Origin and domestication of papaya Y super(h) chromosome

• Published in: Genome research 2015-04, Vol.25 (4), p.524-533
• Main Authors: VanBuren, Robert, Zeng, Fanchang, Chen, Cuixia, Zhang, Jisen, Wai, Ching Man, Han, Jennifer, Aryal, Rishi, Gschwend, Andrea R, Wang, Jianping, Na, Jong-Kuk
• Format: Article
• Language: English
• ISSN: 1088-9051; 1549-5469
• DOI: 10.1101/gr.183905.114

Sex in papaya is controlled by a pair of nascent sex chromosomes. Females are XX, and two slightly different Y chromosomes distinguish males (XY) and hermaphrodites (XY super(h)). The hermaphrodite-specific region of the Y super(h) 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). We used a BAC-by-BAC approach to sequence the MSY and resequence the Y regions of 24 wild males and the Y super(h) regions of 12 cultivated hermaphrodites. The MSY and HSY regions have highly similar gene content and structure, and only 0.4% sequence divergence. 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 super(h) sequence is highly similar to one Y haplotype (MSY3) found only in wild dioecious populations from the north Pacific region of Costa Rica. The low MSY3-Y super(h) divergence supports the hypothesis that hermaphrodite papaya is a product of human domestication. We estimate that Y super(h) arose only similar to 4000 yr ago, well after crop plant domestication in Mesoamerica >6200 yr ago but coinciding with the rise of the Maya civilization. The Y super(h) chromosome has lower nucleotide diversity than the Y, or the genome regions that are not fully sex-linked, consistent with a domestication bottleneck. The identification of the ancestral MSY3 haplotype will expedite investigation of the mutation leading to the domestication of the hermaphrodite Y super(h) chromosome. In turn, this mutation should identify the gene that was affected by the carpel-suppressing mutation that was involved in the evolution of males.