Recent Origin and Divergence of the Two Y Chromosomes in Papaya

Sex determination in papaya is controlled by a pair of primitive sex chromosomes differentiated by an 8.1 Mbp, recombinationally suppressed, hermaphrodite-specific or male-specific region on the Y or Y^h chromosome (MSY or HSY respectively) and its 3.5 Mb X counterpart. Papaya is trioecious with populations consisting of either male (XY) and female (XX) individuals or hermaphrodites (XY^h) and females (XX).  Using a whole genome re-sequencing and BAC by BAC sequencing approach, we characterize the sex chromosomes of ‘AU9’, a wild dioecious variety and compare them to those of ‘SunUp’, a gynodioecious commercial cultivar. The X and Y chromosomes have tenfold less polymorphisms than the autosomal regions, suggesting a possible selective sweep during domestication and selection for hermaphroditism. Gene content and expression is highly conserved between the Y and Y^h chromosomes despite sexual dimorphism between males and hermaphrodites. Ka/Ks ratios of genes on the X chromosomes and the HSY/MSY  are considerably lower than the genome wide average, suggesting the sex chromosome are subjected to strong purifying selection.The low divergence and evidence of a selective sweep between the Y and Y^h chromosomes suggest that hermaphroditism might be a result of domestication in papaya.