The papaya genome project: Fruitful insights, a decade later

Papaya, a fruit crop cultivated in tropical and sub-tropical regions, is known for its nutritional benefits and medicinal applications. The draft genome sequence of ‘SunUp’ papaya was the first commercial transgenic fruit tree to be sequenced. A lack of recent genome duplication may account for the smaller papaya gene number in most functional groups. Transgenesis at three locations is associated with organelle genomic insertions into the nuclear genome. Sex in papaya is controlled by a pair of nascent sex chromosomes with two slightly different Y chromosomes that distinguish males (XY) and hermaphrodites (XY^h). The hermaphrodite specific region of the Y^h chromosome (HSY), its X chromosome counterpart, and the male specific region of the Y (MSY) were sequenced using a BAC by BAC approach. We re-sequenced 24 wild male and 12 cultivated hermaphrodite genomes to characterize the forces shaping Y chromosome evolution, the MSY and HSY shared gene content, and 99.6% sequence identity. The male Y chromosomes formed three distinct populations despite otherwise normal gene flow in the autosomes. Molecular dating, phylogenetic analysis, and population genomic analyses all suggest that the hermaphrodite Y^h chromosome is a product of human domestication about 4000 years ago from a wild dioecious population MSY3 in the northwest pacific region of Costa Rica, coinciding with the rise of the Mayan civilization. The identification of the ancestral MSY3 haplotype will expedite investigation of the mutations leading to the domestication of hermaphrodite Y^h chromosome.