Abstract
The movement of mobile genetic elements (MGEs), including bacteriophages, insertion sequence (IS) elements, and integrative and conjugative elements (ICEs) can have profound effects on bacterial evolution by introducing novel genes, or disrupting the existing ones. Obligate endobacteria are a distinctive group of bacteria that reside within the intracellular compartments of their eukaryotic hosts. Many obligate endobacteria are reproductively dependent on their hosts. Vertical transmission, in addition to degenerative genome contraction and loss of MGEs, makes heritable endobacteria vulnerable to Muller's ratchet, a process that jeopardizes evolutionary longevity of small populations. Mycoplasma-related endobacteria (MRE) are ancient heritable endosymbionts of arbuscular mycorrhizal fungi. Their genomes harbour numerous MGEs. To explore the significance of MGEs in the evolution of MRE and other obligate endobacteria, we analyze the impact of transmission mode, recombination, and evolutionary age on the maintenance of MGEs. Furthermore, we discuss the ability of MGEs to act as sites of gene conversion and recombination in endobacterial genomes. We propose that MGEs are important instruments of genome shuffling, contributing to population heterogeneity and evolutionary longevity in heritable obligate endobacteria.