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345 results for “sex chromosome”
Data from: Evolution and dynamics of germline sex chromosome regulation in D. miranda
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Data from: Snakeskin gourami (Trichopodus pectoralis) exhibits XX/XY sex determination and putative young Y chromosome shares sex chromosomal linkage homologies with those of amniotes
<p class="CxSpFirst"><span>Snakeskin gourami (<i>Trichopodus pectoralis</i>) is one of the most common air-breathing freshwater fish of the Indochina peninsula. It has a high meat yield and is one of the top five aquaculture freshwater fish in Thailand. However, it takes 2–3<b> </b>years for adults to reach sexual maturity. Snakeskin gourami is not externally sexually dimorphic and its sex determination remains unknown, complicating many aspects of broodstock management including sex manipulation. Understanding the sex determination system will contribute significantly towards full-scale commercialization. By characterizing the sex determination system in snakeskin gourami using cytogenetic approaches and Diversity Arrays Technology, we identified sex-specific loci in 16 phenotypic sex assignments of snakeskin gourami. Of the 39 loci present in all males, 4<b> </b>male-linked loci reached the criteria of moderately sex-linked loci (70:30; males:females and 80:20; males:females). By contrast, only one female-linked locus was detected from moderately sex-linked loci. This suggests that snakeskin gourami exhibits an XX/XY sex determination mode. No different chromosomal patterns were observed in karyotype, C-banding, and microsatellite repeat fluorescence <i>in situ</i> hybridization mapping between males and females, and no male-specific loci of 100:0 (males:females) were observed in snakeskin gourami. This suggests that the putative Y chromosome is young and the non-recombination region is very cryptic. A total of<b> </b>10.26% male-linked loci were involved with the sex developmental pathway in vertebrates and 5.13% showed partial homology with several amniote sex chromosomal linkages. Surprisingly, the hypothesis of an ancestral amniote super-sex chromosome with overlaps of partial sex chromosomal linkages was also found in teleosts. This approach provides a solid baseline to reveal the sex determination mechanism<b> </b>and identify potential sex determination regions in teleosts, allowing further investigation of genetic improvements in snakeskin gourami.</span></p>
Genome-wide SNP analysis of Siamese cobra (Naja kaouthia) reveals the molecular basis of transitions between Z and W sex chromosomes and supports the presence of an ancestral super-sex chromosome in amniotes
<p>Elucidation of the process of sex chromosome differentiation is necessary to understand the dynamics of evolutionary mechanisms in organisms. The Siamese cobra (<i>Naja kaouthia</i>) exhibits ZZ/ZW heteromorphic sex chromosomes. The W sex chromosome contains a large number of repeats and shares several amniote sex chromosomal linkages. In conjunction with recent advances in high-throughput sequencing, Diversity Arrays Technology (DArTseq™) provides an effective approach to identify sex-specific loci that are epoch-making, to understand the dynamics of molecular transitions between the Z and W sex chromosomes in a snake lineage. From a total of 543 perfectly sex-linked loci, 90 loci showed partial homology with several amniote sex chromosomal linkages, and 89 loci were homologous to transposable elements, which suggests that recombination suppression may be the crucial step in snake sex chromosome differentiation. Two loci were confirmed as W-specific nucleotides in females but not in males in the population examined by PCR amplification; one of the two loci (locus id: 100002617) was further amplified in females of the Indochinese spitting cobra (<i>N. siamensis</i>) but not in the other 22 snake species examined. Female-specific DArT markers were identified in Siamese cobra. These loci might result from a sex chromosome differentiation process between Z and W and involve putative sex-determination regions in Siamese cobra. Short sequences derived from DArTseq™ technology also shared linkage homologies among amniote sex chromosomes, which supports the hypothesis of an ancestral super-sex chromosome with overlaps of partial sex chromosomal linkages. The locus (id: 100002617) shared in <i>N. kaouthia</i> and <i>N. siamensis</i>, but among 22 other snake species, indicates inheritance from a common ancestor as synapomorphic loci in the <i>Naja</i> lineage. The ease of use of the DArT markers and DArTseq™ platform provides a useful strategy for future research on sex chromosome evolution in snakes.</p>
