The Drosophila Gene Disruption Project (GDP) has created a public collection of 
mutant strains containing single transposon insertions associated with different 
genes. These strains often disrupt gene function directly, allow production of 
new alleles, and have many other applications for analyzing gene function. Here 
we describe the addition of ∼7600 new strains, which were selected from >140,000 
additional P or piggyBac element integrations and 12,500 newly generated 
insertions of the Minos transposon. These additions nearly double the size of 
the collection and increase the number of tagged genes to at least 9440, 
approximately two-thirds of all annotated protein-coding genes. We also compare 
the site specificity of the three major transposons used in the project. All 
three elements insert only rarely within many Polycomb-regulated regions, a 
property that may contribute to the origin of "transposon-free regions" (TFRs) 
in metazoan genomes. Within other genomic regions, Minos transposes essentially 
at random, whereas P or piggyBac elements display distinctive hotspots and 
coldspots. P elements, as previously shown, have a strong preference for 
promoters. In contrast, piggyBac site selectivity suggests that it has evolved 
to reduce deleterious and increase adaptive changes in host gene expression. The 
propensity of Minos to integrate broadly makes possible a hybrid finishing 
strategy for the project that will bring >95% of Drosophila genes under 
experimental control within their native genomic contexts.