title: Sequencing papaya X and Yh chromosomes reveals molecular basis of incipient sex chromosome evolution.
abstract: Sex determination in papaya is controlled by a recently evolved XY chromosome pair, with two slightly different Y chromosomes controlling the development of males (Y) and hermaphrodites (Y(h)). To study the events of early sex chromosome evolution, we sequenced the hermaphrodite-specific region of the Y(h) chromosome (HSY) and its X counterpart, yielding an 8.1-megabase (Mb) HSY pseudomolecule, and a 3.5-Mb sequence for the corresponding X region. The HSY is larger than the X region, mostly due to retrotransposon insertions. The papaya HSY differs from the X region by two large-scale inversions, the first of which likely caused the recombination suppression between the X and Y(h) chromosomes, followed by numerous additional chromosomal rearrangements. Altogether, including the X and/or HSY regions, 124 transcription units were annotated, including 50 functional pairs present in both the X and HSY. Ten HSY genes had functional homologs elsewhere in the papaya autosomal regions, suggesting movement of genes onto the HSY, whereas the X region had none. Sequence divergence between 70 transcripts shared by the X and HSY revealed two evolutionary strata in the X chromosome, corresponding to the two inversions on the HSY, the older of which evolved about 7.0 million years ago. Gene content differences between the HSY and X are greatest in the older stratum, whereas the gene content and order of the collinear regions are identical. Our findings support theoretical models of early sex chromosome evolution.
authors.affiliation: Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
authors.forename: Jianping
authors.initials: J
authors.lastname: Wang
authors.forename: Jong-Kuk
authors.initials: JK
authors.lastname: Na
authors.forename: Qingyi
authors.initials: Q
authors.lastname: Yu
authors.forename: Andrea R
authors.initials: AR
authors.lastname: Gschwend
authors.forename: Jennifer
authors.initials: J
authors.lastname: Han
authors.forename: Fanchang
authors.initials: F
authors.lastname: Zeng
authors.forename: Rishi
authors.initials: R
authors.lastname: Aryal
authors.forename: Robert
authors.initials: R
authors.lastname: VanBuren
authors.forename: Jan E
authors.initials: JE
authors.lastname: Murray
authors.forename: Wenli
authors.initials: W
authors.lastname: Zhang
authors.forename: Rafael
authors.initials: R
authors.lastname: Navajas-Pérez
authors.forename: F Alex
authors.initials: FA
authors.lastname: Feltus
authors.forename: Cornelia
authors.initials: C
authors.lastname: Lemke
authors.forename: Eric J
authors.initials: EJ
authors.lastname: Tong
authors.forename: Cuixia
authors.initials: C
authors.lastname: Chen
authors.forename: Ching Man
authors.initials: CM
authors.lastname: Wai
authors.forename: Ratnesh
authors.initials: R
authors.lastname: Singh
authors.forename: Ming-Li
authors.initials: ML
authors.lastname: Wang
authors.forename: Xiang Jia
authors.initials: XJ
authors.lastname: Min
authors.forename: Maqsudul
authors.initials: M
authors.lastname: Alam
authors.forename: Deborah
authors.initials: D
authors.lastname: Charlesworth
authors.forename: Paul H
authors.initials: PH
authors.lastname: Moore
authors.forename: Jiming
authors.initials: J
authors.lastname: Jiang
authors.forename: Andrew H
authors.initials: AH
authors.lastname: Paterson
authors.forename: Ray
authors.initials: R
authors.lastname: Ming
mesh_terms: D029441:Carica / Q000235:genetics*; D058674:Chromosome Duplication; D007446:Chromosome Inversion; D002874:Chromosome Mapping; D022202:Chromosomes, Artificial, Bacterial; D032461:Chromosomes, Plant; D019143:Evolution, Molecular; D008957:Models, Genetic; D008969:Molecular Sequence Data; D012091:Repetitive Sequences, Nucleic Acid; D018626:Retroelements; D017422:Sequence Analysis, DNA; D012730:Sex Chromosomes
chemical_list: D018626:Retroelements