Data from: Genetic architecture of traits associated with reproductive barriers in Silene: coupling, sex chromosomes and variation
The evolution of reproductive barriers and their underlying genetic architecture is of central importance for the formation of new species. Reproductive barriers can be controlled either by few large-effect loci suggesting strong selection on key traits, or by many small-effect loci, consistent with gradual divergence or with selection on polygenic or multiple traits. Genetic coupling between reproductive barrier loci further promotes divergence, particularly divergence with ongoing gene flow. In this study, we investigated the genetic architectures of ten morphological, phenological and life history traits associated with reproductive barriers between the hybridizing sister species Silene dioica and S. latifolia; both are dioecious with XY sex determination. We used quantitative trait locus (QTL) mapping in two reciprocal F2 crosses. One to six QTLs per trait, including 9 major QTLs (PVE > 20%) were detected, in total, on 11 of 12 linkage groups. We found strong evidence for coupling of QTLs for uncorrelated traits. QTL clusters occurred both on autosomes and on the sex chromosomes. Unexpectedly, QTLs detected in the two F2 crosses differed largely, despite limited phenotypic differences between them and sufficient statistical power. The widely dispersed genetic architectures of traits associated with reproductive barriers suggest gradual divergence or multifarious selection and coupling of the underlying QTLs likely promoted divergence with gene flow in this system. The low congruence of QTLs between the two crosses further points to variable and possibly redundant genetic architectures of traits associated with reproductive barriers, with important implications for the evolutionary dynamics of divergence and speciation.
Data from: Sex-antagonistic genes, XY recombination, and feminized Y chromosomes
The canonical model of sex-chromosome evolution predicts that sex-antagonistic (SA) genes play an instrumental role in the arrest of XY recombination and ensuing Y-chromosome degeneration. Although this model might account for the highly differentiated sex chromosomes of birds and mammals, it does not fit the situation of many lineages of fish, amphibians or non-avian reptiles, where sex chromosomes are maintained homomorphic through occasional XY recombination and/or high turnover rates. Such situations call for alternative explanatory frameworks. A crucial issue at stake is the effect of XY recombination on the dynamics of SA genes and deleterious mutations. Using individual-based simulations, we show that a complete arrest of XY recombination actually benefits females, not males. Male fitness is maximized at different XY-recombination rates depending on SA selection, but never at zero XY recombination. This should consistently favor some level of XY recombination, which in turn generates a recombination load at sex-linked SA genes. Hill-Robertson interferences with deleterious mutations also impede the differentiation of sex-linked SA genes, to the point that males may actually fix feminized phenotypes when SA selection and XY recombination are low. We argue that sex chromosomes might not be a good localization for SA genes, and sex conflicts seem better solved through the differential expression of autosomal genes.
Data from: Sex chromosome turnovers and genetic drift: a simulation study
The recent advances of new genomic technologies has enabled to identify and characterize sex chromosomes in an increasing number of non-model species, revealing that many plants and animals undergo frequent sex chromosome turnovers. What evolutionary forces drive these turnovers remains poorly understood, but it was recently proposed that drift might play a more important role than generally assumed. We analyzed the dynamics of different types of turnovers using individual-based simulations, and show that when mediated by genetic drift, turnovers are usually easier to achieve than substitutions at neutral markers, but that their dynamics and relative likelihoods vary with the type of the resident and emergent sex chromosome system (XY and/or ZW), and the dominance relationships among the sex-determining factors. Focusing on turnovers driven by epistatically dominant mutations, we find that drift-mediated turnovers that preserve the heterogamety pattern are 2-4x more likely than those along which the heterogametic sex changes. This ratio nevertheless decreases along with effective population size, and can even reverse in case of extreme polygyny. This can be attributed to a "drift-induced" selective force, known to influence transitions between male and female heterogamety, but which according to our study, does not affect turnovers that preserve the heterogametic sex.
