W-linked Gene Research Articles

Identification of crucial factors involved in Cynoglossus semilaevis sexual size dimorphism by GWAS and demonstration of zbed1 regulatory network by DAP-seq

Sexual size dimorphism (SSD), whereby females and males exhibit different body sizes, are widely documented in animals. To explore crucial regulators implicated in female-biased SSD of Chinese tongue sole (Cynoglossus semilaevis), GWAS was conducted on 350 females and 59 males. Twenty SNPs and 25 genes including zbed1, nsd3, cdc45, klhl29, and smad4 with -log(p) > 7 were screened, mainly mapping to sex chromosome. The chromosome W-linked gene zbed1 attracted particular attention because it is a master key for cell proliferation. Thus, the regulatory network of zbed1 in C. semilaevis was explored by DAP-seq and 1352 peaks were discovered in the female brain. Moreover, zbed1 potentially regulated hippo signaling pathway, cell cycle, translation, and PI3k-Akt signaling pathway in C. semilaevis. These findings identify crucial SNPs and genes associated with female-biased SSD in C. semilaevis, also provide the first genome-wide survey for the zbed1 regulatory network in fish species.

Schistosome W-Linked Genes Inform Temporal Dynamics of Sex Chromosome Evolution and Suggest Candidate for Sex Determination.

Schistosomes, the human parasites responsible for snail fever, are female-heterogametic. Different parts of their ZW sex chromosomes have stopped recombining in distinct lineages, creating “evolutionary strata” of various ages. Although the Z-chromosome is well characterized at the genomic and molecular level, the W-chromosome has remained largely unstudied from an evolutionary perspective, as only a few W-linked genes have been detected outside of the model species Schistosoma mansoni. Here, we characterize the gene content and evolution of the W-chromosomes of S. mansoni and of the divergent species S. japonicum. We use a combined RNA/DNA k-mer based pipeline to assemble around 100 candidate W-specific transcripts in each of the species. About half of them map to known protein coding genes, the majority homologous to S. mansoni Z-linked genes. We perform an extended analysis of the evolutionary strata present in the two species (including characterizing a previously undetected young stratum in S. japonicum) to infer patterns of sequence and expression evolution of W-linked genes at different time points after recombination was lost. W-linked genes show evidence of degeneration, including high rates of protein evolution and reduced expression. Most are found in young lineage-specific strata, with only a few high expression ancestral W-genes remaining, consistent with the progressive erosion of nonrecombining regions. Among these, the splicing factor u2af2 stands out as a promising candidate for primary sex determination, opening new avenues for understanding the molecular basis of the reproductive biology of this group. Keywords: sex chromosomes, evolutionary strata, W-linked gene, sex determining gene, schistosome parasites.

Multi-Copy Gene Family Evolution on the Avian W Chromosome.

The sex chromosomes often follow unusual evolutionary trajectories. In particular, the sex-limited chromosomes frequently exhibit a small but unusual gene content in numerous species, where many genes have undergone massive gene amplification. The reasons for this remain elusive with a number of recent studies implicating meiotic drive, sperm competition, genetic drift, and gene conversion in the expansion of gene families. However, our understanding is primarily based on Y chromosome studies as few studies have systematically tested for copy number variation on W chromosomes. Here, we conduct a comprehensive investigation into the abundance, variability, and evolution of ampliconic genes on the avian W. First, we quantified gene copy number and variability across the duck W chromosome. We find a limited number of gene families as well as conservation in W-linked gene copy number across duck breeds, indicating that gene amplification may not be such a general feature of sex chromosome evolution as Y studies would initially suggest. Next, we investigated the evolution of HINTW, a prominent ampliconic gene family hypothesized to play a role in female reproduction and oogenesis. In particular, we investigated the factors driving the expansion of HINTW using contrasts between modern chicken and duck breeds selected for different female-specific selection regimes and their wild ancestors. Although we find the potential for selection related to fecundity in explaining small-scale gene amplification of HINTW in the chicken, purifying selection seems to be the dominant mode of evolution in the duck. Together, this challenges the assumption that HINTW is key for female fecundity across the avian phylogeny.

Dynamic evolutionary history and gene content of sex chromosomes across diverse songbirds.

