title: Genomic degradation of a young Y chromosome in Drosophila miranda.
abstract: BACKGROUND
  Y chromosomes are derived from ordinary autosomes and degenerate because of a lack of recombination. Well-studied Y chromosomes only have few of their original genes left and contain little information about their evolutionary origin. Here, we take advantage of the recently formed neo-Y chromosome of Drosophila miranda to study the processes involved in Y degeneration on a genomic scale.
  
  
  RESULTS
  We obtained sequence information from 14 homologous bacterial artificial chromosome (BAC) clones from the neo-X and neo-Y chromosome of D. miranda, encompassing over 2.5 Mb of neo-sex-linked DNA. A large fraction of neo-Y DNA is composed of repetitive and transposable-element-derived DNA (20% of total DNA) relative to their homologous neo-X linked regions (1%). The overlapping regions of the neo-sex linked BAC clones contain 118 gene pairs, half of which are pseudogenized on the neo-Y. Pseudogenes evolve significantly faster on the neo-Y than functional genes, and both functional and non-functional genes show higher rates of protein evolution on the neo-Y relative to their neo-X homologs. No heterogeneity in levels of degeneration was detected among the regions investigated. Functional genes on the neo-Y are under stronger evolutionary constraint on the neo-X, but genes were found to degenerate randomly on the neo-Y with regards to their function or sex-biased expression patterns.
  
  
  CONCLUSIONS
  Patterns of genome evolution in D. miranda demonstrate that degeneration of a recently formed Y chromosome can proceed very rapidly, by both an accumulation of repetitive DNA and degeneration of protein-coding genes. Our data support a random model of Y inactivation, with little heterogeneity in degeneration among genomic regions, or between functional classes of genes or genes with sex-biased expression patterns.
authors.affiliation: Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA. dbachtrog@ucsd.edu
authors.forename: Doris
authors.initials: D
authors.lastname: Bachtrog
authors.forename: Emily
authors.initials: E
authors.lastname: Hom
authors.forename: Karen M
authors.initials: KM
authors.lastname: Wong
authors.forename: Xulio
authors.initials: X
authors.lastname: Maside
authors.forename: Pieter
authors.initials: P
authors.lastname: de Jong
mesh_terms: D000818:Animals; D022202:Chromosomes, Artificial, Bacterial / Q000235:genetics; D004251:DNA Transposable Elements / Q000235:genetics; D004330:Drosophila / Q000235:genetics*; D019143:Evolution, Molecular; D005260:Female; D005786:Gene Expression Regulation; D049750:Genome, Insect; D019476:Insect Proteins / Q000235:genetics; D008297:Male; D017422:Sequence Analysis, DNA; D019849:Sex Determination Processes; D014998:Y Chromosome / Q000378:metabolism*
chemical_list: D004251:DNA Transposable Elements; D019476:Insect Proteins