A Large Expansion of the HSFY Gene Family in Cattle Shows Dispersion across Yq and Testis-Specific Expression

Hamilton, Christine K.; Révay, Tamás; Domander, Robin; Favetta, Laura A.; King, W. A.

doi:10.1371/journal.pone.0017790

Cited by 27 publications

(36 citation statements)

References 42 publications

(66 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Further work will be required to determine whether the repetitive long arm of SSCY contains ampliconic genes, as found in the male-specific regions of Y chromosomes of other species (e.g. [13,14,20,21]).…”

Section: Resultsmentioning

confidence: 99%

Regions of XY homology in the pig X chromosome and the boundary of the pseudoautosomal region

et al. 2013

View full text Add to dashboard Cite

BackgroundSex chromosomes are subject to evolutionary pressures distinct from the remainder of the genome, shaping their structure and sequence content. We are interested in the sex chromosomes of domestic pigs (Sus scrofa), how their structure and gene content compares and contrasts with other mammalian species, and the role of sex-linked genes in fertility. This requires an understanding of the XY-homologous sequence on these chromosomes.To this end, we performed microarray-based comparative genomic hybridisation (array-CGH) with male and female Duroc genomic DNA on a pig X-chromosome BAC tiling-path microarray. Putative XY-homologous BACs from regions of interest were subsequently FISH mapped.ResultsWe show that the porcine PAR is approximately 6.5-6.9 Mb at the beginning of the short arm of the X, with gene content reflective of the artiodactyl common ancestor. Our array-CGH data also shows an XY-homologous region close to the end of the X long arm, spanning three X BACs. These BACs were FISH mapped, and paint the entire long arm of SSCY. Further clones of interest revealed X-autosomal homology or regions containing repetitive content.ConclusionsThis study has identified regions of XY homology in the pig genome, and defined the boundary of the PAR on the X chromosome. This adds to our understanding of the evolution of the sex chromosomes in different mammalian lineages, and will prove valuable for future comparative genomic work in suids and for the construction and annotation of the genome sequence for the sex chromosomes. Our finding that the SSCYq repetitive content has corresponding sequence on the X chromosome gives further insight into structure of SSCY, and suggests further functionally important sequences remain to be discovered on the X and Y.

show abstract

Section: Resultsmentioning

confidence: 99%

Regions of XY homology in the pig X chromosome and the boundary of the pseudoautosomal region

et al. 2013

View full text Add to dashboard Cite

show abstract

“…4) (Murphy et al 2006). With few exceptions, we observed widespread signatures of positive selection among lineage-specific ampliconic gene families in carnivores (e.g., FLJ36031Y), mouse (e.g., Ssty and Sly), cattle (HSFY) (Hamilton et al 2011), and primates (DAZ ). By contrast, evidence of positive selection was virtually absent in the analyses of single-copy, ubiquitously expressed X degenerate genes (Table 2; Supplemental Fig.…”

Section: Wwwgenomeorgmentioning

confidence: 87%

Comparative analysis of mammalian Y chromosomes illuminates ancestral structure and lineage-specific evolution

et al. 2013

View full text Add to dashboard Cite

Although more than thirty mammalian genomes have been sequenced to draft quality, very few of these include the Y chromosome. This has limited our understanding of the evolutionary dynamics of gene persistence and loss, our ability to identify conserved regulatory elements, as well our knowledge of the extent to which different types of selection act to maintain genes within this unique genomic environment. Here, we present the first MSY (male-specific region of the Y chromosome) sequences from two carnivores, the domestic dog and cat. By combining these with other available MSY data, our multiordinal comparison allows for the first accounting of levels of selection constraining the evolution of eutherian Y chromosomes. Despite gene gain and loss across the phylogeny, we show the eutherian ancestor retained a core set of 17 MSY genes, most being constrained by negative selection for nearly 100 million years. The X-degenerate and ampliconic gene classes are partitioned into distinct chromosomal domains in most mammals, but were radically restructured on the human lineage. We identified multiple conserved noncoding elements that potentially regulate eutherian MSY genes. The acquisition of novel ampliconic gene families was accompanied by signatures of positive selection and has differentially impacted the degeneration and expansion of MSY gene repertoires in different species.[Supplemental material is available for this article.]Y chromosomes have arisen independently in divergent evolutionary lineages across the eukaryotic tree of life

show abstract

“…As with HSFX/HSFY comparisons in other species (e.g. Hamilton et al, 2011), there is little sequence identity between the X and Y copies. Indeed, the only alignable region is the DNA binding domain.…”

Section: Discussionmentioning

confidence: 88%

“…Mammalian HSFY seems present in low but variable copy number across many species, with between two and eight copies in cats (Pearks Wilkerson et al 2008; Murphy et al 2006), at least one retroposed active copy in mice (Kinoshita et al 2006) and the two active copies in humans (Tessari et al 2004) plus several pseudogene copies, one of which is found on chromosome 22. In cattle, the gene family has amplified to at least 70 copies (Hamilton et al 2011; Yue et al 2014). Recent work suggests that the amplification in cattle occurred after their divergence with sheep, and so is likely an independent amplification to that in pigs (Chang et al 2013).…”

Section: Introductionmentioning

confidence: 99%

Expansion of theHSFYgene family in pig lineages

Skinner

Lachani

Sargent

et al. 2014

Preprint

View full text Add to dashboard Cite

Amplified gene families on sex chromosomes can harbour genes with important biological functions, especially relating to fertility. The HSFY family has amplified on the Y chromosome of the domestic pig (Sus scrofa), in an apparently independent event to an HSFY expansion on the Y chromosome of cattle (Bos taurus). Although the biological functions of HSFY genes are poorly understood, they appear to be involved in gametogenesis in a number of mammalian species, and, in cattle, HSFY gene copy number correlates with levels of fertility.We have investigated the HSFY family in domestic pigs, and other suid species including warthogs, bushpigs, babirusas and peccaries. The domestic pig contains at least two amplified variants of HSFY, distinguished predominantly by presence or absence of a SINE within the intron. Both these variants are expressed in testis, and both are present in approximately 50 copies each in a single cluster on the short arm of the Y. The longer form has multiple nonsense mutations rendering it likely non-functional, but many of the shorter forms still have coding potential. Other suid species also have these two variants of HSFY, and estimates of copy number suggest the HSFY family may have amplified independently twice during suid evolution.Given the association of HSFY gene copy number with fertility in cattle, HSFY is likely to play an

show abstract

A Large Expansion of the HSFY Gene Family in Cattle Shows Dispersion across Yq and Testis-Specific Expression

Cited by 27 publications

References 42 publications

Regions of XY homology in the pig X chromosome and the boundary of the pseudoautosomal region

Regions of XY homology in the pig X chromosome and the boundary of the pseudoautosomal region

Comparative analysis of mammalian Y chromosomes illuminates ancestral structure and lineage-specific evolution

Expansion of theHSFYgene family in pig lineages

Contact Info

Product

Resources

About