Organismal phylogeny and distribution of lineage-specific gene clusters.

<p>The organismal phylogeny is inferred from the concatenated protein alignment of 105 single-copy genes shared by all lineages (with 44,919 aligned amino acid sites), the three phylogenetic methods used (<i>i.e.</i>, maximum likelihood, parsimony, and Bayesian) all produced the same tree topology with strong support (<i>i.e.</i>, all internal nodes received 100% bootstrap support using the maximum likelihood method and >97% clade credibility using the Bayesian method). The branch lengthes shown in this figure is based on the maximum likelihood result. The numbers above a branch and proceeded by a ‘+’ sign indicate the number of homologous gene clusters that are uniquely present in all daughter lineages; the numbers below a branch and proceeded by a ‘−’ sign indicate the number of homologous gene clusters that are uniquely absent. For example, 52 gene clusters are shared by all four ‘<i>Candidatus</i> Phytoplasma’ genomes and do not contain homolog from any of the other eight genomes analyzed (<i>i.e.</i>, represent possible gene gain events in the common ancestor of ‘<i>Ca.</i> Phytoplasma’ lineages); similarly, 27 gene clusters are missing from the four ‘<i>Ca.</i> Phytoplasma’ genomes but are present in all other eight genomes (<i>i.e.</i>, represent possible gene loss events in the common ancestor of ‘<i>Ca.</i> Phytoplasma’ lineages).