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The MSY sequences from wild males include three distinct haplotypes, associated with the populations’ geographic locations, but gene flow is detected for other genomic regions.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.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.

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Finally the MSY and HSY share a “collinear region,” adjacent to border B of inversion 2, which includes 18 genes, all with X and MSY (and HSY) copies, and two pseudogenes.

Repetitive sequences make up ∼79.2% of the MSY pseudomolecule, similar to the HSY, which has 79.3% repetitive element content. chromosome and the differences found between all such chromosomes and the Y of males.

AU9 was collected from a papaya breeding program at Griffith University in Queensland, Australia, which was traced back to a papaya breeding program in Israel with plants of unknown origin.

Because of the pericentric location and high repeat content of the Y-linked region, we sequenced the papaya MSY using a reiterative BAC-by-BAC approach.

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.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).The MSY and HSY sequences are collinear, except for an 8398-bp insertion in the MSY corresponding to a newly integrated Ty3-gypsy retrotransposon; this transposon insertion is the cause of the earlier overestimation of the 1.4% sequence divergence between MSY and HSY, which was based on only one pair of homologous BACs (Yu et al. There may be other small-scale differences between the HSY and MSY because of small sequence gaps in both assemblies.Most BACs are complete, but some highly repetitive BACs (-like retrotransposon insertion in the first intron of the HSY allele, resulting in a transcript with a partial sequence of the second intron (Ueno et al. Ninety-four transcription units were annotated on both Y chromosomes.The previously sequenced HSY and X revealed two major inversions, one of which (inversion 1) was inferred to have caused the initial recombination suppression between the X and Y chromosomes (Ming et al. In both the MSY and the HSY, inversion 1 includes 30 of the 66 intact Y-linked genes, including all 16 that have no X-linked counterparts, as well as 21 pseudogene sequences (Supplemental Table 1).

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