BackgroundThe papaya Y-linked region showed clear population structure, resulting in the detection of the ancestral male population that domesticated hermaphrodite papayas were selected from. The same populations were used to study nucleotide diversity and population structure in X-linked region. ResultsDiversity is very low for all genes in the X-linked region in wild dioecious population, with nucleotide diversity πsyn = 0.00017, tenfold lower than the autosomal πsyn = 0.0017 and twelvefold lower than the Y-linked region πsyn = 0.0021. Analysis of the X-linked sequences shows an undivided population, suggesting a geographically wide diversity-reducing event, whereas two sub populations were observed in the autosomes separating gynodioecy and dioecy and three sub populations in the Y-linked region separating three male populations. The extremely low diversity in papaya X-linked region was probably caused by a recent, strong selective sweep before domestication, involving either the spread of a recessive mutation in an X-linked gene that is beneficial to males, or a partially dominant mutation that benefitted females or both sexes. Nucleotide diversity in the domesticated X samples is about half that in the wild Xs, probably due to the bottleneck when hermaphrodites were selected during domestication. ConclusionsThe extreme low nucleotide diversity in papaya X-linked region is much greater than observed in humans, great apes, and the neo-X chromosome of Drosophila miranda, which show the expected pattern of Y-linked genes < X-linked genes < autosomal genes), whereas papaya shows an unprecedented pattern of X-linked genes < autosomal genes < Y-linked genes.