A new plant sex-linked gene with high sequence diversity and possible introgression of the X copy

We describe patterns of DNA sequence diversity in a newly identified sex-linked gene, SlX9/SlY9, in Silene latifolia (Caryophyllaceae). The copies on both sex chromosomes seem to be functional, and each maps close to the respective X- and Y-linked copy of another sex-linked gene pair, SlCypX/SlCypY. The Y-linked copy has low diversity, similar to what has been found for several other Y-linked genes in S. latifolia, and consistent with the theoretical expectations of hitch-hiking processes occurring on a non-recombining chromosome. However, SlX9 has higher diversity than other genes on the S. latifolia X chromosome. We evaluate the hypothesis of introgression from the closely related species S. dioica as an explanation for the high sequence diversity observed.     

A sex-chromosome mutation in Silene latifolia

Silene latifolia is dioecious, yet rare hermaphrodites have been found, and such natural mutants can provide valuable insight into genetic mechanisms. Here, we describe a hermaphrodite-inducing mutation that is almost certainly localized to the gynoecium-suppression region of the Y chromosome in S. latifolia. The mutant Y chromosome was passed through the megaspore, and the presence of two X chromosomes was not necessary for seed development in the parent. This result supports a lack of degeneration of the Y chromosome in S. latifolia, consistent with the relatively recent formation of the sex chromosomes in this species. When crossed to wild-type plants, hermaphrodites performed poorly as females, producing low seed numbers. When hermaphrodites were pollen donors, the sex ratio of offspring they produced through crosses was biased towards females. This suggests that hermaphroditic S. latifolia would fail to thrive and potentially explains the rarity of hermaphrodites in natural populations of S. latifolia. These results indicate that the Y chromosome in Silene latifolia remains very similar to the X, perhaps mostly differing in the primary sex determination regions.     

Nucleotide diversity in Silene latifolia autosomal and sex-linked genes

The plant Silene latifolia has separate sexes and sex chromosomes, and is of interest for studying the early stages of sex chromosome evolution, especially the evolution of non-recombining regions on the Y chromosome. Hitch-hiking processes associated with ongoing genetic degeneration of the non-recombining Y chromosome are predicted to reduce Y-linked genes'' effective population sizes, and S. latifolia Y-linked genes indeed have lower diversity than X-linked ones. We tested whether this represents a true diversity reduction on the Y, versus the alternative possibility, elevated diversity at X-linked genes, by collecting new data on nucleotide diversity for autosomal genes, which had previously been little studied. We find clear evidence that Y-linked genes have reduced diversity. However, another alternative explanation for a low Y effective size is a high variance in male reproductive success. Autosomal genes should then also have lower diversity than expected, relative to the X, but this is not found in our loci. Taking into account the higher mutation rate of Y-linked genes, their low sequence diversity indicates a strong effect of within-population hitch-hiking on the Y chromosome.     

Recent Spread of a Retrotransposon in the Silene latifolia Genome, Apart From the Y Chromosome

Transposable elements often accumulate in nonrecombining regions, such as Y chromosomes. Contrary to this trend, a new Silene retrotransposon described here, has spread recently all over the genome of plant Silene latifolia, except its Y chromosome. This coincided with the latest steps of sex chromosome evolution in this species.     

Identifying new sex-linked genes through BAC sequencing in the dioecious plant Silene latifolia

Background

Silene latifolia represents one of the best-studied plant sex chromosome systems. A new approach using RNA-seq data has recently identified hundreds of new sex-linked genes in this species. However, this approach is expected to miss genes that are either not expressed or are expressed at low levels in the tissue(s) used for RNA-seq. Therefore other independent approaches are needed to discover such sex-linked genes.

Results

Here we used 10 well-characterized S. latifolia sex-linked genes and their homologs in Silene vulgaris, a species without sex chromosomes, to screen BAC libraries of both species. We isolated and sequenced 4 Mb of BAC clones of S. latifolia X and Y and S. vulgaris genomic regions, which yielded 59 new sex-linked genes (with S. vulgaris homologs for some of them). We assembled sequences that we believe represent the tip of the Xq arm. These sequences are clearly not pseudoautosomal, so we infer that the S. latifolia X has a single pseudoautosomal region (PAR) on the Xp arm. The estimated mean gene density in X BACs is 2.2 times lower than that in S. vulgaris BACs, agreeing with the genome size difference between these species. Gene density was estimated to be extremely low in the Y BAC clones. We compared our BAC-located genes with the sex-linked genes identified in previous RNA-seq studies, and found that about half of them (those with low expression in flower buds) were not identified as sex-linked in previous RNA-seq studies. We compiled a set of ~70 validated X/Y genes and X-hemizygous genes (without Y copies) from the literature, and used these genes to show that X-hemizygous genes have a higher probability of being undetected by the RNA-seq approach, compared with X/Y genes; we used this to estimate that about 30 % of our BAC-located genes must be X-hemizygous. The estimate is similar when we use BAC-located genes that have S. vulgaris homologs, which excludes genes that were gained by the X chromosome.

