Birth of a new gene on the Y chromosome of Drosophila melanogaster

Proc Natl Acad Sci U S A. 2015 Oct 6;112(40):12450-5. doi: 10.1073/pnas.1516543112. Epub 2015 Sep 18.


Contrary to the pattern seen in mammalian sex chromosomes, where most Y-linked genes have X-linked homologs, the Drosophila X and Y chromosomes appear to be unrelated. Most of the Y-linked genes have autosomal paralogs, so autosome-to-Y transposition must be the main source of Drosophila Y-linked genes. Here we show how these genes were acquired. We found a previously unidentified gene (flagrante delicto Y, FDY) that originated from a recent duplication of the autosomal gene vig2 to the Y chromosome of Drosophila melanogaster. Four contiguous genes were duplicated along with vig2, but they became pseudogenes through the accumulation of deletions and transposable element insertions, whereas FDY remained functional, acquired testis-specific expression, and now accounts for ∼20% of the vig2-like mRNA in testis. FDY is absent in the closest relatives of D. melanogaster, and DNA sequence divergence indicates that the duplication to the Y chromosome occurred ∼2 million years ago. Thus, FDY provides a snapshot of the early stages of the establishment of a Y-linked gene and demonstrates how the Drosophila Y has been accumulating autosomal genes.

Keywords: Drosophila melanogaster; FDY; PacBio; Y chromosome; vig2.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Chromosome Mapping
  • Chromosomes, Insect / genetics
  • Drosophila Proteins / classification
  • Drosophila Proteins / genetics
  • Drosophila melanogaster / genetics*
  • Female
  • Gene Duplication
  • Gene Expression
  • Genes, Insect / genetics*
  • Genes, Y-Linked / genetics*
  • INDEL Mutation
  • Male
  • Molecular Sequence Data
  • Phylogeny
  • Reverse Transcriptase Polymerase Chain Reaction
  • X Chromosome / genetics
  • Y Chromosome / genetics*


  • Drosophila Proteins
  • FDY protein, Drosophila

Associated data

  • GENBANK/BK009307
  • GENBANK/BK009348
  • GENBANK/BK009349
  • GENBANK/BK009350
  • GENBANK/BK009351
  • GENBANK/BK009352
  • GENBANK/BK009353
  • GENBANK/BK009354
  • GENBANK/BK009355
  • GENBANK/KR781487