Rapid divergence and expansion of the X chromosome in papaya

Andrea R. Gschwend, Qingyi Yu, Eric J. Tong, Fanchang Zeng, Jennifer Han, Robert VanBuren, Rishi Aryal, Deborah Charlesworth, Paul H. Moore, Andrew H. Paterson, Ray Ming

Research output: Contribution to journalArticlepeer-review


X chromosomes have long been thought to conserve the structure and gene content of the ancestral autosome from which the sex chromosomes evolved. We compared the recently evolved papaya sex chromosomes with a homologous autosome of a close relative, the monoecious Vasconcellea monoica, to infer changes since recombination stopped between the papaya sex chromosomes. We sequenced 12 V. monoica bacterial artificial chromosomes, 11 corresponding to the papaya X-specific region, and 1 to a papaya autosomal region. The combined V. monoica X-orthologous sequences are much shorter (1.10 Mb) than the corresponding papaya region (2.56 Mb). Given that the V. monoica genome is 41% larger than that of papaya, this finding suggests considerable expansion of the papaya X; expansion is supported by a higher repetitive sequence content of the X compared with the papaya autosomal sequence. The alignable regions include 27 transcriptencoding sequences, only 6 of which are functional X/V. monoica gene pairs. Sequence divergence from the V. monoica orthologs is almost identical for papaya X and Y alleles; the Carica-Vasconcellea split therefore occurred before the papaya sex chromosomes stopped recombining, making V. monoica a suitable outgroup for inferring changes in papaya sex chromosomes. The papaya X and the hermaphrodite-specific region of the Yh chromosome and V. monoica have all gained and lost genes, including a surprising amount of changes in the X.

Original languageEnglish (US)
Pages (from-to)13716-13721
Number of pages6
JournalProceedings of the National Academy of Sciences of the United States of America
Issue number34
StatePublished - Aug 21 2012


  • Carica papaya
  • Centromere of X chromosome
  • Gene gains and losses
  • Sex chromosome evolution
  • Suppression of recombination

ASJC Scopus subject areas

  • General


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