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chromosome (HSY) and its X chromosome counterpart were sequenced and analyzed previously.

We now report the sequence of the entire male-specific region of the Y (MSY).

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Such genes would be candidates for the female suppressor involved in the early stages of sex chromosome evolution in this species. 2014), and the genes involved in their initial evolution cannot be identified, because many subsequent changes, including gene gains and losses, have occurred (Hughes et al. Here, we describe complete sequencing of the AU9 MSY.

The sex chromosomes in other organisms, such as mammals, are ancient (Veyrunes et al. Moreover, sequencing multiple individuals of both males and hermaphrodites is necessary, because the origin or origins of hermaphrodites are unknown, and the AU9 MSY might not be closely related to the ancestor of the HSY, as we indeed show to be the case.

The Y chromosome has lower nucleotide diversity than the Y, or the genome regions that are not fully sex-linked, consistent with a domestication bottleneck.

Moreover, sequences from multiple individuals are needed, because the HSY and MSY of any single varieties may include mutations in genes that are not responsible for the phenotypic difference in their gender; only fixed differences between the Y and Y are candidates for causing the functional difference (though variants in individual varieties can help exclude candidate genes because the female-suppressor is dominant, causing maleness or hermaphroditism in the heterozygous XY or XY, is ancestral in papaya and identify the origin of the derived MSY or HSY by resequencing male and hermaphrodite genomes sampled from wild and domesticated populations; (3) use the sequences from wild populations to estimate diversity and thus test the domestication hypothesis independently of the molecular dating based on MSY–HSY divergence; and (4) use the sequences from wild populations to discover genes with fixed differences between the sets of Y-specific sequences of males and hermaphrodites, where the differences may affect gene functions, to generate candidate genes for the Y-linked carpel suppressor.

The Y and Y diverged very recently is therefore important, because it suggests that the number of fixed differences between the two chromosomes may be small.

We used a BAC-by-BAC approach to sequence the MSY and resequence the Y regions of 24 wild males and the Y regions of 12 cultivated hermaphrodites.

The MSY and HSY regions have highly similar gene content and structure, and only 0.4% sequence divergence.

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There is no direct archaeological evidence for the center of origin of papaya, but the presence of natural populations in Mexico and Central America and the cultivation in Mexico and Belize predating the Spaniards suggest a Mesoamerican origin (Colunga-García Marín and Zizumbo-Villarreal 2004).