Songbirds have a species number close to that of mammals and are classic models for studying speciation and sexual selection. Sex chromosomes are hotspots of both processes, yet their evolutionary history in songbirds remains unclear. We characterized genomes of 11 songbird species, with 5 genomes of bird-of-paradise species. We conclude that songbird sex chromosomes have undergone four periods of recombination suppression before species radiation, producing a gradient of pairwise sequence divergence termed 'evolutionary strata'. The latest stratum was probably due to a songbird-specific burst of retrotransposon CR1-E1 elements at its boundary, instead of the chromosome inversion generally assumed for suppressing sex-linked recombination. The formation of evolutionary strata has reshaped the genomic architecture of both sex chromosomes. We find stepwise variations of Z-linked inversions, repeat and guanine-cytosine (GC) contents, as well as W-linked gene loss rate associated with the age of strata. A few W-linked genes have been preserved for their essential functions, indicated by higher and broader expression of lizard orthologues compared with those of other sex-linked genes. We also find a different degree of accelerated evolution of Z-linked genes versus autosomal genes among species, potentially reflecting diversified intensity of sexual selection. Our results uncover the dynamic evolutionary history of songbird sex chromosomes and provide insights into the mechanisms of recombination suppression.

Masculinization-Related Genes and Cell-Mass Structures During Early Gonadal Differentiation in the African Clawed Frog Xenopus laevis.

The African clawed frog Xenopus laevis has a female heterogametic ZZ/ZW-type sex-determining system. We previously discovered a W-linked female sex-determining gene dm-W that is involved in ovary formation, probably through the up-regulation of the estrogen synthesis genes cyp19a1 and foxl2. We also reported that a unique "mass-in-line structure", which disappears from ZZ gonads during early testicular development, might serve as the basis for ovary differentiation in ZW gonads. However, the molecular mechanisms underlying early masculinization are poorly understood. To elucidate the development of bipotential gonads into testes after sex determination in this species, we focused on the orthologs of five mammalian sex-related genes: three nuclear factor genes, dax1, sf1 (also known as ad4bp), and sox9, and two genes encoding members of the tumor growth factor-β (TGF-β) family, anti-Müllerian hormone (amh) and inhibin βb (inhbb). Quantitative RT-PCR analysis revealed that the expression of dax1, sox9, amh, and inhbb or sf1 was greatly or slightly higher in ZZ than in ZW gonads during early sex development. In situ hybridization analysis revealed that amh and inhbb mRNAs were expressed in somatic cells on the inner and outer sides of cell masses in the mass-in-line structure, respectively, in the developing ZZ gonads. Interestingly, estrogen exposure prevented the disappearance of the mass-in-line structure in early developing ZZ tadpoles. These findings suggest that TGF-β signaling is involved in the destruction of the mass-in-line structure, which may be maintained by estrogen.

Cell-mass structures expressing the aromatase gene Cyp19a1 lead to ovarian cavities in Xenopus laevis.

The African clawed frog, Xenopus laevis, has a ZZ/ZW-type sex-determination system. We previously reported that a W-linked gene, Dm-W, can determine development as a female. However, the mechanisms of early sex differentiation remain unclear. We used microarrays to screen for genes with sexually dimorphic expression in ZZ and ZW gonads during early sex differentiation in X laevis and found several steroidogenic genes. Importantly, the steroid 17α-hydroxylase gene Cyp17a1 and the aromatase gene Cyp19a1 were highly expressed in ZZ and ZW gonads, respectively, just after sex determination. At this stage, we found that Cyp17a1, Cyp19a1, or both were expressed in the ZZ and ZW gonads in a unique mass-in-line structure, in which several masses of cells, each surrounded by a basement membrane, were aligned along the anteroposterior axis. In fact, during sex differentiation, ovarian cavities formed inside each mass of Cyp17a1- and Cyp19a1-positive cells in the ZW gonads. However, the mass-in-line structure disappeared during testicular development in the ZZ testes. These results suggested that the mass-in-line structure found in both ZZ and ZW gonads just after sex determination might be formed in advance to produce ovarian cavities and then oocytes. Consequently, we propose a view that the default sex may be female in the morphological aspect of gonads in X laevis.

