Intergenic transposable elements are not randomly distributed in bacteria.

Insertion sequences (ISs) are mobile genetic elements in bacterial genomes. In general, intergenic IS elements are probably less deleterious for their hosts than intragenic ISs, simply because they have a lower likelihood of disrupting native genes. However, since promoters, Shine-Dalgarno sequences, and transcription factor binding sites are intergenic and upstream of genes, I hypothesized that not all neighboring gene orientations (NGOs) are selectively equivalent for IS insertion. To test this, I analyzed the NGOs of all intergenic ISs in 326 fully sequenced bacterial chromosomes. Of the 116 genomes with enough IS elements for statistical analysis, 68 have significantly more ISs between convergently oriented genes than expected, and 46 have significantly fewer ISs between divergently oriented genes. This suggests that natural selection molds intergenic IS distributions because they are least intrusive between convergent gene pairs and most intrusive between divergent gene pairs.