title: Extremely low nucleotide diversity in the X-linked region of papaya caused by a strong selective sweep.
abstract: The papaya Y-linked region showed clear population structure, resulting in the detection of the ancestral male population that domesticated hermaphrodite papayas were selected from. The same populations were used to study nucleotide diversity and population structure in the X-linked region.
  
  
  
  Diversity is very low for all genes in the X-linked region in the wild dioecious population, with nucleotide diversity πsyn= 0.00017, tenfold lower than the autosomal region (πsyn= 0.0017) and 12-fold lower than the Y-linked region (πsyn= 0.0021). Analysis of the X-linked sequences shows an undivided population, suggesting a geographically wide diversity-reducing event, whereas two subpopulations were observed in the autosomes separating gynodioecy and dioecy and three subpopulations in the Y-linked region separating three male populations. The extremely low diversity in the papaya X-linked region was probably caused by a recent, strong selective sweep before domestication, involving either the spread of a recessive mutation in an X-linked gene that is beneficial to males or a partially dominant mutation that benefitted females or both sexes. Nucleotide diversity in the domesticated X samples is about half that in the wild Xs, probably due to the bottleneck when hermaphrodites were selected during domestication.
  
  
  
  The extreme low nucleotide diversity in the papaya X-linked region is much greater than observed in humans, great apes, and the neo-X chromosome of Drosophila miranda, which show the expected pattern of Y-linked genes < X-linked genes < autosomal genes; papaya shows an unprecedented pattern of X-linked genes < autosomal genes < Y-linked genes.
authors.affiliation: FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China.|Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
authors.forename: Robert
authors.initials: R
authors.lastname: VanBuren
authors.affiliation: FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China.|Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
authors.forename: Ching Man
authors.initials: CM
authors.lastname: Wai
authors.affiliation: FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology 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, IL, 61801, USA.
authors.forename: Jennifer
authors.initials: J
authors.lastname: Han
authors.affiliation: Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
authors.forename: Jie
authors.initials: J
authors.lastname: Arro
authors.affiliation: FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China.
authors.forename: Zhicong
authors.initials: Z
authors.lastname: Lin
authors.affiliation: FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China.
authors.forename: Zhenyang
authors.initials: Z
authors.lastname: Liao
authors.affiliation: Texas A&M AgriLife Research, Department of Plant Pathology & Microbiology, Texas A&M University System, Dallas, TX, 75252, USA.
authors.forename: Qingyi
authors.initials: Q
authors.lastname: Yu
authors.affiliation: Hawaii Agriculture Research Center, Kunia, HI, 96759, USA.
authors.forename: Ming-Li
authors.initials: ML
authors.lastname: Wang
authors.affiliation: USDA-ARS, Pacific Basin Agricultural Research Center, Hilo, HI, 96720, USA.
authors.forename: Francis
authors.initials: F
authors.lastname: Zee
authors.affiliation: Department of Botany, Miami University, Oxford, OH, 45056, USA.
authors.forename: Richard C
authors.initials: RC
authors.lastname: Moore
authors.affiliation: Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, EH9 3JT, UK.
authors.forename: Deborah
authors.initials: D
authors.lastname: Charlesworth
authors.affiliation: FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China. rming@life.uiuc.edu.|Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA. rming@life.uiuc.edu.
authors.forename: Ray
authors.initials: R
authors.lastname: Ming
mesh_terms: D029441:Carica / Q000235:genetics*; D032461:Chromosomes, Plant / Q000235:genetics*; D005260:Female; D050172:Genes, X-Linked / Q000235:genetics; D050173:Genes, Y-Linked / Q000235:genetics; D014644:Genetic Variation; D006239:Haplotypes; D006801:Humans; D008297:Male; D009154:Mutation; D009711:Nucleotides / Q000235:genetics*; D017422:Sequence Analysis, DNA; D019849:Sex Determination Processes
chemical_list: D009711:Nucleotides