Additional file 1:

Genome information data.

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Additional file 2:

Trends between genome size and gene count in different bacterial phyla. Columns correspond to the genome size (left axis), and the points correspond to the gene count (right axis). Red and blue colours correspond to host dependent (HD) and free-living (FL) bacteria, respectively. Other phyla: Aquifex, Thermotoga, Chlorobium, Dehalococcoides, Deinococci, Thermus, Fusobacteria, and planctomyces. Taxa are listed in Additional file 1.

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Additional file 3:

Schematic representation of strategy used to identify essential and lost COGs. FL corresponds to free-living and OI corresponds to obligate intracellular bacteria.

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Additional file 4:

Comparison of the sets of lost COGs. Venn diagram shows the number of shared and group-specific COGs lost in obligate intracellular bacteria and conserved in their close free-living relatives in alpha- and gamma-proteobacteria. Mycobacterium leprae lost only 63% of these COGs, however its genome content is rapidly degrading according to the high number of pseudogene [27].

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Additional file 5:

Distribution of the common loss proportion, simulated from 2000 re-samplings. The number of COGs lost by each phylum is fixed and equals the observed loss numbers. Red dashed lines represent the 2.5% and 97.5% quantiles and blue line indicates the observed common loss proportion. 100 COGs were lost in concert among the obligate intracellular bacteria over the 969 COGs that are lost by at least one of the studied bacteria, which give a proportion of 0.1032 (100/969). The number of common COGs lost was significantly more important than expected if the loss were random (Randomization test, n = 2000, p < 10^-6).

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Additional file 6:

Probability of losing at least 100 COGs in common Curve describing the probability of losing at least 100 COGs in common with respect to the theoretical probability of random loss (p0). The red point corresponds to the probability-threshold under which the hypothesis of independent loss between phyla is rejected (with α = 5%).

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Additional file 7:

Mean number of genes per Mb encoding for intracellular trafficking. *p-values < 0.05 are shown in bold to indicate significant differences between mutualists and parasites (Wilcoxon rank sum test).

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Additional file 8:

COGs involved in transcription.

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Additional file 9:

COGs involved in intracellular trafficking and secretion.

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Additional file 10:

Distribution of COGs lost by small free-living bacteria among the set of 100 COGs lost in common by obligate intracellular bacteria and among all other COGs.

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Additional file 11:

Probability of losing at least 100 COGs in common among the 969 COGs lost at least by one obligate intracellular bacterium. Curve describing the probability of losing at least 100 COGs in common with respect to the theoretical probability of random loss (p0). The red point corresponds to the probability-threshold under which the hypothesis of independent loss between phyla is rejected (with α = 5%).

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