A physical map of the papaya MSY was constructed from the AU9 male BAC library, using probes from BACs in the HSY physical map (Gschwend et al. Candidate BACs were confirmed by a combination of PCR and BAC end sequencing, and gaps in the physical map were filled using chromosome walking (see Methods).
The MSY physical map consists of a minimum tiling path of 99 BACs (Supplemental Fig.
The identification of the ancestral MSY3 haplotype will expedite investigation of the mutation leading to the domestication of the hermaphrodite Y Gender in papaya is genetically controlled by a sex-linked region that behaves like an XY sex chromosome, and maleness versus hermaphroditism is controlled by slightly different sex-specific Y chromosome regions, Y (HSY) in hermaphrodites and Y (MSY) in males. The corresponding region of the X is only 3.5 Mb, and both the Y and Y) is inviable, and the embryos abort 25–50 d after pollination, suggesting that the Y chromosome types are similar and that both are missing an essential gene that is functional in the X.
In contrast, the corresponding X region has a total repetitive element content of 67.2%, lower than either Y chromosome though higher than the papaya genome-wide average of 51.9% (Ming et al. 2) and males from 24 dioecious wild papaya accessions collected from 10 populations across Costa Rica for whole-genome resequencing (Supplemental Table 5).
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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