Data from: Identifying homomorphic sex chromosomes from wild-caught adults with limited genomic resources
We demonstrate a genotyping-by-sequencing approach to identify homomorphic sex chromosomes and their homolog in a distantly related reference genome, based on noninvasive sampling of wild-caught individuals, in the moor frog Rana arvalis. Double-digest RADseq libraries were generated using buccal swabs from 30 males and 21 females from the same population. Search for sex-limited markers from the unfiltered data set (411 446 RAD tags) was more successful than searches from a filtered data set (33 073 RAD tags) for markers showing sex differences in heterozygosity or in allele frequencies. Altogether, we obtained 292 putatively sex-linked RAD loci, 98% of which point to male heterogamety. We could map 15 of them to the Xenopus tropicalis genome, all but one on chromosome pair 1, which seems regularly co-opted for sex determination among amphibians. The most efficient mapping strategy was a three-step hierarchical approach, where R. arvalis reads were first mapped to a low-coverage genome of Rana temporaria (17 My divergence), then the R. temporaria scaffolds to the Nanorana parkeri genome (90 My divergence), and finally the N. parkeri scaffolds to the X. tropicalis genome (210 My). We validated our conclusions with PCR primers amplifying part of Dmrt1, a candidate sex determination gene mapping to chromosome 1: a sex-diagnostic allele was present in all 30 males but in none of the 21 females. Our approach is likely to be productive in many situations where biological samples and/or genomic resources are limited.
Data from: Genetic architecture of isolation between two species of Silene with sex chromosomes and Haldane's rule
Examination of the genetic architecture of hybrid breakdown can provide insight into the genetic mechanisms of commonly observed isolating phenomena such as Haldane's rule. We used line-cross analysis to dissect the genetic architecture of divergence between two plant species that exhibit Haldane's rule for male sterility and rarity, Silene latifolia and Silene diclinis. We made 15 types of crosses, including reciprocal F1, F2, backcrosses, and later-generation crosses, grew the seeds to flowering, and measured the number of viable ovules, proportion of viable pollen, and sex ratio. Typically, Haldane's rule for male rarity in XY animal hybrids is explained by interactions involving recessive X-linked alleles that are deleterious when hemizygous (dominance theory), while sterility is explained by rapid evolution of spermatogenesis genes (faster-male evolution). In contrast, we found that the genetic mechanisms underlying Haldane's rule between the two Silene species did not follow these conventions. Dominance theory was sufficient to explain male sterility, but male rarity likely involved faster-male evolution. We also found an effect of the neo-sex chromosomes of S. diclinis on the extreme rarity of some hybrid males. Our findings suggest that the genetic architecture of Haldane's rule in dioecious plants may differ from those commonly found in animals.
Data from: Sex-chromosome turnovers induced by deleterious mutation load
In sharp contrast with mammals and birds, many cold-blooded vertebrates present homomorphic sex chromosomes. Empirical evidence supports a role for frequent turnovers, which replace non-recombining sex chromosomes before they have time to decay. Three main mechanisms have been proposed for such turnovers, relying either on neutral processes, sex-ratio selection, or intrinsic benefits of the new sex-determining genes (due e.g. to linkage with sexually antagonistic mutations). Here we suggest an additional mechanism, arising from the load of deleterious mutations that accumulate on non-recombining sex chromosomes. In the absence of dosage compensation, this load should progressively lower survival rate in the heterogametic sex. Turnovers should occur when this cost outweighs the benefits gained from any sexually antagonistic genes carried by the non-recombining sex chromosome. We use individual-based simulations of a Muller's ratchet process to test this prediction, and investigate how the relevant parameters (effective population size, strength and dominance of deleterious mutations, size of non-recombining segment, and strength of sexually antagonistic selection) are expected to affect the rate of turnovers.
Data from: Getting a full dose? Reconsidering sex chromosome dosage compensation in the silkworm, Bombyx mori
Dosage compensation – equalizing gene expression levels in response to differences in gene dose or copy number – is classically considered to play a critical role in the evolution of heteromorphic sex chromosomes. As the X and Y diverge through degradation and gene loss on the Y (or the W in female-heterogametic ZW taxa), it is expected that dosage compensation will evolve to correct for sex-specific differences in gene dose. While this is observed in some organisms, recent genome-wide expression studies in other taxa have revealed striking exceptions. In particular, reports that both birds and the silkworm moth (Bombyx mori) lack dosage compensation have spurred speculation that this is the rule for all female-heterogametic taxa. Here we revisit the issue of dosage compensation in silkworm by replicating and extending the previous analysis. Contrary to previous reports, our efforts reveal that the global male:female expression ratio does not differ between the Z and autosomes, a pattern typically associated with dosage compensated taxa. We believe the previous report of unequal male:female ratios on the Z reflects artifacts of microarray normalization in conjunction with not testing a major assumption that the male:female global expression ratio was unbiased for autosomal loci. However, we also find that the global Z chromosome expression is significantly reduced relative to autosomes, a pattern not expected in dosage compensated taxa. This combination of male:female parity with an overall reduction in expression for sex-linked loci is not consistent with the prevailing evolutionary theory of sex chromosome evolution and dosage compensation.
