Indeed, in a large virulence plasmid of Shigella flexnery, an astonishing 153 (53%) ORFs are related to known and putative IS elements; no known bacterial plasmid has been described previously with such a high proportion of IS elements, and four new IS elements have been definitively identified (Venkatesan et al., 2001). Additionally, metagenomic sequencing has yielded a flood of bacterial genome data that confirm the presence of increasing numbers of mobile elements in all analyzed bacterial genomes. This has naturally led to the development of evolutionary studies where consistent IS annotation across many different genomes has become necessary, and several

alternatives are now available for comparison and enhanced understanding of their evolutionary this website and functional roles (Siguier et al., 2006; Wagner et al., 2007). Piscirickettsia salmonis

is the etiologic agent of salmonid rickettsial septicemia, or piscirickettsiosis (Fryer et al., 1990), which is an aggressive infectious disease that has affected salmonid fish since the late 1980s (Bravo & Campos, 1989; Graggero et al., 1995; Marshall et al., 2007). Piscirickettsia salmonis is a facultative intracellular Gram-negative bacterium (Mauel et al., 2008; STA-9090 Mikalsen et al., 2008; Gómez et al., 2009) that was initially described as a Rickettsia-like for obligate intracellular Alphaproteobacteria. Recently, it was reclassified

as a Gammaproteobacteria that closely resembles Legionella and Francisella species (Fryer & Hedrick, 2003). This ambiguity misled researchers for more than a decade; therefore, its biology, epidemiology and genetics are almost totally unknown. Nevertheless, it is known that this bacterium persists in sea water (Olivares & Marshall, 2010), maintaining its infective potential under rough environmental conditions (Lannan & Fryer, 1994). This vitality suggests that its genetic background should be sufficiently versatile to adapt easily to changing stressful conditions. In fact, our laboratory has demonstrated that under limiting in vitro conditions, morphological and genetic changes are consistently observed (Rojas et al., 2008). Thus, the report of the first IS sequence in this genome strengthened the belief that the genome of P. salmonis might show a surprising degree of complexity and plasticity. As our laboratory can successfully grow this bacterium in liquid media (Gómez et al., 2009; E. González, F. Gómez, V. Henríquez, S. H. Marshall & C. Altamirano, unpublished data), based on increasing evidence of the adaptive potential of this bacterium (Rojas et al., 2008, 2009, 2010), we decided to evaluate the quality of the bacterial genome to determine whether the observed morphological changes and adaptability have a genetic background.