RT Journal
A1 VanBuren, Robert
A1 Zeng, Fanchang
A1 Chen, Cuixia
A1 Zhang, Jisen
A1 Wai, Ching Man
A1 Han, Jennifer
A1 Aryal, Rishi
A1 Gschwend, Andrea R.
A1 Wang, Jianping
A1 Na, Jong-Kuk
A1 Huang, Lixian
A1 Zhang, Lingmao
A1 Miao, Wenjing
A1 Gou, Jiqing
A1 Arro, Jie
A1 Guyot, Romain
A1 Moore, Richard C.
A1 Wang, Ming-Li
A1 Zee, Francis
A1 Charlesworth, Deborah
A1 Moore, Paul H.
A1 Yu, Qingyi
A1 Ming, Ray
T1 Origin and domestication of papaya Yh chromosome
JF Genome Research 
JO Genome Research 
YR 2015 
FD April 01 
VO 25 
IS 4 
SP 524 
OP 533 
DO 10.1101/gr.183905.114 
UL http://genome.cshlp.org/content/25/4/524.abstract 
AB 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 (XYh). The hermaphrodite-specific region of the Yh 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 Yh 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 Yh 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-Yh divergence supports the hypothesis that hermaphrodite papaya is a product of human domestication. We estimate that Yh arose only ∼4000 yr ago, well after crop plant domestication in Mesoamerica >6200 yr ago but coinciding with the rise of the Maya civilization. The Yh 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 Yh 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.