title: Abundant and species-specific DINE-1 transposable elements in 12 Drosophila genomes.
abstract: BACKGROUND
  Miniature inverted-repeat transposable elements (MITEs) are non-autonomous DNA-mediated transposable elements (TEs) derived from autonomous TEs. Unlike in many plants or animals, MITEs and other types of DNA-mediated TEs were previously thought to be either rare or absent in Drosophila. Most other TE families in Drosophila exist at low or intermediate copy number (around < 100 per genome).
  
  
  RESULTS
  We present evidence here that the dispersed repeat Drosophila interspersed element 1 (DINE-1; also named INE-1 and DNAREP1) is a highly abundant DNA-mediated TE containing inverted repeats found in all 12 sequenced Drosophila genomes. All DINE-1s share a similar sequence structure, but are more homogeneous within species than they are among species. The inferred phylogenetic relationship of the DINE-1 consensus sequence from each species is generally consistent with the known species phylogeny, suggesting vertical transmission as the major mechanism for DINE-1 propagation. Exceptions observed in D. willistoni and D. ananassae could be due to either horizontal transfer or reactivation of ancestral copies. Our analysis of pairwise percentage identity of DINE-1 copies within species suggests that the transpositional activity of DINE-1 is extremely dynamic, with some lineages showing evidence for recent transpositional bursts and other lineages appearing to have silenced their DINE-1s for long periods of time. We also find that all species have many DINE-1 insertions in introns and adjacent to protein-coding genes. Finally, we discuss our results in light of a recent proposal that DINE-1s belong to the Helitron family of TEs.
  
  
  CONCLUSIONS
  We find that all 12 Drosophila species with whole-genome sequence contain the high copy element DINE-1. Although all DINE-1s share a similar structure, species-specific variation in the distribution of average pairwise divergence suggests that DINE-1 has gone through multiple independent cycles of activation and suppression. DINE-1 also has had a significant impact on gene structure evolution.
authors.affiliation: Institute of Genetics, National Yang-Ming University, Taipei 112, Taiwan. hy31@cornell.edu
authors.forename: Hsiao-Pei
authors.initials: HP
authors.lastname: Yang
authors.forename: Daniel A
authors.initials: DA
authors.lastname: Barbash
mesh_terms: D000818:Animals; D001483:Base Sequence; D004251:DNA Transposable Elements / Q000235:genetics*; D004330:Drosophila / Q000145:classification / Q000235:genetics*; D019143:Evolution, Molecular; D014644:Genetic Variation; D049750:Genome, Insect; D008969:Molecular Sequence Data; D016254:Mutagenesis, Insertional; D010802:Phylogeny; D017422:Sequence Analysis, DNA; D013045:Species Specificity
chemical_list: D004251:DNA Transposable Elements