Genome Biol Evol. 2010;2:584-90. doi: 10.1093/gbe/evq040. Epub 2010 Jul 8.
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.
插入序列（IS）是细菌基因组中的可移动遗传元件。一般来说，基因间的 IS 元件对其宿主的危害性可能小于基因内的 IS 元件，这仅仅是因为它们破坏宿主固有基因的可能性较低。然而，由于启动子、Shine-Dalgarno 序列和转录因子结合位点是基因间的，并且位于基因的上游，所以我假设并非所有相邻基因取向（NGO）对于 IS 插入都是具有选择性等价性的。为了验证这一点，我分析了 326 个完全测序的细菌染色体中所有基因间 IS 的 NGOs。在 116 个具有足够 IS 元素进行统计分析的基因组中，有 68 个在趋同取向的基因之间的 IS 数量显著多于预期，而有 46 个在发散取向的基因之间的 IS 数量显著少于预期。这表明自然选择塑造了基因间 IS 的分布，因为它们在趋同基因对之间的干扰最小，而在发散基因对之间的干扰最大。
