D’Auria et al. BMC Genomics 2010, 11:181 http://www.biomedcentral.com/1471-2164/11/181 Page 4 of 13 Figure 2 Pangenome state. Rarefaction curves applied to different strains of L. pneumophila (5 genomes), E. coli (8 genomes), Streptococcus pyogenes (8 genomes), S. agalactiae (8 genomes), and Staphilococcus aureus (9 genomes). See Additional file 6 for accession numbers of used genomes. for defense mechanisms (V) and intracellular trafficking, secretion and vesicular transport (U) categories. Genomic islands Although the five strains are highly syntenic, most of the genes that do not belong to the core genome are part of genomic islands, absent in at least one of the genomes. Table 2 reports the islands identified for each strain, Fig- ure 4 describes the island positions for each genome fol- lowing Table 2 classifications, while Figure 5a shows the hypothesis of islands histories according to the MLST tree topology obtained by D’Auria et al. [9]. Figure 5b shows the alignment of the five genomes, the locally col- linear blocks and the position of the islands according to their genome locations. Twenty-eight islands were identi- fied belonging to six different types (see Additional File 1). Only one island (R1, see below) is present in all five genomes; eighteen are strain-specific, probably acquired by horizontal gene transfer (HGT) events; five are common to Lpa/Lpc genomes (probably acquired by the Lpa/Lpc common ancestor), whereas one island (DT3, see below) could be interpreted as having been lost in the common ancestor of Lpa/Lpc genomes. Resistance-related islands (R) We have identified two types of resistance-related islands, R1 and R2 (see Figure 4 and Figure 5, blue track). R1 maintains the same position, around 60 Kb at the beginning of the chromosome, in the five strains, inserted in a tRNAasn site, although the organization and content is different. In Lpa, Lpc and Lpg, the island is similar and contains several hypothetical proteins as well as a methylase (lpa00094, LPC_0075, lpg0060), fol- lowed by a multi-drug resistance protein (lpa00095, LPC_0076, lpg0061). In the Paris strain, the island also begins with a methylase (lpp0063) and in the Lens strain with a putative transposase (lpl0064). However, although the position of the gene coding for the methylase is quite similar in both genomes, the alignment is differ- ent, due to a relatively big deletion in Lpl, whereas in Lpp it is followed by the antibiotic persistence-related system HipB/HipA (lpp0065, lpp0064) with no homolog in other Legionella strains. Although the mechanism of this system is still not well known, much evidence points to HipA as a toxin with bacteriostatic activity which binds DNA/RNA, blocking macromolecule synth- esis until HipB binds HipA, releasing the DNA/RNA so microbial cells can survive extended exposure to drugs [22,23]. This island is followed by various phage-related proteins, elements of the Xre family of transcriptional regulators, an LvrA protein, and three transporters (lpp0077, lpp0078, lpp0079) of which the lpp0077 is similar to the acriflavine multi-drug efflux pump [24].