title: Deciphering neo-sex and B chromosome evolution by the draft genome of Drosophila albomicans.
abstract: BACKGROUND
  Drosophila albomicans is a unique model organism for studying both sex chromosome and B chromosome evolution. A pair of its autosomes comprising roughly 40% of the whole genome has fused to the ancient X and Y chromosomes only about 0.12 million years ago, thereby creating the youngest and most gene-rich neo-sex system reported to date. This species also possesses recently derived B chromosomes that show non-Mendelian inheritance and significantly influence fertility.
  
  
  METHODS
  We sequenced male flies with B chromosomes at 124.5-fold genome coverage using next-generation sequencing. To characterize neo-Y specific changes and B chromosome sequences, we also sequenced inbred female flies derived from the same strain but without B's at 28.5-fold.
  
  
  RESULTS
  We assembled a female genome and placed 53% of the sequence and 85% of the annotated proteins into specific chromosomes, by comparison with the 12 Drosophila genomes. Despite its very recent origin, the non-recombining neo-Y chromosome shows various signs of degeneration, including a significant enrichment of non-functional genes compared to the neo-X, and an excess of tandem duplications relative to other chromosomes. We also characterized a B-chromosome linked scaffold that contains an actively transcribed unit and shows sequence similarity to the subcentromeric regions of both the ancient X and the neo-X chromosome.
  
  
  CONCLUSIONS
  Our results provide novel insights into the very early stages of sex chromosome evolution and B chromosome origination, and suggest an unprecedented connection between the births of these two systems in D. albomicans.
authors.affiliation: CAS-Max Planck Junior Research Group, State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China.
authors.forename: Qi
authors.initials: Q
authors.lastname: Zhou
authors.forename: Hong-mei
authors.initials: HM
authors.lastname: Zhu
authors.forename: Quan-fei
authors.initials: QF
authors.lastname: Huang
authors.forename: Li
authors.initials: L
authors.lastname: Zhao
authors.forename: Guo-jie
authors.initials: GJ
authors.lastname: Zhang
authors.forename: Scott W
authors.initials: SW
authors.lastname: Roy
authors.forename: Beatriz
authors.initials: B
authors.lastname: Vicoso
authors.forename: Zhao-lin
authors.initials: ZL
authors.lastname: Xuan
authors.forename: Jue
authors.initials: J
authors.lastname: Ruan
authors.forename: Yue
authors.initials: Y
authors.lastname: Zhang
authors.forename: Ruo-ping
authors.initials: RP
authors.lastname: Zhao
authors.forename: Chen
authors.initials: C
authors.lastname: Ye
authors.forename: Xiu-qing
authors.initials: XQ
authors.lastname: Zhang
authors.forename: Jun
authors.initials: J
authors.lastname: Wang
authors.forename: Wen
authors.initials: W
authors.lastname: Wang
authors.forename: Doris
authors.initials: D
authors.lastname: Bachtrog
mesh_terms: D000818:Animals; D058674:Chromosome Duplication / Q000235:genetics; D059006:Chromosomes, Insect / Q000235:genetics*; D004330:Drosophila / Q000235:genetics*; D019143:Evolution, Molecular; D005260:Female; D049750:Genome, Insect / Q000235:genetics*; D008297:Male; D058977:Molecular Sequence Annotation; D010802:Phylogeny; D011995:Recombination, Genetic / Q000235:genetics*; D014960:X Chromosome / Q000235:genetics*; D014998:Y Chromosome / Q000235:genetics*