Origin and domestication of papaya Yh chromosome
- Robert VanBuren1,2,9,
- Fanchang Zeng2,9,
- Cuixia Chen2,9,
- Jisen Zhang1,9,
- Ching Man Wai2,
- Jennifer Han2,
- Rishi Aryal2,
- Andrea R. Gschwend2,
- Jianping Wang2,
- Jong-Kuk Na2,
- Lixian Huang1,
- Lingmao Zhang1,
- Wenjing Miao1,
- Jiqing Gou3,
- Jie Arro2,
- Romain Guyot4,
- Richard C. Moore5,
- Ming-Li Wang6,
- Francis Zee7,
- Deborah Charlesworth8,
- Paul H. Moore6,
- Qingyi Yu3 and
- Ray Ming1,2
- 1FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China;
- 2Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA;
- 3Texas A&M AgriLife Research, Department of Plant Pathology and Microbiology, Texas A&M University System, Dallas, Texas 75252, USA;
- 4IRD, UMR DIADE, EVODYN, BP 64501, 34394 Montpellier Cedex 5, France;
- 5Department of Botany, Miami University, Oxford, Ohio 45056, USA;
- 6Hawaii Agriculture Research Center, Kunia, Hawaii 96759, USA;
- 7USDA-ARS, Pacific Basin Agricultural Research Center, Hilo, Hawaii 96720, USA;
- 8Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3JT, United Kingdom
- Corresponding author: rming{at}life.uiuc.edu
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↵9 These authors contributed equally to this work.
Abstract
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.
Footnotes
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[Supplemental material is available for this article.]
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Article published online before print. Article, supplemental material, and publication date are at http://www.genome.org/cgi/doi/10.1101/gr.183905.114.
- Received September 14, 2014.
- Accepted February 9, 2015.
This article is distributed exclusively by Cold Spring Harbor Laboratory Press for the first six months after the full-issue publication date (see http://genome.cshlp.org/site/misc/terms.xhtml). After six months, it is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/.