Supplementary Note 1 Papaya male flowers are derived from carpel abortion, but the female flower is a morphological anomaly1. According to Storey2, the female flower is “derived by the loss of all elements of the ancestral gynoecium expecting (sic) (excepting) the ventral carpellary bundle system, and replacement of the rest of the carpellary structure by a set of ancestral stamens which have become carpellodic in form by transmutation”.
1. Storey, W. B. Pistillate papaya flower: A morphological anomaly. Science 163, 401-405 (1969).
2. Storey, W. B. Theory of the derivations of the unisexual flowers of Caricaceae. Agronomia Tropical17, 273-321 (1967).
Supplementary Note 2
PSDM marker is developed by Urasaki et al.1 and Nafp by Parasnis et al2.
1. Urasaki,N. et al. A male and hermaphrodite specific RAPD marker for papaya (Carica papaya L.). Theor. Appl. Genet.104, 281-285 (2002).
2. Parasnis, A. S. Gupta, V. S. Tamhankar, S. A. Ranjekar, P. K. A highly reliable sex diagnostic PCR assay for mass screening of papaya seedlings. Mol. Breeding6, 337-344 (2000).
Supplementary Note 3
The extremely high rate of DNA polymorphism in the papaya MSY region appears to be a result of the divergence and degeneration of this region. A significant portion of the random markers (38%) on the physical map of MSY also detected repetitive sequences, a feature typical of Y chromosomes1. The decrease in gene density and increase in retroelement density revealed by random sequencing of the MSY are direct evidence for the degeneration of MSY in papaya. Roughly one third of the MSY is degenerated, reinforcing the notion that this is a primitive Y chromosome at the beginning stage of a degeneration process.
1. Skaletsky, H. et al. The male-specific region of the human Y chromosome is a mosaic of discrete sequence classes. Nature423, 825-837 (2003).