PAIS database

Insertion sequences (IS) are abundant mobile genetic elements that substantially affect evolution and ecological adaptation of prokaryotes. However, the environmental distribution of IS and their impact on ecosystems remain underexplored. We screened 10,740 metagenomes from all major ecosystems to compile the Prokaryotic Atlas of Insertion Sequences (PAIS), which includes 4.1 million IS. Using PAIS, we show that the global IS distribution is shaped by founder effects with high ecosystem and sample specificity, elucidate the effects of IS on host metabolism, and demonstrate that IS mediate horizontal gene transfer in the deep biosphere, especially when influenced by human activity like mining. We explore PAIS’ potential in biotechnology using a neural network approach for ecotone detection and possible application of diverse IS for genome editing.