D’Auria et al. BMC Genomics 2010, 11:181 http://www.biomedcentral.com/1471-2164/11/181 Page 3 of 13 Figure 1 Pangenome overview. The Venn diagram showing the core genome and the genes specific of the strains L. pneumophila Alcoy, Philadelphia, Lens, Paris and Corby. Genes overlapping at least 70% length and 80% of similarity were considered orthologs. (71.2%) with Lpp; and 1,802 (56.4%) and 1,776 (55.4%) with Lpg, respectively. Similarly, Lpp and Lpl also seem to be close-related with a shared genome of 2,207 genes out of 2,877 for Lpl (76.7%) and 3,026 for Lpp (73%). Finally, Lpg seems to be the most distantly related, shar- ing 2,207 genes with Lpl (75%) and 1,792 (60.1%) with Lpp. Figure 2 shows the application of the rarefaction methodology on the gene clusters from multiple gen- omes belonging to the same species. L. pneumophila tends to reach a plateau, although, according to Tettelin and collaborators [18], it should be considered an open pangenome similarly to what happens in other patho- genic organisms, such as the pangenomes from the same species of Streptococcus agalactiae, S. pyogenes and Staphylococcus aureus [18,19]. In the case of E. coli, despite the growing number of complete genomes, its pangenome is still far from fully described [17]. It has also been reported that clinically related pathogenic bac- teria posses a lower level of variation than free-living bacteria, which is probably due to niche restriction that could lead to a wider core genome [20,21]. Functional classification of core and dispensable genes Genes belonging to the core and dispensable genomes have been classified according to their predicted func- tion based on COG categories (Figure 3). L. pneumo- phila is characterized by quite a high number of hypothetical proteins, for which annotation is still incomplete. Of the 1,979 genes belonging to the core genome, 1,131 (57%) were attributed to a COG category (e value less than 10-15), and in the case of dispensable genome, only 179 out of 978 (18.2%). These results are in agreement with those obtained in other studies, where hypothetical genes, and even genes with unknown function are, in the majority, in the dispensable genome [18]. Although the major proportion of the CDSs for which a function could be predicted (according to the COG database) falls within the core genome, minor dif- ferences between the two compartments were observed