Data from: Homologous sex chromosomes in three deeply divergent anuran species
Comparative genomic studies are revealing that, in sharp contrast with the strong stability found in birds and mammals, sex determination mechanisms are surprisingly labile in cold-blooded vertebrates, with frequent transitions between different pairs of sex chromosomes. It was recently suggested that, in context of this high turnover, some chromosome pairs might be more likely than others to be co-opted as sex chromosomes. Empirical support, however, is still very limited. Here we show that sex-linked markers from three highly divergent groups of anurans map to Xenopus tropicalis scaffold 1, a large part of which is homologous to the avian sex chromosome. Accordingly, the bird sex determination gene DMRT1, known to play a key role in sex differentiation across many animal lineages, is sex-linked in all three groups. Our data provide strong support for the idea that some chromosome pairs are more likely than others to be co-opted as sex chromosomes, because they harbor key genes from the sex determination pathway.
Data from: Introgression maintains the genetic integrity of the sex-determining chromosome of the fungus Neurospora tetrasperma
Genome evolution is driven by a complex interplay of factors, including selection, recombination, and introgression. The regions determining sexual identity are particularly dynamic parts of eukaryotic genomes that are prone to molecular degeneration associated with suppressed recombination. In the fungus Neurospora tetrasperma, it has been proposed that this molecular degeneration is counteracted by the introgression of non-degenerated DNA from closely related species. In this study, we used comparative and population genomic analyses of variation among 92 genomes from eight phylogenetically and reproductively isolated lineages of N. tetrasperma, and its three closest relatives, to investigate the factors shaping the evolutionary history of the genomes. We found that suppressed recombination extends across at least 6 Mbp (~63%) of the mating-type (mat) chromosome in N. tetrasperma, and is associated with decreased genetic diversity, which is likely the result primarily of selection at linked sites. Furthermore, analyses of molecular evolution revealed an increased mutational load in this region, relative to recombining regions. However, comparative genomic and phylogenetic analyses indicate that the mat chromosomes are temporarily regenerated via introgression from sister species; six out of eight lineages show introgression into one of their mat chromosomes, with at least three other Neurospora species acting as donors. The introgressed tracts have been driven to fixation in lineages, suggesting that they confer an adaptive advantage in natural populations, and our analyses support the presence of selective sweeps in at least one of the lineages. Thus, these data strongly support the previously hypothesized role of introgression as a mechanism for the maintenance of mating-type determining chromosomal regions.
FIGURES 1–2. Endecous ubajarensis n in A new species of Endecous Saussure, 1878 (Orthoptera, Gryllidae) from northeast Brazil with the first X X 0 chromosomal sex system in Gryllidae
FIGURES 1–2. Endecous ubajarensis n. sp. habitus. 1—holotype male; 2—paratype female UBA02.