Conclusions

Our BAC sequencing identified 59 new sex-linked genes, and our analysis of these BAC-located genes, in combination with RNA-seq data suggests that gene losses from the S. latifolia Y chromosome could be as high as 30 %, higher than previous estimates of 10-20 %.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1698-7) contains supplementary material, which is available to authorized users.     

MK17, a specific marker closely linked to the gynoecium suppression region on the Y chromosome in Silene latifolia

The aim of this work was to isolate new DNA markers linked to the Silene latifolia Y chromosome. To do this we created a chromosome-specific plasmid library after DOP-PCR amplification of laser-microdissected Y-chromosomes. The library screening led to the isolation of several clones yielding mostly to exclusive male specific hybridization signals. Subsequent PCR confirmed the Y-unique linkage for one of the sequences. This DNA sequence called MK17 has no homology to any known DNA sequence and it is not expressed. Based on PCR and Southern analyses, MK17 is present only in dioecious species of the Elisanthe section of the genus Silene (S. latifolia, S. dioica, and S. diclinis) and it is absent in related gynodioecious and hermaphroditic species. The mapping analysis using a panel of deletion mutants showed that MK17 is closely linked to the region controlling suppression of gynoecium development. Hence MK17 represents a valuable marker to isolate genes controlling the gynoecium development suppression on the Y chromosome of S. latifolia.     

DNA diversity in sex-linked and autosomal genes of the plant species Silene latifolia and Silene dioica

The relatively recent origin of sex chromosomes in the plant genus Silene provides an opportunity to study the early stages of sex chromosome evolution and, potentially, to test between the different population genetic processes likely to operate in nonrecombining chromosomes such as Y chromosomes. We previously reported much lower nucleotide polymorphism in a Y-linked gene (SlY1) of the plant Silene latifolia than in the homologous X-linked gene (SlX1). Here, we report a more extensive study of nucleotide diversity in these sex-linked genes, including a larger S. latifolia sample and a sample from the closely related species Silene dioica, and we also study the diversity of an autosomal gene, CCLS37.1. We demonstrate that nucleotide diversity in the Y-linked genes of both S. latifolia and S. dioica is very low compared with that of the X-linked gene. However, the autosomal gene also has low DNA polymorphism, which may be due to a selective sweep. We use a single individual of the related hermaphrodite species Silene conica, as an outgroup to show that the low SlY1 diversity is not due to a lower mutation rate than that for the X-linked gene. We also investigate several other possibilities for the low SlY1 diversity, including differential gene flow between the two species for Y-linked, X-linked, and autosomal genes. The frequency spectrum of nucleotide polymorphism on the Y chromosome deviates significantly from that expected under a selective-sweep model. However, we detect population subdivision in both S. latifolia and S. dioica, so it is not simple to test for selective sweeps. We also discuss the possibility that Y-linked diversity is reduced due to highly variable male reproductive success, and we conclude that this explanation is unlikely.     

The role of chromosomal rearrangements in the evolution of <Emphasis Type="Italic">Silene latifolia</Emphasis> sex chromosomes

Silene latifolia is a model plant for studies of the early steps of sex chromosome evolution. In comparison to mammalian sex chromosomes that evolved 300 mya, sex chromosomes of S. latifolia appeared approximately 20 mya. Here, we combine results from physical mapping of sex-linked genes using polymerase chain reaction on microdissected arms of the S. latifolia X chromosome, and fluorescence in situ hybridization analysis of a new cytogenetic marker, Silene tandem repeat accumulated on the Y chromosome. The data are interpreted in the light of current genetic linkage maps of the X chromosome and a physical map of the Y chromosome. Our results identify the position of the centromere relative to the mapped genes on the X chromosome. We suggest that the evolution of the S. latifolia Y chromosome has been accompanied by at least one paracentric and one pericentric inversion. These results indicate that large chromosomal rearrangements have played an important role in Y chromosome evolution in S. latifolia and that chromosomal rearrangements are an integral part of sex chromosome evolution.     

