| | | Bacteria have compound genomes. Core genes confer basic functions that are shared by most bacteria and mostly support a common phylogenetic history, so they can provide a stable basis for taxonomy. By contrast, accessory genes provide most of the functions that make bacteria interesting: pathogenesis, symbiosis, resistance to antibiotics or other toxins, metabolism of unusual compounds, and so on. The set of accessory genes varies even among strains of the same species, and these genes are carried by mobile elements that frequently move between species. They are mostly on plasmids, on chromids (previously called second chromosomes) or on genomic islands in the chromosome. The result is a mismatch between taxonomy and function: the species name does not necessarily indicate exactly what the organism can do. I will illustrate these issues using analyses of published bacterial genomes and our own data on the genomic diversity of Rhizobium leguminosarum and other root-nodule symbiotic bacteria. |
