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

Abstract

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.

Figure 1.

Schematic representation of the MSY chromosome gene content of six mammals. Different gene/sequence classes are displayed in different colors (roughly following Skaletsky et al. 2003; Hughes et al. 2005, , for clarity). Mouse physical mapping data are from Mazeyrat et al. (1998). Each sequence schematic is drawn to a different scale to emphasize differences in single-copy X-degenerate gene compaction.

Figure 2.

Fluorescent in situ hybridization and qPCR of dog NOR, PAR, and ampliconic genes. (A) Dog has six autosomal NORs (CFA7, 17, 20; arrows), and one on Y. A total of seven NORs are observed in males and six in females (not shown). (Red) NOR probe. (Green) PAR probe (represented by BAC clone RPCI-183L18). (B) NOR probe (green on Yp+Ycen) and PAR probe (red on Yq) are at opposite ends of the dog Y. (C) Zoomed dog Y showing the location of NOR and the PAR in relation to the centromere. Dog Y is sub-metacentric. (D) KAL1 and TBL1 containing BAC clones hybridize to distal Xp and Yq. (E) TSPY and CUL4BY cDNA probes localize to Ycen-proximal Yq. (F) Quantitative PCR results for SRY and TSPY/TSPYL in three male domestic dogs.

Figure 3.

MSY chromosome rearrangements. Estimate of chromosome rearrangement and gain/loss events within the MSY of six mammalian Y chromosomes. Fifteen of 17 MSY chromosome genes present on the ancestral eutherian MSY are indicated by numbered arrows, with the name and location of the X chromosome gametologs displayed on the right. TSPY and RPS4Y are both dispersed multicopy gene families in multiple species and cannot be confidently assigned to a single position in the terminal taxa, nor in the ancestor. Arrows indicate the gene orientation within each chromosome. Rectangles on each branch represent the minimum number of rearrangements. Inferred gene losses are shown at the right side of each branch, while inferred gene gains are shown on the left side of each branch. Mouse physical mapping data are from Mazeyrat et al. (1998).

Figure 4.

Sequence conservation across five mammalian Y chromosomes. The cat Y chromosome sequence is shown as the reference. Five-way (human, chimpanzee, rhesus, dog, and cat) sequence conservation is calculated and shown by blue columns (bottom panel). The conservation between cat X and Y chromosome sequences is shown by red/green columns (top panel). Gene boundaries are shown below each panel with blue brackets, with arrows defining orientation. Vertical red bars at the bottom of each panel indicate known gene exons. Green triangles along the bottom indicate the locations of conserved elements with potential secondary structure based on significant RNAz scores. Black lines at the bottom indicate the coding region span of each gene (dashed lines indicate conserved coding sequences identified in other mammals but not cat).