Non canonical bases differentially represented in the sex chromosomes of the dioecious plant Silene latifolia
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Sex-specific splicing of Z- and W-borne nr5a1 alleles suggests sex determination is controlled by chromosome conformation
<p><i>Pogona vitticeps</i> has female heterogamety (ZZ/ZW) but the master sex determining gene is unknown, as is the case for all reptiles. We show that <i>nr5a1</i>, a gene that is essential in mammalian sex determination, has alleles on the Z and W chromosomes (Z-<i>nr5a1</i> and W-<i>nr5a1</i>), which are both expressed and can recombine. Three transcript isoforms of Z-<i>nr5a1</i> were detected in gonads of adult ZZ males, two of which encode a functional protein. However, ZW females produced sixteen isoforms, most of which contained premature stop codons. The array of transcripts produced by the W-borne allele (W-<i>nr5a1</i>) is likely to produce truncated polypeptides that could act as a competitive inhibitor to the full-length intact protein. We hypothesize that an altered configuration of the W chromosomes affects the conformation of the primary transcript generating inhibitory W-borne isoforms that suppress testis determination. Under this hypothesis, the GSD system of <i>P. vitticeps</i> is a W-borne dominant female-determiner that may be controlled epigenetically.</p>
Sex chromosome differentiation via changes in the Y chromosome repeat landscape in African annual killifishes Nothobranchius furzeri and N. kadleci
<p><span>Repetitive DNA represents an important driver of sex chromosome differentiation. Yet repetitive sequences tend to be misrepresented or overlooked in genomic studies. We analysed repetitive landscape of sex chromosomes in several populations of a turquoise killifish <em>Nothobranchius</em> <em>furzeri</em> and its sister species <em>N</em>. <em>kadleci</em> (Teleostei: Nothobranchiidae), representatives of African annual killifishes with high rate of karyotype and sex chromosome evolution. We combined bioinformatic analyses of repeatome with molecular cytogenetic techniques such as comparative genomic hybridization, fluorescence in situ hybridization with satellite sequences, genes for ribosomal RNAs (rDNA) and bacterial artificial chromosomes (BACs) and immunostaining of </span><span>SYCP3 and MLH1 proteins, which marked lateral elements of synaptonemal complexes and recombination sites, respectively</span><span>. We revealed that <em>N</em>. <em>furzeri</em> and <em>N</em>. <em>kadleci</em> share the XY sex chromosome system, which is thus much older than previously assumed. Sex chromosomes are mostly heteromorphic as evidenced by distinct distribution of satellite DNAs and major rDNA. Yet, the heteromorphic X and Y sex chromosomes pair almost exclusively regularly in meiosis, which implies synaptic adjustment. Physical mapping of BACs identified inversions on Y chromosomes of the <em>N</em>. <em>kadleci</em> populations, similar to the pattern previously reported in <em>N</em>. <em>furzeri</em>. Yet, the repetitive DNA landscape of X and Y sex chromosomes either diverged in parallel in populations of both species, or it evolved in their common ancestor and thus predates the inversions. The observed differentiation via repeat repatterning thus cannot be explained by the classical sexual antagonistic model. Rather, we hypothesized that relaxed meiotic drive and recombination reduced by neutral processes could drive changes in repeatome and secondary inversions could be maintained </span><span>by sexually antagonistic regulatory effects resulting from evolution of dosage compensation. </span><span><br></span></p>
Data from: The evolutionary dynamics of sexually antagonistic mutations in pseudoautosomal regions of sex chromosomes
Sex chromosomes can evolve gene contents that differ from the rest of the genome, as well as larger sex differences in gene expression compared with autosomes. This probably occurs because fully sex-linked beneficial mutations substitute at different rates from autosomal ones, especially when fitness effects are sexually antagonistic (SA). The evolutionary properties of genes located in the recombining pseudo-autosomal region (PAR) of a sex chromosome have not previously been modelled in detail. Such PAR genes differ from classical sex-linked genes by having two alleles at a locus in both sexes; in contrast to autosomal genes, however, variants can become associated with gender. The evolutionary fates of PAR genes may therefore differ from those of either autosomal or fully sex-linked genes. Here, we model their evolutionary dynamics by deriving expressions for the selective advantages of PAR gene mutations under different conditions. We show that, unless selection is very strong, the probability of invasion of a population by an SA mutation is usually similar to that of an autosomal mutation, unless there is close linkage to the sex-determining region. Most PAR genes should thus evolve similarly to autosomal rather than sex-linked genes, unless recombination is very rare in the PAR.
Figure 5. Male C in Sex chromosome polymorphism in Bulgarian populations of Microtus guentheri (Danford & Alston, 1880)
Figure 5. Male C-banded karyotype of the Guenther's vole from Rodop Mountains.
Figure 4 in Sex chromosome polymorphism in Bulgarian populations of Microtus guentheri (Danford & Alston, 1880)
Figure 4. Female metaphase plate and its karyotype of the Guenther's vole from Rodop Mountains.
Figure 2 in Sex chromosome polymorphism in Bulgarian populations of Microtus guentheri (Danford & Alston, 1880)
Figure 2. Female metaphase plate and its karyotype of the Guenther's vole from Strandzha Mountain.
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