The Dynamic Nature of Genomes across the Tree of Life

Genomes are dynamic in lineages across the tree of life. Among bacteria and archaea, for example, DNA content varies throughout life cycles, and nonbinary cell division in diverse lineages indicates the need for coordination of the inheritance of genomes. These observations contrast with the textbook view that bacterial and archaeal genomes are monoploid (i.e., single copied) and fixed both within species and throughout an individual’s lifetime. Here, we synthesize information on three aspects of dynamic genomes from exemplars representing a diverse array of bacterial and archaeal lineages: 1) ploidy level variation, 2) epigenetic mechanisms, and 3) lifecyclevariation.Forexample, theEuryarchaeotaanalyzedtodateareallpolyploid,as is thebacteriumEpulopiscium thatcontainsup to tens of thousands of copies of its genome and reproduces by viviparity. The bacteriumDeinococcus radiodurans and the archaeon Halobacterium sp. NRC-1 can repair a highly fragmented genome within a few hours. Moreover, bacterial genera such as Dermocarpella and Planctomyces reproduce by fission (i.e., generating many cells from one cell) and budding, respectively, high-lighting the need for regulation of genome inheritance in these lineages. Combining these data with our previous work on wide-spread genome dynamics among eukaryotes, we hypothesize that dynamic genomes are a rule rather than the exception across the tree of life. Further, we speculate that all domains may have the ability to distinguish germline from somatic DNA and that this ability may have been present the last universal common ancestor. Key words: LUCA, life cycle variation, polyploidy, epigenetics, genome