Dynamic gene order on the <Emphasis Type="Italic">Silene latifolia</Emphasis> Y chromosome

Dioecious Silene latifolia evolved heteromorphic sex chromosomes within the last ten million years, making it a species of choice for studies of the early stages of sex chromosome evolution in plants. About a dozen genes have been isolated from its sex chromosomes and basic genetic and deletion maps exist for the X and Y chromosomes. However, discrepancies between Y chromosome maps led to the proposal that individual Y chromosomes may differ in gene order. Here, we use an alternative approach, with fluorescence in situ hybridization (FISH), to locate individual genes on S. latifolia sex chromosomes. We demonstrate that gene order on the Y chromosome differs between plants from two populations. We suggest that dynamic gene order may be a general property of Y chromosomes in species with XY systems, in view of recent work demonstrating that the gene order on the Y chromosomes of humans and chimpanzees are dramatically different.     

Accumulation of chloroplast DNA sequences on the Y chromosome of Silene latifolia

Silene latifolia is a model dioecious plant with heteromorphic sex chromosomes. The Y chromosome is the largest in this species. Theoretical models propose an accumulation of repetitive DNA sequences in non-recombining parts of the Y chromosome. In this study, we isolated a BAC7H5 clone preferentially hybridizing to the Y chromosome of S. latifolia. Sequence analysis revealed that this BAC7H5 contains part of the chloroplast genome, indicating that these chloroplast sequences have accumulated on the Y chromosome and also may contribute to its large size. We constructed Y chromosome- and X chromosome-specific libraries and screened them to find Y- and/or X-linked copies of chloroplast sequences. Sequence analysis revealed higher divergence of a non-genic region of the chloroplast sequences located on the Y chromosome while genic regions tested showed only very low (max 0.9%) divergence from their chloroplast homologues.     

