Heteromorphic sex chromosomes (XY/ZW) can often be distinguished from autosomes by the absence of recombination in at least a part of their length and Y/W chromosome degeneration [1, 2]. Plants with sex chromosomes have evolved rarely but repeatedly in many plant lineages, and sex chromosomes have reached various levels of differentiation . In Asparagus officinalis and Carica papaya for example, X and Y chromosomes have diverged little and recombine along most of their length [4–6] whereas in Rumex acetosa and Silene latifolia, the sex chromosomes in males are largely non-recombining [7, 8]. In S. latifolia, X and Y chromosomes can recombine only in the regions known as pseudoautosomal regions (PARs). Westergaard  originally identified one PAR on each of the q-arms of Silene latifolia sex chromosomes. Later, Lengerova et al. (2003)  using fluorescent in situ hybridization (FISH) revealed that the X PAR is located on the p-arm, whereas the PAR on the Y chromosome is located on the q-arm. More recently, Scotti and Delph  proposed that PARs exist on both ends of the X and Y chromosomes, similar to the situation in humans . A further similarity to mammalian sex chromosomes is that the S. latifolia sex chromosomes diverged gradually , which led to the formation of evolutionary strata. Comparisons between the evolutionarily young S. latifolia sex chromosomes (about 10 million years [12, 13]) and those of eutherian mammals (about 110 million years ) have revealed that similar processes are involved in the evolution of sex chromosomes in both animals and plants.
The sex chromosomes of S. latifolia most likely evolved from a single pair of autosomes as previously shown [12, 13], with one autosome of the gynodioecious relative S. vulgaris, a species lacking sex chromosomes, carrying homologues of S. latifolia sex-linked genes [12, 13]. Silene latifolia and S. vulgaris have the same haploid chromosome number (n = 12), but differ substantially in genome size. The Silene latifolia haploid genome is 2646 Mbp in females , with the X chromosome being about 400 Mbp in length , whereas the haploid genome size of S. vulgaris is 1103Mbp  and autosomes are about 100 Mbp long.
In this study we analyzed a part of the S. latifolia PAR located on the p-arm of the X chromosome and on the q-arm of the Y chromosome (henceforth referred to as PAR) and of the corresponding S. vulgaris autosome, in order to study collinearity and divergence between these chromosome parts and to assess whether the S. latifolia PAR has characteristics in common with animal PARs. Furthermore, we investigate whether the S. latifolia size increase relative to S. vulgaris reflects the increase in size of the entire X chromosome or more closely resembles the increase seen in S. latifolia autosomes.
In mammalian genomes, PARs have several interesting properties including increased GC content, higher mutation rates and a level of recombination higher than in the rest of the genome [18, 19] due to the necessity for crossing over in this region . PARs in mice and the human PAR1 appear to serve a critical function in spermatogenesis, as indicated by the fact that their absence prevents X and Y chromosome segregation during male meiosis, causing male sterility [21–23]. However, PARs differ widely in size among mammals (covering about 4 % of the Y chromosome in humans [24, 25] and mice , about 8 % in cattle  and about 24 % in dogs [28, 29]), with most eutherians sharing the same genes situated closest to the telomere but having the pseudoautosomal boundary (PAB), separating the PAR from the sex-specific part of the sex chromosomes, at variable positions . In mice, the PAB is located in the gene Fxy. Exons 1–3 are located in the X specific part, while exons 4–10 are located in the PAR . The segment of this gene located in the PAR has a higher GC content than its X-specific portion [30, 31].
In order to analyze the S. latifolia PAR and the corresponding region on the S. vulgaris autosome, we first established and screened a bacterial artificial chromosome (BAC) library of S. latifolia with the marker ScOPA09 that has previously been found to be located in the PAR of the closely related dioecious species S. dioica and has successfully been identified and used for mapping S. latifolia sex chromosomes . The marker ScOPA09 is located in the S. latifolia PAR which is known to recombine once per generation in males  and makes up about 10 % of the Y chromosome [34, 35]. In S. vulgaris, the marker OPA is lacking. We therefore first sequenced a clone of the S. latifolia BAC library containing the marker ScOPA09. Sequencing was performed by Sanger and 454 pyrosequencing to explore the suitability of different sequencing strategies for BAC assembly. From these sequences we identified new markers and used them to screen the S. vulgaris BAC library for a homologous clone. Both BAC sequences were assembled into >100,000 bp-long scaffolds using GS De Novo Assembler (Roche).
Here we present the results of a genomic comparison between an area located in the PAR of the X chromosome p-arm and in the q-arm of the Y chromosome of the dioecious plant species S. latifolia and its homologous autosomal area in the closely related gynodioecious species S. vulgaris. Our results identify the first physically mapped genes located in the Silene PAR and reveal characteristics of a plant pseudoautosomal region.