobagrus ussuriensis (Bagridae, Siluriformes) based on a chromosome-level genome

Pseudobagrus ussuriensis is an aquaculture catfish with significant sexual dimorphism. In this study, a chromosome-level genome with a size of 741.97 Mb was assembled for female P. ussuriensis. A total of 26 chromosome-level contigs covering 97.34% of the whole-genome assembly were obtained with an N50 of 28.53 Mb and an L50 of 11. A total of 24,075 protein-coding genes were identified, with 91.54% (22,039) genes being functionally annotated. Based on the genome assembly, four chromosome evolution clusters of catfishes were identified and the formation process of P. ussuriensis chromosomes was predicted. A total of 55 sex-related quantitative trait loci (QTLs) with a phenotypic variance explained value of 100% were located on chromosome 8 (chr08). The QTLs and other previously identified sex-specific markers were located in a sex-determining region of 16.83 Mb (from 6.90 to 23.73 Mb) on chr08, which was predicted as the X chromosome. The sex-determining region comprised 554 genes, with 135 of which being differently expressed between males and females/pseudofemales, and 16 candidate sex-determining genes were screened out. The results of this study provided a useful chromosome-level genome for genetic, genomic and evolutionary studies of P. ussuriensis, and also be useful for further studies on sex-determination mechanism analysis and sex-control breeding of this fish.

Sex determination mechanisms and sex control approaches in aquaculture animals

Aquaculture is one of the most efficient modes of animal protein production and plays an important role in global food security. Aquaculture animals exhibit extraordinarily diverse sexual phenotypes and underlying mechanisms, providing an ideal system to perform sex determination research, one of the important areas in life science. Moreover, sex is also one of the most valuable traits because sexual dimorphism in growth, size, and other economic characteristics commonly exist in aquaculture animals. Here, we synthesize current knowledge of sex determination mechanisms, sex chromosome evolution, reproduction strategies, and sexual dimorphism, and also review several approaches for sex control in aquaculture animals, including artificial gynogenesis, application of sex-specific or sex chromosome-linked markers, artificial sex reversal, as well as gene editing. We anticipate that better understanding of sex determination mechanisms and innovation of sex control approaches will facilitate sustainable development of aquaculture.

The chromosome-level genome assembly of the Japanese yellowtail jack Seriola aureovittata provides insights into genome evolution and efficient oxygen transport

Fishes of the genus Seriola are widely farmed and highly valued in global aquaculture production. To further understand their economically important traits and help improve aquaculture product quality and sustainability, we performed a chromosome-level genome construction for Seriola aureovittata. Combining two technologies, PacBio and BGISEQ-500, we assembled 649.86 Mb S. aureovittata genome sequences with a contig N50 of 22.21 Mb, and 98% of BUSCO genes were detected in total. The initial assembly was then further scaffolded into 24 pseudochromosomes using Hi-C data, indicating the high quality of the genome. Genome evolution analysis showed that many genes related to fatty acid metabolism and oxygen binding, or transport were expanded, which provided insights into the metabolic characteristics of fatty acids and efficient oxygen transport. Based on the genome data, we confirmed the evolutionary relationship of S. aureovittata, S. dorsalis and S. lalandi and identified chr12 as the putative sex chromosome of S. aureovittata. Our chromosome-level genome assembly provides a genetic foundation for the phylogenetic and taxonomic investigation of different Seriola species. Moreover, the genome will provide an important genomic resource for further biological and aquaculture studies of S. aureovittata.

Inactivated Whole Vaccine Inhibits Lethal Vibrio harveyi Infection in Oplegnathus punctatus

Aquaculture plays a key role in food production globally and provides a valuable source of protein and nutrition, addressing a worldwide growing demand. Oplegnathus punctatus (spotted knifejaw) is an economically important fish species with a high market value and demand. Previous studies on O. punctatus focused mainly on gonadal development, chromosomal microstructure, selective breeding, characterization of immune genes, and viral diseases. There is no published scientific research regarding vibriosis in this fish species. In this study, two potential pathogenic bacteria, Vibrio harveyi and Enterococcus gallinarum, were isolated from moribund cultured O. punctatus. The sequence of the universal 16S rDNA gene was used to identify potential pathogenic bacteria isolated from the moribund O. punctatus, and morphological assessments and API20E tests of the bacterial isolates were conducted to verify the identity and biochemical characteristics of the isolates. Injection of E. gallinarum did not lead to mortality in O. punctatus during the 21 days of observation. In contrast, fish died overnight when challenged with V. harveyi at 1.25 × 105 CFU/g body weight, suggesting that the cause of death of the cultured O. punctatus was V. harveyi infection. Antimicrobial sensitivity analyses revealed that the V. harveyi strain NTOU is sensitive to flumequine, doxycycline, oxolinic acid, and amoxycillin. Importantly, we demonstrated for the first time that intraperitoneal administration of an inactivated V. harveyi whole-cell vaccine resulted in a high level of protection against V. harveyi infection in O. punctatus.