Evolution of Neo-Sex Chromosomes in Silene diclinis

A small cluster of dioecious species in the plant genus Silene has evolved chromosomal sex determination and sex chromosomes relatively recently, within the last 10 million years (MY). Five dioecious Silene species (section Elisanthe) are very closely related (1–2 MY of divergence) and it was previously thought that all five have similar sex chromosomes. Here we demonstrate that in one of these species, Silene diclinis, the sex chromosomes have been significantly rearranged, resulting in the formation of neo-sex chromosomes. Fluorescence in situ hybridization with genic and repetitive probes revealed that in S. diclinis a reciprocal translocation has occurred between the ancestral Y chromosome and an autosome, resulting in chromosomes designated Y1 and Y2. Both Y1 and Y2 chromosomes are male specific. Y1 pairs with the X chromosome and with the autosome (the neo-X), which cosegregates with X. Y2 pairs only with the neo-X, forming a chain X-Y1-neo-X-Y2 in male meiosis. Despite very recent formation of the neo-sex chromosomes in S. diclinis, they are present in all surveyed individuals throughout the species range. Evolution of neo-sex chromosomes may be the cause of partial reproductive isolation of this species and could have been the isolating mechanism that drove speciation of S. diclinis.PAIRING of homologous chromosomes during meiosis, in the majority of diploid plants and animals, leads to the formation of bivalents at first metaphase and subsequently the correct segregation of the chromosomes. Chromosomal translocations that produce multivalents usually result in unbalanced segregation, which consequently affects fertility. However, chain or ring configurations appear to be stably inherited in some species. An extreme example is found in the plant genus Oenothera, where many species display a ring involving all 14 chromosomes (Cleland 1972). In animals these configurations may include sex chromosomes, resulting in the formation of multiple X and Y chromosomes. For example, the monotreme platypus possesses five X and five Y chromosomes that form a chain of alternating X and Y chromosomes in male meiosis (Bick and Sharman 1975; Gruetzner et al. 2006). Such chains are formed due to several interchromosomal translocation events, including sex chromosome–autosome translocations (Gruetzner et al. 2006). Since sex chromosomes are rare in plants, examples of plant sex-linked chromosome multiples have been reported on only a few occasions. A chain of four X and five Y has been identified in an East African mistletoe Viscum fischeri (Wiens and Barlow 1975) and a chain of two X and two Y has been found in Humulus lupulus ssp. cordifolius (Shephard et al. 2000). Trivalent formation comprising Y1 X Y2 has been observed both in H. japonicus (Shephard et al. 2000) and in a number of dioecious species in the genus Rumex (Cunado et al. 2007; Navajas-Perez et al. 2009). Here we report that the plant species Silene diclinis has multiple sex chromosomes that form a chain of four during meiosis metaphase I.S. diclinis is a member of a small group of dioecious species (having separate male and female plants) in section Elisanthe in the plant genus Silene (Caryophyllaceae). The other members of this group are S. latifolia, S. dioica, S. heuffelii, and S. marizii (Prentice 1978). The presence of large heteromorphic sex chromosomes in S. latifolia and S. dioica has been known for many years (Westergaard 1958). Due to the ease of cytogenetic identification of the sex chromosomes, the clear morphological difference between the sexes and the short generation time, S. latifolia was used in early genetic research concerning sex determination in plants. The male was shown to be the heterogametic sex (XY) with the larger Y chromosome having a decisive role in sex determination (Westergaard 1958). Since then, S. latifolia has become a species of choice for studies in plant genetics, ecology, and evolution (Bernasconi et al. 2009). It is particularly useful for studies of sex chromosome evolution because the sex chromosomes in Silene are of relatively recent origin compared to those of mammals (Charlesworth 2002; Ming and Moore 2007; Marais et al. 2008).Experimental crosses involving all five dioecious species in Silene section Elisanthe in various pairwise combinations have produced viable hybrids and, although some combinations were less successful than others, the formation of these hybrids suggests a close relationship within this group (Prentice 1978). This close relationship is also illustrated by DNA sequence comparisons that show that interspecific silent divergence between these species does not exceed 2%, which is comparable to intraspecific polymorphism in S. latifolia (Ironside and Filatov 2005). S. diclinis is a rare and restricted endemic, found only in Southern Valencia, Spain in an area smaller than 18 × 9 km (Prentice 1976; Montesinos et al. 2006). Of the other four Elisanthe species, only S. latifolia occurs in this region, and experimental crosses between these two species are the least successful (Prentice 1978). Hybrids between S. latifolia and S. dioica occur naturally in regions where their populations coincide (Baker 1948) but no natural hybrids of S. diclinis and S. latifolia have been reported.Cytogenetic analysis of S. diclinis has been limited. Examination of mitotic metaphase spreads in root tip squash preparations from adult male and female plants indicated that the male had one X and one Y chromosome. Both chromosomes were large but the difference between them was slight (van Nigtevecht and Prentice 1985). Regular pairing of chromosomes with 12 bivalents at metaphase I in pollen mother cells has been reported (Morisset and Bozman 1969). However, these observations were made without the benefit of a marker for the Y chromosome. Recently, sequences with homology to an Ogre retrotransposon have been isolated from S. latifolia and used as probes in fluorescence in situ hybridization (FISH) experiments on mitotic (Cermak et al. 2008) and both mitotic and meiotic (Filatov et al. 2009) chromosome spreads. The pattern of hybridization showed that these sequences are widespread over the X chromosome and all of the autosomes but are mainly confined to a small section at the pairing region of the Y chromosome in S. latifolia. Therefore, these probes “paint” all the chromosomes apart from the Y, providing a “negative paint” for the Y chromosome. By using one of these probes (clone 4.2) on meiotic spreads of S. dioica and S. marizii, we confirmed that these species have sex chromosomes similar to those of S. latifolia (Filatov et al. 2009). The X and Y formed a rod bivalent and the Y chromosome was larger than both the X and autosomes.In this article we report our FISH experiments with S. diclinis using the negative paint probe together with probes containing S. latifolia sex-linked gene sequences. We demonstrate that S. diclinis males have two Y chromosomes that differ in the distribution of the paint signal and these gene sequences. In meiotic metaphase I, one Y pairs with the X and an autosome while the second Y pairs with the other arm of this autosome, forming a chain of four chromosomes. We suggest that an autosome–Y reciprocal translocation was involved in the evolution of neo-sex chromosomes in this species.     

Searching for guidance cues: Follow the Sidestep trail

Recombination restriction between evolving sex chromosomes leads to the degeneration of the chromosome that is present only in the heterogametic sex (the Y chromosome in XY species). The evolutionary forces driving Y chromosome degeneration, however, are still under debate and include positive and negative selection models. In a recent study, we showed that the rate of accumulation of loss-of-function mutations on the neo-Y chromosome of Drosophila miranda is compatible with the process of Muller's ratchet, the stochastic loss of the best mutational class of individuals from a small asexual population. Purifying selection at amino acid sites can accelerate the ratchet, and the speed of degeneration depends on the number of genes still present on the evolving Y chromosome. Our study shows that Y chromosome degeneration does not require the action of selective sweeps at linked sites, and can take place under realistic parameters of purifying selection only.     

