Bosi et al. BMC Genomics 2011, 12:403 http://www.biomedcentral.com/1471-2164/12/403 respect to the whole dataset (10% and 5%, respectively, see below), suggesting that plasmids from these micro- organisms might really have more genes of chromoso- mal origin that what is seen in other species. PAGs and plasmids size In principle, the acquisition and the maintainance of exo- geneous DNA by a plasmid molecule might lead to the expansion of its coding capabilities and, parallely, to an increase of its size. Moreover, it might be expected that larger plasmids possess a higher number of “entry points” for exogeneous DNA in respect to smaller ones, thus somehow promoting the acquisition of novel genetic material. To test these hypotheses, we compared the num- ber of PAGs possessed by each plasmid with its size (Fig- ure 4). We found only a slightly positive correlation (R2 = 0.21) between the length (in bp) of each plasmid and its PAGs content. Indeed, within our dataset we retrieved plasmids completely riddled in PAGs as, for example, Far04_lp28-1 plasmid from Borrelia garinii Far04 (27689 nt) where we found almost 80% of atypical genes. Conver- sely, in a plasmid of similar size (e.g. pXAG81 from Xanthomonas axonopodis pv. Glycines, 26721 bp) we were not able to detect any PAG. This finding might suggest that plasmids can undergo recombination with other informative molecules and/or HGT regardless of their size. Moreover, this might also indicate that, the acquisi- tion of foreign DNA might not be the only force driving the growth and the expansion of plasmids coding capabil- ities and that other molecular mechanisms (e.g. gene duplication) might play a certain role. Similar trends (with R2 values raging from 0.24 to 0.48 were observed) also when PAGs dataset retrieved with lower CI thresholds were analyzed (Additional file 5). Figure 4 PAGs and plamids size. Scatterplot illustrating the correlation existing between plasmids size and their PAGs content. Page 6 of 12 PAGs functions We aimed at identifying the most represented functions performed by PAGs. To fulfill this task we adopted the computational pipeline implemented in Blast2GO (B2GO) [37] and performed an automated functional annotation. For most of PAGs it was not possible to identify any associated function. This was somehow expected, since it has already been shown [3] that the function of most of the plasmid encoded proteins is still unknown. Specifically, on a total of 8065 sequences used as input for B2GO, 803 PAGs did not retrieve any BLAST hit and 4795 retrieved an hypothetical ortholog in the database (in almost all cases corresponding to the query itself) but did not produce any mapping to a known biological function. Hence, overall, an important fraction of PAGs (5598 sequences, almost 68% of the total) could not be linked to any hit in functional data- bases and, as a consequence, to any known biological function. For the remaining 2467, it was possible to retrieve a putative biological process. For clarity pur- poses, we show only those biological process that pos- sessed at least 70 representatives within the PAGs dataset (Figure 5, complete results are shown as Addi- tional file 6). As shown in Figure 5, most of the PAGs encoded pro- teins (around 22% of all the annotated ones) are asso- ciated to those molecular functions that are able to catalyze the movement of DNA among and within infor- mative molecules, that is DNA integration, transposition 12 s 10 G P A 8 d e issgn 6 a fo% 4 2 0 ten ion td no is ic no ss ss ss sse ino tr s no ss ss ry no sse sse ìss ce iili,tfttrrcsednpddeonpanoegauno−ANDR ittrgaenADN iii,trssadeeononpa−TADNm jitaguonC tseengahoP iitttssobnaeoonpeR iiitt/rcxudeanodO iiilttrrrrccsyccyoepenheaoba− iiittrccysxeophenbuonA iliiltrrcccycxceopobadeaabooonmM ilittrrccopbooneeaPm iltrcaepADN ittrsanpnoaoC liilttrccscopoeedoeueabNm iiiltrsssangnaSm ttrsssoeonepeR iiiillttttrrccysvsopehenobanueboea−mW trcsseueonepoRm iiillftrcccdaoeuoeoammM iiiilllttrrccyscopenhbodanoaaeuCm iittrccysyzponheboneeoCm iiiittttrrrccysvseoepenheaebodnaedP iiiltsnnaanadaPmm Figure 5 PAGs functions. Histogram showing the distribution of the main biological processes in which PAGs are involved. Red bars refer to processes generally related to DNA mobilization.