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New Insights Into Mammalian Sex Chromosome Structure and Evolution Using High-Quality Sequences From Bovine X and Y Chromosomes

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New Insights Into Mammalian Sex Chromosome Structure and Evolution Using High-Quality Sequences From Bovine X and Y Chromosomes

Ruijie Liu et al. BMC Genomics.

Abstract

Background: Mammalian X chromosomes are mainly euchromatic with a similar size and structure among species whereas Y chromosomes are smaller, have undergone substantial evolutionary changes and accumulated male specific genes and genes involved in sex determination. The pseudoautosomal region (PAR) is conserved on the X and Y and pair during meiosis. The structure, evolution and function of mammalian sex chromosomes, particularly the Y chromsome, is still poorly understood because few species have high quality sex chromosome assemblies.

Results: Here we report the first bovine sex chromosome assemblies that include the complete PAR spanning 6.84 Mb and three Y chromosome X-degenerate (X-d) regions. The PAR comprises 31 genes, including genes that are missing from the X chromosome in current cattle, sheep and goat reference genomes. Twenty-nine PAR genes are single-copy genes and two are multi-copy gene families, OBP, which has 3 copies and BDA20, which has 4 copies. The Y chromosome X-d1, 2a and 2b regions contain 11, 2 and 2 gametologs, respectively.

Conclusions: The ruminant PAR comprises 31 genes and is similar to the PAR of pig and dog but extends further than those of human and horse. Differences in the pseudoautosomal boundaries are consistent with evolutionary divergence times. A bovidae-specific expansion of members of the lipocalin gene family in the PAR reported here, may affect immune-modulation and anti-inflammatory responses in ruminants. Comparison of the X-d regions of Y chromosomes across species revealed that five of the X-Y gametologs, which are known to be global regulators of gene activity and candidate sexual dimorphism genes, are conserved.

Keywords: Bovine; Genomes; Livestock; Pseudoautosomal region; Sex chromosomes.

Conflict of interest statement

The authors declare that they have no competing interests.

Figures

Fig. 1
Fig. 1
Comparison of the Brahman X and Angus Y cattle chromosome pseudoautosomal regions (PARs) and adjacent sequence. The x-axis is Angus Y chromosome and y-axis is Brahman X chromosome. The cattle PAR is located between PLCXD1 and GPR143, 3286 bp distal to GPR143. The X and Y chromosome PAR genes (dark blue) share the same gene content and gene order. Gene families OBP and BDA20 are highlighted in yellow and orange. The X chromosome PAR is assembled in one contig while the Y chromosome PAR has two contig gaps. SHROOM2 is located distal to the pseudoautosomal boundary (PAB) on the X chromosome, which is found inverted on the Y chromosome X-d1 region
Fig. 2
Fig. 2
A gene map of X-Y homologous genes outside the cattle PAR. X-degenerate (X-d1, Xd2a and X-d2b) and ampliconic regions are indicated. 14 X-Y paired genes and 6 multi-copy genes are shown. Of 11 genes located in X-d1 (light blue), all but RPL23AY have homologous on the chromosome 19. Gene orientations are not consistent for X-Y paired genes. Multi-copy genes (yellow) and bovine-specific Y genes (asterisk) are indicated
Fig. 3
Fig. 3
Comparison of the X chromosome PAR genes in cattle and other mammals. PAR genes (dark blue) and X specific genes (light blue) are indicated for each species. Red dashed lines represent genes with different order relative to the Brahman cattle. The pseudoautosomal boundary gene is the same in all ruminants except goat which has an inversion. Copy number of OBP and BDA20 varies among species. The copy number of OBP and BDA20 are listed in Additional file 1: Table S4. BDA20 is ruminant specific whereas OBP is found in all mammals except human. Assemblies for pig, Hereford cattle, sheep and goat show a truncated PAR. The numbers above each species name represent the approximate PAR size
Fig. 4
Fig. 4
Comparison of Y chromosome X-degenerate regions in cattle and other mammals. The human Y chromosome is different from other mammals with 7 X-d regions and one unique X-transposed region (pink). Eight X-d1 genes are shared among cattle, pig and horse but the gene order and orientation are not the same. The cattle X-d2 is split into and X-d2a X-d2b regions with 2 and 3 genes respectively. The cattle Y chromosome diagram does not include the unknown heterochromatic regions

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