Comparative Organization and Gene Expression Profiles of the Porcine Pseudoautosomal Region

Abstract

The pseudoautosomal region (PAR) has important biological functions in spermatogenesis, male fertility and early development. Even though pig (Sus scrofa, SSC) is an agriculturally and biomedically important species, and its genome is sequenced, current knowledge about the porcine PAR is sparse. Here we defined the PAR in SSCXp/Yp by demarcating the sequence of the pseudoautosomal boundary at X:6,743,567 bp in intron 3-4 of SHROOM2 and showed that SHROOM2 is truncated in SSCY. Cytogenetic mapping of 20 BAC clones containing 15 PAR and X-specific genes revealed that the pig PAR is largely collinear with other mammalian PARs or Xp terminal regions. The results improved the current SSCX sequence assembly and facilitated distinction between the PAR and X-specific genes to study their expression in adult and embryonic tissues. A pilot analysis showed that the PAR genes are expressed at higher levels than X-specific genes during early development, whereas the expression of PAR genes was higher at day 60 compared to day 26, and higher in embryonic tissues compared to placenta. The findings advance the knowledge about the comparative organization of the PAR in mammals and suggest that the region might have important functions in early development in pigs.

The pig X and Y Chromosomes: structure, sequence, and evolution

“…The precise location of the PAR boundary was recently confirmed to be within the gene SHROOM2 (Das et al 2013). A 33-kb region containing a lincRNA with homology to the PAR (X-WTSI: 1,840,693-1,874,130) can be found on Xq 853,886,764), and most likely arose via duplication and transposition from the PAR onto Xq.…”

The Eutherian Pseudoautosomal Region

“…In the following decades, these observations were validated and further information regarding the structure/gene content was obtained in mice and men through studies of male meiosis [Oliver-Bonet et al, 2006;Kauppi et al, 2011], linkage analysis, gene mapping Perry et al, 2001], and sex chromosome sequencing [Skaletsky et al, 2003;Ross et al, 2005;Soh et al, 2014]. The presence of the PAR has also been acknowledged in all domestic animals and a few wild mammals [Van Laere et al, 2008;Raudsepp et al, 2012;Das et al, 2013] and is thought to be a common feature of eutherian sex chromosomes. The presently known exceptions are some species of arvicoline and gerbilline rodents, such as the Mediterranean pine vole and Mongolian gerbil that, like in marsupials, have asynaptic and achiasmatic sex chromosomes with no PAR [de la Fuente et al, 2012].…”

“…Moreover, the sequence data includes only 12 genes (UCSC) compared to 18 reported in the contig [Raudsepp and Chowdhary, 2008]. Notably, both the contig map and reference assembly do not show the SHOX gene -a biomedically important gene in the human PAR1 (see below) and a known PAR locus in pigs [Das et al, 2013] and carnivores [Li et al, 2013]. Currently, efforts are underway to reconstruct the equine PAR by long-read next-generation sequencing using the minimum BAC tiling path of the region (our unpublished data).…”

“…3 ). However, the region was properly demarcated and mapped only recently by using array comparative hybridization and FISH analysis of a pig X-chromosome BAC tilingpath microarray [Skinner et al, 2013], and by FISH mapping and sequence analysis of 20 BAC clones containing 12 porcine orthologs of eutherian PAR genes [Das et al, 2013]. Both studies show that the pig has a single PAR that has similar gene content and order as other eutherian PARs or Xp terminal regions ( fig.…”

“…2 ). The pig PAB is located in SHROOM2 [Das et al, 2013], and the size of the PAR is 6.5-6.9 Mb [Das et al, 2013;Skinner et al, 2013]. Since Xpter sequence assembly in the pig reference genome susScr3 (UCSC) has yet to be finalized, this estimate is approximate.…”