Sex-Specific Genomic Region Identification and Molecular Sex Marker Development of Rock Bream (Oplegnathus fasciatus)

Rock bream (Oplegnathus fasciatus) is a valuable commercial marine teleost species, which exhibits sexual dimorphism in growth performance. However, the absence of a rapid and cost-effective sex identification method based on sex-specific genetic marker has impeded study on sex determination mechanisms and breeding applications. In the present study, we firstly developed the PCR method for identifying potential sex-specific sequences in Oplegnathus fasciatus with the next-generation sequencing. Sex-specific genomic regions/loci for sex determination were discovered on Chr2 and Chr6 by genome-wide association analysis, sequencing depth, and heterozygosity comparison between females and males. Candidate sex-determining genes (CCDC63, ITR, WNT4) were furtherly detected in transcriptome data of testes and ovaries. Taken together, a male-specific 34-bp deletion on the Chr2 was identified and developed into molecular marker of sex for O. fasciatus. After validation in individuals with known phenotypic sexes, the accuracy was 100%. This study gives an insight into the mechanism of sex determination in O. fasciatus, and the gender marker is crucial both for future genomic research and for development of efficient and sustainable aquaculture practice.

Chromosome-Level Assembly of the Southern Rock Bream (Oplegnathus fasciatus) Genome Using PacBio and Hi-C Technologies

The Rock Bream (Oplegnathus fasciatus) is an economically important rocky reef fish of the Northwest Pacific Ocean. In recent years, it has been cultivated as an important edible fish in coastal areas of China. Despite its economic importance, genome-wide adaptions of domesticated O. fasciatus are largely unknown. Here we report a chromosome-level reference genome of female O. fasciatus (from the southern population in the subtropical region) using the PacBio single molecule sequencing technique (SMRT) and High-through chromosome conformation capture (Hi-C) technologies. The genome was assembled into 120 contigs with a total length of 732.95 Mb and a contig N50 length of 27.33 Mb. After chromosome-level scaffolding, 24 chromosomes with a total length of 723.22 Mb were constructed. Moreover, a total of 27,015 protein-coding genes and 5,880 ncRNAs were annotated in the reference genome. This reference genome of O. fasciatus will provide an important resource not only for basic ecological and population genetic studies but also for dissect artificial selection mechanisms in marine aquaculture.

A Chromosome-Level Genome Assembly of Mozambique Tilapia (Oreochromis mossambicus) Reveals the Structure of Sex Determining Regions

The Mozambique tilapia (Oreochromis mossambicus) is a fascinating taxon for evolutionary and ecological research. It is an important food fish and one of the most widely distributed tilapias. Because males grow faster than females, genetically male tilapia are preferred in aquaculture. However, studies of sex determination and sex control in O. mossambicus have been hindered by the limited characterization of the genome. To address this gap, we assembled a high-quality genome of O. mossambicus, using a combination of high coverage of Illumina and Nanopore reads, coupled with Hi-C and RNA-Seq data. Our genome assembly spans 1,007 Mb with a scaffold N50 of 11.38 Mb. We successfully anchored and oriented 98.6% of the genome on 22 linkage groups (LGs). Based on re-sequencing data for male and female fishes from three families, O. mossambicus segregates both an XY system on LG14 and a ZW system on LG3. The sex-patterned SNPs shared by two XY families narrowed the sex determining regions to ∼3 Mb on LG14. The shared sex-patterned SNPs included two deleterious missense mutations in ahnak and rhbdd1, indicating the possible roles of these two genes in sex determination. This annotated chromosome-level genome assembly and identification of sex determining regions represents a valuable resource to help understand the evolution of genetic sex determination in tilapias.