Genetic and functional analysis of DD44, a sex-linked gene from the dioecious plant Silene latifolia,provides clues to early events in sex chromosome evolution

Silene latifolia is a dioecious plant with heteromorphic sex chromosomes. The sex chromosomes of S. latifolia provide an opportunity to study the early events in sex chromosome evolution because of their relatively recent emergence. In this article, we present the genetic and physical mapping, expression analysis, and molecular evolutionary analysis of a sex-linked gene from S. latifolia, DD44 (Differential Display 44). DD44 is homologous to the oligomycin sensitivity-conferring protein, an essential component of the mitochondrial ATP synthase, and is ubiquitously expressed in both sexes. We have been able to genetically map DD44 to a region of the Y chromosome that is genetically linked to the carpel-suppressing locus. Although we have physically mapped DD44 to the distal end of the long arm of the X chromosome using fluorescence in situ hybridization (FISH), DD44 maps to the opposite arm of the Y chromosome as determined by our genetic map. These data suggest that chromosomal rearrangements have occurred on the Y chromosome, which may have contributed to the genetic isolation of the Y chromosome. We discuss the implications of these results with respect to the structural and functional evolution of the S. latifolia Y chromosome.     

Flower scent composition in night-flowering Silene species (Caryophyllaceae)

Floral scent of 13 night-flowering Silene species (Caryophyllaceae) was collected by headspace adsorption and analysed via gas chromatography and mass spectrometry. Benzenoids together with isoprenoids dominated the scent in all species. Among the benzenoids, benzaldehyde (Silene subconica 35.5%, Silene succulenta 23.1%, Silene sericea 15.6%, Silene vulgaris 12.2%, and Silene nutans 9.9%), methylbenzoate (Silene saxifraga 96.1%, S. succulenta 15.2%), benzyl acetate (Silene dichotoma 37.8%, S. nutans 30.1%, Silene italica 9.0%, and Silene latifolia 5.5%), or benzyl alcohol (Silene viscosa 36.1%) occur in the largest amounts. p-Cresol is only found in the floral scent of S. dichotoma (28.5%). Among the isoprenoids, monoterpenes occur in the largest amounts (myrcene 23% in Silene chlorantha, trans-β-ocimene 27.2% in S. nutans and 34.9% in S. sericea, fenchyl acetate 12.7% in S. chlorantha, β-linalool 40.5% in S. chlorantha and 14.5% in S. italica). Relatively high amounts of lilac compounds occur in S. latifolia (49.1%), Silene otites (35.7%), S. subconica (15.2%), and S. vulgaris (59.6%). Higher amounts of sesquiterpenes (isoprenoids) were only found in Silene vallesia with β-bourbonene and γ-muurolene.The vast majority of chemicals identified are common components of a wide array of scented angiosperm flowers. Nevertheless, the results conform most strongly with the findings in other night-blooming and/or moth-pollinated flowers. All investigated Silene species follow the general trend of floral scent compounds typical for moth-pollinated flowers, i.e. flowers having acyclic terpene alcohols (e.g. linalool), aromatic alcohols (benzyl alcohol, 2-phenylethanol) and esters derived from them, and small amounts of nitrogen-containing compounds.     

Disentangling the effects of mating systems and mutation rates on cytoplamic diversity in gynodioecious Silene nutans and dioecious Silene otites

Many flowering plant species exhibit a variety of distinct sexual morphs, the two most common cases being the co-occurrence of females and males (dioecy) or the co-occurrence of hermaphrodites and females (gynodioecy). In this study, we compared DNA sequence variability of the three genomes (nuclear, mitochondrial and chloroplastic) of a gynodioecious species, Silene nutans, with that of a closely related dioecious species, Silene otites. In the light of theoretical models, we expect cytoplasmic diversity to differ between the two species due to the selective dynamics that acts on cytoplasmic genomes in gynodioecious species: under an epidemic scenario, the gynodioecious species is expected to exhibit lower cytoplasmic diversity than the dioecious species, while the opposite is expected in the case of balancing selection maintaining sterility cytoplasms in the gynodioecious species. We found no difference between the species for nuclear gene diversity, but, for the cytoplasmic loci, the gynodioecious S. nutans had more haplotypes, and higher nucleotide diversity, than the dioecious relative, S. otites, even though the latter has a relatively high rate of mitochondrial synonymous substitutions, and therefore presumably a higher mutation rate. Therefore, as the mitochondrial mutation rate cannot account for the higher cytoplasmic diversity found in S. nutans, our findings support the hypothesis that gynodioecy in S. nutans has been maintained by balancing selection rather than by epidemic-like dynamics.     

