title: Origin and domestication of papaya Yh chromosome.
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 (XY(h)). The hermaphrodite-specific region of the Y(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(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 ∼ 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.
authors.affiliation: FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China; Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA;
authors.forename: Robert
authors.initials: R
authors.lastname: VanBuren
authors.affiliation: Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA;
authors.forename: Fanchang
authors.initials: F
authors.lastname: Zeng
authors.affiliation: Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA;
authors.forename: Cuixia
authors.initials: C
authors.lastname: Chen
authors.affiliation: FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China;
authors.forename: Jisen
authors.initials: J
authors.lastname: Zhang
authors.affiliation: Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA;
authors.forename: Ching Man
authors.initials: CM
authors.lastname: Wai
authors.affiliation: Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA;
authors.forename: Jennifer
authors.initials: J
authors.lastname: Han
authors.affiliation: Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA;
authors.forename: Rishi
authors.initials: R
authors.lastname: Aryal
authors.affiliation: Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA;
authors.forename: Andrea R
authors.initials: AR
authors.lastname: Gschwend
authors.affiliation: Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA;
authors.forename: Jianping
authors.initials: J
authors.lastname: Wang
authors.affiliation: Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA;
authors.forename: Jong-Kuk
authors.initials: JK
authors.lastname: Na
authors.affiliation: FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China;
authors.forename: Lixian
authors.initials: L
authors.lastname: Huang
authors.affiliation: FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China;
authors.forename: Lingmao
authors.initials: L
authors.lastname: Zhang
authors.affiliation: FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China;
authors.forename: Wenjing
authors.initials: W
authors.lastname: Miao
authors.affiliation: Texas A&M AgriLife Research, Department of Plant Pathology and Microbiology, Texas A&M University System, Dallas, Texas 75252, USA;
authors.forename: Jiqing
authors.initials: J
authors.lastname: Gou
authors.affiliation: Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA;
authors.forename: Jie
authors.initials: J
authors.lastname: Arro
authors.affiliation: IRD, UMR DIADE, EVODYN, BP 64501, 34394 Montpellier Cedex 5, France;
authors.forename: Romain
authors.initials: R
authors.lastname: Guyot
authors.affiliation: Department of Botany, Miami University, Oxford, Ohio 45056, USA;
authors.forename: Richard C
authors.initials: RC
authors.lastname: Moore
authors.affiliation: Hawaii Agriculture Research Center, Kunia, Hawaii 96759, USA;
authors.forename: Ming-Li
authors.initials: ML
authors.lastname: Wang
authors.affiliation: USDA-ARS, Pacific Basin Agricultural Research Center, Hilo, Hawaii 96720, USA;
authors.forename: Francis
authors.initials: F
authors.lastname: Zee
authors.affiliation: Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3JT, United Kingdom.
authors.forename: Deborah
authors.initials: D
authors.lastname: Charlesworth
authors.affiliation: Hawaii Agriculture Research Center, Kunia, Hawaii 96759, USA;
authors.forename: Paul H
authors.initials: PH
authors.lastname: Moore
authors.affiliation: Texas A&M AgriLife Research, Department of Plant Pathology and Microbiology, Texas A&M University System, Dallas, Texas 75252, USA;
authors.forename: Qingyi
authors.initials: Q
authors.lastname: Yu
authors.affiliation: FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China; Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA;
authors.forename: Ray
authors.initials: R
authors.lastname: Ming
mesh_terms: D001483:Base Sequence; D029441:Carica / Q000235:genetics*; D032461:Chromosomes, Plant / Q000235:genetics*; D051456:Gene Flow / Q000235:genetics; D006239:Haplotypes / Q000235:genetics; D057850:Hermaphroditic Organisms / Q000235:genetics; D008969:Molecular Sequence Data; D000069600:Plant Breeding; D020641:Polymorphism, Single Nucleotide; D017422:Sequence Analysis, DNA; D012723:Sex; D012730:Sex Chromosomes / Q000235:genetics*; D019849:Sex Determination Processes / Q000235:genetics*