The Neolithic revolution of bacterial genomes Alex Mira, Ravindra Pushker, Francisco Rodríguez-Valera  Trends in Microbiology  Volume 14, Issue 5, Pages 200-206 (May 2006) DOI: 10.1016/j.tim.2006.03.001 Copyright © 2006 Elsevier Ltd Terms and Conditions

Figure 1 IS expansions in human-related species. DNA sequence similarity between pairs of paralogous genes (blue crosses) and between pairs of IS elements (red crosses) is indicated across different bacterial species. Chromosomal location of the first gene for each pair is shown on the x-axis. (a) Bordetella pertussis Tohama I and Bordetella bronchiseptica RB50; (b) Shigella flexneri 2a and Escherichia coli K12. Bacteria specialized in humans are shown on the left, whereas related species that are not human specialists are shown on the right. Species associated with humans (B. pertussis and S. flexneri) show a recent explosion of IS elements across their genomes. Trends in Microbiology 2006 14, 200-206DOI: (10.1016/j.tim.2006.03.001) Copyright © 2006 Elsevier Ltd Terms and Conditions

Figure 2 IS expansions in species that are presumably unrelated to humans. DNA sequence similarity is indicated between pairs of paralogous genes (blue crosses) and between pairs of IS elements (red crosses). (a) Wolbachia pipientis (which causes cytoplasmic incompatibility in the fruit fly Drosophila melanogaster) and Photorhabdus luminescens (a mutualistic symbiont with a restricted host range to the nematode Heterorhabditis bacteriophora) are animal-associated. (b) Geobacter metallireducens and Shewanella oneidensis are metal reducers from the terrestrial subsurface. Trends in Microbiology 2006 14, 200-206DOI: (10.1016/j.tim.2006.03.001) Copyright © 2006 Elsevier Ltd Terms and Conditions

Figure 3 IS expansions in bacteria that are specialized in agricultural plants, in farm animals and in food processing. DNA sequence similarity is indicated between pairs of paralogous genes (blue crosses) and between pairs of IS elements (red crosses) across different bacterial species. (a) Pseudomonas syringae pv. tomato and Pseudomonas aeruginosa PA01; (b) Burkholderia mallei ATCC 23344 and Burkholderia pseudomallei K96243; (c) Lactococcus lactis subsp. lactis and Lactobacillus acidophilus NCFM. Specialized strains are shown on the left and non-specialized related strains are shown on the right. Trends in Microbiology 2006 14, 200-206DOI: (10.1016/j.tim.2006.03.001) Copyright © 2006 Elsevier Ltd Terms and Conditions

Figure 4 IS expansions in species under potential human influence. DNA sequence similarity is indicated between pairs of paralogous genes (blue crosses) and between pairs of IS elements (red crosses) across selected bacterial species. Chromosomal location of the first gene for each pair is shown on the x-axis. (a) Bradyrhizobium japonicum USDA 110 and Mesorhizobium loti MAFF303099; (b) Halobacterium salinarum NRC-1 and Haloarcula marismortui ATCC 43049. Species on the left show recent IS element expansions that are not found in closely related species (right), which is hypothesized to be the result of niche specialization. Trends in Microbiology 2006 14, 200-206DOI: (10.1016/j.tim.2006.03.001) Copyright © 2006 Elsevier Ltd Terms and Conditions