TY  - JOUR
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
Y1  - 2015/04/01 
JF  - Genome Research 
JO  - Genome Research 
SP  - 524 
EP  - 533 
DO  - 10.1101/gr.183905.114 
VL  - 25 
IS  - 4 
UR  - http://genome.cshlp.org/content/25/4/524.abstract 
N2  - 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. 
ER  -