The first complete T2T Assemblies of Cattle and Sheep Y-Chromosomes uncover remarkable divergence in structure and gene content

Abstract

Reference genomes of cattle and sheep have lacked contiguous assemblies of the sex-determining Y chromosome. We assembled complete and gapless telomere to telomere (T2T) Y chromosomes for these species. The pseudo-autosomal regions were similar in length, but the total chromosome size was substantially different, with the cattle Y more than twice the length of the sheep Y. The length disparity was accounted for by expanded ampliconic region in cattle. The genic amplification in cattle contrasts with pseudogenization in sheep suggesting opposite evolutionary mechanisms since their divergence 18MYA. The centromeres also differed dramatically despite the close relationship between these species at the overall genome sequence level. These Y chromosome have been added to the current reference assemblies in GenBank opening new opportunities for the study of evolution and variation while supporting efforts to improve sustainability in these important livestock species that generally use sire-driven genetic improvement strategies.

Figure 1.

Global structure of the cattle and sheep Y chromosomes The structure of the cattle and the sheep Y-chromosomes showing the differences and the similarities between the two species. (A) The self-identity dotplots highlight the mosaic of repetitive sequence on the q-arms while the tracks below it show the different sequence classes and the gene annotation. (B) The repeat content annotation indicates that more than half of both Y-chromosomes is repetitive DNA. (C) Centromere content and organization shows that the two Y-chromosomes have tandemly arrayed repeat unit at the centromere; while the cattle centromeric repeat is organized into a higher order repeat (HOR) of a 73bp monomer, the sheep repeat unit is a composite of a tandem LINE and SINE element with spacer DNA between the copies.

Figure 2:

Ampliconic genes content comparison between cattle and sheep (A) The copy distribution of the protein-coding and the pseudogene copies of the ampliconic genes families on the cattle and sheep Y-chromosomes show remarkable differences. (B) The gene density of the ampliconic genes across the Y-chromosomes calculated in 100kb bin sizes highlighting the loci of the protein-coding genes on the upper tracks and the pseudogenes on the lower tracks. There are no protein-coding copies of TSPY1 on the Sheep-Y on the lower panel a TSPY1 island (high blue clustered spike) is located on the cattle-Y harboring a tandem array of 44 copies out of the total 68 protein-coding copies on the chromosome. More pseudogenes are found on the Sheep-Y relative to the protein-coding genes suggesting that some of the ampliconic genes are being pseudogenized, losing their protein-coding capabilities.

Figure 3:

Content and organization of the Y-chromosome centromeres (A) The Cattle-Y centromere is organized as a tandem array of highly identical higher-order repeat (HOR) unit spanning 2.5Mb. The 3.7kb HOR contains copies of a 73bp monomeric unit arranged into four segments where segments 1 and 3 are tandem arrays of 5 copies (5-mer) and 6 copies (6-mer) respectively while segments 2 and 4 contain copies of the monomeric unit but not in tandem arrays as in segments 1 and 3. (B) The Sheep-Y centromere spanning about 118kb organized as an array of a 2.5kb composite repeat unit comprising a B0V-A2 SINE and a BovB LINE tranposable elements embedded between two segments of DNA.