D’Auria et al. BMC Genomics 2010, 11:181 http://www.biomedcentral.com/1471-2164/11/181 Table 2: Accessory genes islands (Continued) ND10 Paris ND11 Alcoy Corby ND12 Lens ND13 Corby No clear role Mainly transposases No clear role No clear role 2725059 - 2776774 3003085 - 3015471 3443118 - 3451379 2824095 - 2849378 2833804 - 2842585 61 28 14 16 10 51716 12387 8262 25284 8782 Page 7 of 13 + + + - + 37 37.15 35.00 36.77 37.42 First column describes the name of the island and the genome of provenance. Following columns report a short description, the position on the genomes, the number of CDSs contained in the island, the length, the presence (+)/absence (-) of transposase genes and the GC content. those of the Lpg genome. Conversely, core HelABC genes in Lpa and Lpc are highly related. DNA transfer-related islands (DT) Three DT islands have been identified (DT1, DT2 and DT3). DT1 and DT2 correspond to the Trb-2 and Trb-1 islands described by Glöckner and collaborator for the Corby strain [7]. We have found that both islands are also present in the Alcoy strain, although DT2a is shorter than DT2c, thus suggesting that Lpa and Lpc acquired these systems via DNA transfer prior to their divergence (see Figure 5, green track). Some remarkable features of DT1 are: a phage repressor (lpa00219, LPC_0166), a set of tra and trb (conjugal transfer pro- teins) operons, a putative lamboid prophage Rac inte- grase (lpa00266, LPC_0199), another integrase (lpa00270, LPC_0202), an htpX protease (lpa00275, LPC_0205), and a prophage regulatory protein alpA (lpa00278, LPC_0208). In the DT2 island, both strains share a putative RNA helicase (lpa00835, LPC_2785), two putative restriction enzymes (LPC_2788, LPC_2790, lpa00832, and lpa_00829) and the set of the tra and trb operons. Glöckner and collaborators [7] described that Trb-1 (here DT2) is active and could be transferred to other Legionella. In both genomes, DT1 and DT2 are integrated, respectively, at the tmRNA and tRNApro sites. Finally, we have identified a DNA transfer island, DT3, in all strains with the exception of the Corby and Alcoy ones. It is worth mentioning that this island was pre- viously described in Lpg and Lpp, as an integrated plas- mid-like element [5,29]. It contains lvh (Legionella vir homolog), a type IV secretion system involved in conju- gation [30,31]. The lvr (Legionella vir region) is located downstream where LvrA is homologous to the CsrA repressor, important for the inhibition of post-exponen- tial phase activity (such as DNA transfer) [32]. A CRISPR system was identified at the beginning of this island. Figure 4 Strain related orthology maps. Strain related orthology maps. Each map shows comparative analysis based on each genome. From outside to inside: ring 1, gene positions according with COG categories color code; ring 2, GC content; ring 3, GC Skew; ring 4, island positions (color code according with islands legend); rings 5 to 8 show the BLAST homology for each gene versus the other four genomes (color code according with genomes legend).