Triploid plover female provides support for a role of the W chromosome in avian sex determination

Two models, Z Dosage and Dominant W, have been proposed to explain sex determination in birds, in which males are characterized by the presence of two Z chromosomes, and females are hemizygous with a Z and a W chromosome. According to the Z Dosage model, high dosage of a Z-linked gene triggers male development, whereas the Dominant W model postulates that a still unknown W-linked gene triggers female development. Using 33 polymorphic microsatellite markers, we describe a female triploid Kentish plover Charadrius alexandrinus identified by characteristic triallelic genotypes at 14 autosomal markers that produced viable diploid offspring. Chromatogram analysis showed that the sex chromosome composition of this female was ZZW. Together with two previously described ZZW female birds, our results suggest a prominent role for a female determining gene on the W chromosome. These results imply that avian sex determination is more dynamic and complex than currently envisioned.

Sex chromosome evolution in moths and butterflies

Lepidoptera, i.e. moths and butterflies, have a female heterogametic sex chromosome system, with most females having a WZ constitution while males are ZZ. Besides this predominant WZ/ZZ system, Z/ZZ, WZ(1)Z(2)/Z(1)Z(1)Z(2)Z(2) and W(1)W(2)Z/ZZ systems also occur. Sex is determined by an unknown W-linked gene or genes in Bombyx mori, but by dosage-dependent and equally unknown Z-linked genes in all Z/ZZ species. The female heterogametic sex chromosome system has been conserved for at least 180MY in the phylogenetic branch that combines Lepidoptera and Trichoptera. The W chromosome, which is present in most lepidopteran species, was incorporated in the sex chromosome system much later, about 90-100MY ago. The Z chromosomes are highly conserved among Lepidoptera, much like the Z in birds or the X in mammals. The W, on the other hand, is evolving rapidly. It is crammed with repetitive elements which appear to have a high turnover rate but poor in or even devoid of protein-coding genes. It has frequently undergone fusion with autosomes or sporadically lost altogether.

A ZZ/ZW‐type sex determination in Xenopus laevis

Genetic sex-determining systems in vertebrates include two basic types of heterogamety, which are represented by the XX/XY and ZZ/ZW types. Both types occur among amphibian species. Little is known, however, about the molecular mechanisms underlying amphibian sex determination. Recently, a W-linked gene, DM-W, was isolated as a paralog of DMRT1 in the African clawed frog Xenopus laevis, which has a female heterogametic ZZ/ZW-type sex-determining system. The DNA-binding domain of DM-W shows high sequence identity with that of DMRT1, but DM-W does not contain a domain with homology to DMRT1's transactivation domain. Importantly, phenotypic analysis of transgenic individuals bearing a DM-W-expression or -knockdown vector strongly suggested that DM-W acts as a female sex-determining gene in this species. In this minireview, we briefly describe the sex-determining systems in amphibians, discuss recent findings from the discovery of the DM-W gene in terms of its molecular evolution and its function in sex determination and ovary formation, and introduce a new model for the ZZ/ZW-type sex determination elicited by DM-W and DMRT1 in X. laevis. Finally, we discuss sex-determining systems and germ-cell development during vertebrate evolution, especially in view of a conserved role of DMRT1 in gonadal masculinization.

Opposite roles ofDMRT1and its W-linked paralogue,DM-W, in sexual dimorphism ofXenopus laevis: implications of a ZZ/ZW-type sex-determining system

A Y-linked gene, DMY/dmrt1bY, in teleost fish medka and a Z-linked gene, DMRT1, in chicken are both required for male sex determination. We recently isolated a W-linked gene, DM-W, as a paralogue of DMRT1 in Xenopus laevis, which has a ZZ/ZW-type sex-determining system. The DNA-binding domain of DM-W shows high sequence identity with that of DMRT1, but DM-W has no significant sequence similarity with the transactivation domain of DMRT1. Here, we first show colocalization of DM-W and DMRT1 in the somatic cells surrounding primordial germ cells in ZW gonad during sex determination. We next examined characteristics of DM-W and DMRT1 as a transcription factor in vitro. DM-W and DMRT1 shared a DNA-binding sequence. Importantly, DM-W dose-dependently antagonized the transcriptional activity of DMRT1 on a DMRT1-driven luciferase reporter system in 293 cells. We also examined roles of DM-W or DMRT1 in gonadal formation. Some transgenic ZW tadpoles bearing a DM-W knockdown vector had gonads with a testicular structure, and two developed into frogs with testicular gonads. Ectopic DMRT1 induced primary testicular development in some ZW individuals. These observations indicated that DM-W and DMRT1 could have opposite functions in the sex determination. Our findings support a novel model for a ZZ/ZW-type system in which DM-W directs female sex as a sex-determining gene, by antagonizing DMRT1. Additionally, they suggest that DM-W diverged from DMRT1 as a dominant-negative type gene, i.e. as a ;neofunctionalization' gene for the ZZ/ZW-type system. Finally, we discuss a conserved role of DMRT1 in testis formation during vertebrate evolution.

