Canis lupus familiaris isolate:Yoclon | breed:Yorkshire terrier Genome sequencing and assembly. Canis lupus familiaris isolate:Yoclon | breed:Yorkshire terrier

We provided a new assembly of canine Y chromosome that is absent from the previously published dog reference genome, but revealed no potential genomic variations that could explain the pathogenesis of DSD. However, an extensive stochastic anomaly of methylome was discovered in each of the XY DSD dogs. Persistent abnormal hypermethylation of the SRY gene was observed together with its down-regulated mRNA and protein expression. Failure of SRY expression due to hypermethylation was further correlated with silencing of a serial of testis determining genes, including SOX9, SF1, SOX8, AMH and DMRT1 in an early embryonic development stage at E34 in the XYDSD gonad, and high activation of the female specific genes, including FOXL1, RSPO1, CYP19A1, Wnt4, ERα and ERβ, after one postnatal year in the ovotestis. Our results demonstrate that incomplete demethylation on the SRY gene is the driving cause of XYDSD in these XY DSD dogs, indicating a central role of epigenetic regulation in sex determination.