Horizon 1 1 17 ACL : Articles dans des revues avec comité de lecture répertoriées par l'AERES Genome Research 524-533 AMERIQUE CENTRALE COSTA RICA 2015 fdi:010064149 ENG Genome Research 1088-9051 ISI:000352139200007 4 10.1101/gr.183905.114 https://www.documentation.ird.fr/hor/fdi:010064149 https://www.documentation.ird.fr/intranet/publi/2015/05/010064149.pdf 25 Horizon (IRD) 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 Y-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-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-h divergence supports the hypothesis that hermaphrodite papaya is a product of human domestication. We estimate that Y-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-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-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. 076 ; 020 UR232 Chine