Inducible Mis- and Over-Expression of PKCIW Regulates the Expression of AMH and P450arom in Chicken Embryo Fibroblast

Sex in birds is determined genetically as in mammals and a Z-linked gene DMRT1 is required for testis development. But it remains possible that the W chromosome contains a similarly critical factor for female development. The W-linked gene PKCIW was put forward as the seductive candidate for avian sex determination and/or sex differentiation. Mis-expression and over-expression of PKCIW were performed respectively in male and female chicken embryo fibroblast with tet-on inducible expression system in this study. The results of RT-PCR showed that with the PKCIW recombinant vector introducing, PKCIW mRNA expression was significantly improved in female chicken embryo fibroblast and was close to that of the female controls and in male chicken embryo fibroblast, in which normally there was no expression. Both misand over-expression of PKCIW led to up-regulated expression of P450arom and down-regulated expression of AMH, while large increase of P450arom in female and large decrease of AMH in male appeared. With misand over-expression of PKCIW, there was no significant change of FOXL2, SOX9, DMRT1 and ATP5A1W mRNA expression. These results showed the possible regulatory effect of PKCIW on AMH and P450arom in transcription level.

Xenopus W-Linked DM-W Induces Foxl2 and Cyp19 Expression during Ovary Formation

The molecular mechanisms of vertebrate ZZ/ZW-type sex-determining systems remain unclear. We recently indicated that a W-linked gene, DM-W is a likely ovary-determining gene in Xenopus laevis. We first examined whether Cyp19 for estrogen-synthesizing enzyme P450 aromatase and Foxl2 showed female-specific expression in developing gonads. Both genes showed much higher expression in ZW than in ZZ gonads during and after sex determination. Importantly, transgenic ZZ gonads expressing exogenous DM-W at the sex-determining stage showed a ZW-type pattern of Cyp19 and Foxl2 expression. These results suggest that DM-W up-regulates Cyp19 and Foxl2 expression to guide primary ovary development in X. laevis.

Sequence Analysis of Full-Length cDNA of Sex Chromosome-Linked Novel Gene 2d-2F9 inGallus gallus

We obtained two novel W chromosome-linked chick genes by the use of female-male subtraction macroarrays, one of which, 2d-2F9, (recorded as AB188527 in DDBJ) did not have sufficient length (776 bp) to reveal its real form or characteristics. Hence, we obtained full-length Z-linked and W-linked 2d-2F9 genes of 2596 bp and 2589 bp respectively by the oligo-capping and RACE methods. Sequence analysis of these genes not only revealed that there is a counterpart of the W-linked 2d-2F9 gene on the Z chromosome, but also that there is a low homologous area at 5'-UTR between the W- and Z-kinked genes. Using this information, we designed a set of primers to identify sex and to select clones having the Z and W-linked gene (named 2d-2F9-Z and 2d-2F9-W), and also prepared two sets of primers for RT-PCR. These genes were found to be expressed constitutively and ubiquitously from the early embryo to the hatched chick, and they were assigned to the AAA ATP-superfamily.

