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Figure 5 | BMC Genomics

Figure 5

From: Inter- and intra-specific pan-genomes of Borrelia burgdorferi sensu lato: genome stability and adaptive radiation

Figure 5

Phylogenetic correlation of B. burgdorferi s. l. and B. burgdorferi s. s pan- genomes. (A) Pan-genome sizes, calculated in permutations where the B31 genome is used as reference, are plotted against the number n of genomes in the comparisons. Data points were fitted with negative exponential growth models (see Methods) [69]. The least-square fitted model for B. burgdorferi s.l. (solid orange line) takes the following parameter values (and respective standard errors): D=0.995 (0.0121), tg(θ)=0.00725 (0.00083),κ=0.0445 (0.0187), and τ n =3.47 (1.06). The model fit has an R2=0.7479. The model for B. burgdorferi s.s. (solid black line) has the following parameter values (and respective standard errors): D=1.001 (0.00276), tg(θ)=0.000917 (0.00027),κ=0.01446 (0.0088), and τ n =2.287 (0.857). The model fit has an R2=0.6065. (B) The same pan-genome calculations were fitted linearly with the sub-tree length of genomes in comparison, according to the neutral coalescence model: Ωn0+ωTn, where ω is the rate of gene acquisition [77]. The linear model for B. burgdorferi s.l. has Ω0=1458 (3.8) and ω=260.3 (3.5) with a greatly improved R2=0.8762 (p<2e-16). The linear model for B. burgdorferi s.s. has Ω0=1501 (0.91) and ω=202.3 (0.05) with a slightly improved R2=0.6126 (p<2e-16). The improvement is due to a tighter fit of predicted pan-genome sizes with the tree lengths, in which some groups of genomes are more phylogenetically diverse (thus having larger pan-genome sizes) than others albeit the total number of genomes in comparison remain the same (e.g. comparing n=8, in blue, in the two panels).

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