An accumulation of tandem DNA repeats on the Y chromosome in Silene latifolia during early stages of sex chromosome evolution

Sex chromosomes in mammals are about 300 million years old and typically have a highly degenerated Y chromosome. The sex chromosomes in the dioecious plant Silene latifolia in contrast, represent an early stage of evolution in which functional X–Y gene pairs are still frequent. In this study, we characterize a novel tandem repeat called TRAYC, which has accumulated on the Y chromosome in S. latifolia. Its presence demonstrates that processes of satellite accumulation are at work even in this early stage of sex chromosome evolution. The presence of TRAYC in other species of the Elisanthe section suggests that this repeat had spread after the sex chromosomes evolved but before speciation within this section. TRAYC possesses a palindromic character and a strong potential to form secondary structures, which could play a role in satellite evolution. TRAYC accumulation is most prominent near the centromere of the Y chromosome. We propose a role for the centromere as a starting point for the cessation of recombination between the X and Y chromosomes.     

Sequence diversity patterns suggesting balancing selection in partially sex‐linked genes of the plant Silene latifolia are not generated by demographic history or gene flow

DNA sequence diversity in genes in the partially sex‐linked pseudoautosomal region (PAR) of the sex chromosomes of the plant Silene latifolia is higher than expected from within‐species diversity of other genes. This could be the footprint of sexually antagonistic (SA) alleles that are maintained by balancing selection in a PAR gene (or genes) and affect polymorphism in linked genome regions. SA selection is predicted to occur during sex chromosome evolution, but it is important to test whether the unexpectedly high sequence polymorphism could be explained without it, purely by the combined effects of partial linkage with the sex‐determining region and the population's demographic history, including possible introgression from Silene dioica. To test this, we applied approximate Bayesian computation‐based model choice to autosomal sequence diversity data, to find the most plausible scenario for the recent history of S. latifolia and then to estimate the posterior density of the most relevant parameters. We then used these densities to simulate variation to be expected at PAR genes. We conclude that an excess of variants at high frequencies at PAR genes should arise in S. latifolia populations only for genes with strong associations with fully sex‐linked genes, which requires closer linkage with the fully sex‐linked region than that estimated for the PAR genes where apparent deviations from neutrality were observed. These results support the need to invoke selection to explain the S. latifolia PAR gene diversity, and encourage further work to test the possibility of balancing selection due to sexual antagonism.     

Testing for the Footprint of Sexually Antagonistic Polymorphisms in the Pseudoautosomal Region of a Plant Sex Chromosome Pair

The existence of sexually antagonistic (SA) polymorphism is widely considered the most likely explanation for the evolution of suppressed recombination of sex chromosome pairs. This explanation is largely untested empirically, and no such polymorphisms have been identified, other than in fish, where no evidence directly implicates these genes in events causing loss of recombination. We tested for the presence of loci with SA polymorphism in the plant Silene latifolia, which is dioecious (with separate male and female individuals) and has a pair of highly heteromorphic sex chromosomes, with XY males. Suppressed recombination between much of the Y and X sex chromosomes evolved in several steps, and the results in Bergero et al. (2013) show that it is still ongoing in the recombining or pseudoautosomal, regions (PARs) of these chromosomes. We used molecular evolutionary approaches to test for the footprints of SA polymorphisms, based on sequence diversity levels in S. latifolia PAR genes identified by genetic mapping. Nucleotide diversity is high for at least four of six PAR genes identified, and our data suggest the existence of polymorphisms maintained by balancing selection in this genome region, since molecular evolutionary (HKA) tests exclude an elevated mutation rate, and other tests also suggest balancing selection. The presence of sexually antagonistic alleles at a locus or loci in the PAR is suggested by the very different X and Y chromosome allele frequencies for at least one PAR gene.     

Structure and evolution of <Emphasis Type="Italic">Apetala3</Emphasis>, a sex-linked gene in <Emphasis Type="Italic">Silene latifolia</Emphasis>

Background  

The evolution of sex chromosomes is often accompanied by gene or chromosome rearrangements. Recently, the gene AP3 was characterized in the dioecious plant species Silene latifolia. It was suggested that this gene had been transferred from an autosome to the Y chromosome.