Genetic mapping of Z chromosome and identification of W chromosome-specific markers in the silkworm, Bombyx mori

In the silkworm, Bombyx mori, the female is the heterogametic (ZW) sex and the male is homogametic (ZZ). The female heterogamety is a typical situation in the insect order Lepidoptera. Although the W chromosome in silkworm is strongly female determining, no W-linked gene for a morphological character has been found on it. The Z chromosome carries important traits of economic value as well as genes for various phenotypic traits, but only 2% of molecular information based on its relative size is known. Studies conducted so far indicate that the Z-linked genes are not dosage compensated. In the present study, we constructed a genetic map of randomly amplified polymorphic DNA fragments (RAPD), simple sequence repeats (SSR), and fluorescent intersimple sequence repeat PCR (FISSR) markers for the Z chromosome using a backcross mapping population. A total of 16 Z-linked markers were identified, characterized, and mapped using od, a recessive trait for translucent skin as an anchor marker yielding a total recombination map of 334.5 cM. The linkage distances obtained suggested that the markers were distributed throughout the Z chromosome. Four RAPD and four SSR markers that were linked to W chromosome were also identified. The proposed mapping approach should be useful to identify and map sex-linked traits in the silkworm. The economic and evolutionary significance of Z- and W-linked genes in silkworm, in particular, and lepidopterans, in general, is discussed.

Adaptive molecular evolution of HINTW, a female-specific gene in birds.

It is well established that many genes on the male-specific Y chromosome of organisms such as mammals are involved in male reproduction and may evolve rapidly because of positive selection on male reproductive traits. In contrast, very little is known about the function and evolution of W-linked genes restricted to the female genome of organisms with female heterogamety. For birds (males ZZ, females ZW), only one W-linked gene (HINTW) is sufficiently different from its Z-linked homolog to indicate a female-specific function. Here, we report that HINTW shows evidence of adaptive molecular evolution, implying strong positive selection for new functional properties in female birds. Moreover, because HINTW is expressed in the gonads of female birds just before sexual differentiation and is thus a candidate for sex determination, it suggests adaptive evolution related to female development. This provides the first example of Darwinian evolution of a gene restricted to the female genome of any organism. Given that HINTW exists in multiple copies on W, similar to some testis-specific genes amplified on mammalian Y, avian HINTW may thus potentially represent a female parallel to the organization and evolution of Y chromosome genes involved in male reproduction and development.

Sex identification in birds

Visually identifying the sex of a bird can be difficult. It cannot be done in half the world's species when they are adults, and virtually none can be sexed as chicks. Despite this, the sex of a bird is vital for aviculture, scientific research, and conservation. Over the years, surgery and chromosome inspection have been used for sex identification. At present, these techniques are being eclipsed by the use of DNA. DNA can be used because a male bird has two Z sex chromosomes, whereas the female has a Z and a W. Consequently, the presence of a W unique DNA sequence will identify a bird as female. However, the isolation of a W-linked marker can be laborious. This is being remedied through the use of two DNA amplification reactions, known as random amplification of polymorphic DNA (RAPD) and amplified fragment length polymorphs (AFLP). Unfortunately, the markers they yield are often nonfunctional DNA. This type of DNA is a mild parasite and makes up about 95% of the genome. It also evolves rapidly so that a test based on such a sequence will only work in a single species or a few close relatives. More recently, a W-linked gene has been found. This is named CHD1-W, and it evolves far more slowly than nonfunctional DNA. It can be used to sex all birds, barring ratites such as the ostrich. The technique is simple, cheap, and effective. To conclude, DNA sex identification is demonstrated in three situations: an experiment that has shown that birds can control the sex of their offspring; a race to identify the sex of the last wild Spix's Macaw from moulted feathers; and as a valuable aid to breeding in zoos.

Sex identification in birds using two CHD genes.

In theory, birds should control the sex ratio of the offspring they produce. In practice, we have very limited evidence to support this idea because of our difficulty in sexing nestling birds. In addition, extinction is facing an increasing number of birds. Our ability to help includes captive breeding which, again, is difficult if male and female adults cannot be recognized. Here we describe the discovery of a W-linked gene in the Great tit (Parus major). It is named CHD-W (chromodomain-helicase-DNA-binding protein W-linked), it is highly conserved and it is W-chromosome linked in a range of bird species. These birds also possess a second, non-W-linked CHD gene (CHD-NW). A single, simple polymerase chain reaction technique based on both genes can be used to identify the sex in a wide variety of birds.

CDNA Cloning of a Z- and W-Linked Gene in Gallinaceous Birds

cDNA Cloning of a Z- and W-Linked Gene in Gallinaceous Birds