Phylogenetic position of the Paulinella chromatophore within the cyanobacteria inferred by complete rRNA operon sequence comparisons. The tree topology was generated by maximum likelihood (ML) analyses using the GTR+I+Γ model. The nodal support values are bootstrap values ≥ 50% obtained by ML (100 replicates), neighbor-joining (NJ; GTR+I+Γ model; 1000 repl.), maximum parsimony (MP; 1000 repl.), and Bayesian posterior probabilities (≥ 0.95). Branches in bold have maximal support (100%; 1.00) by all methods; interrupted branches were graphically reduced to 30% of their original length. Taxa in bold were newly determined for this study; strain designations and EMBL/GENBANK accession numbers are also given. Cyanobacterial clade abbreviations: GBACT (Gloeobacter), PSAN (Pseudanabaena), S/P/M (Synechocystis/Pleurocapsa/Microcystis), OSC (Oscillatoria), LEPT (Leptolyngbya), NOST (Nostoc), and PHOR (Phormidium): modified sequence groups after ; YELLOST (thermophilic "Synechococcus" from Yellowstone NP), THERMOSY (Thermosynechococcus), CHROO (Chroococcidiopsis), PRCHX (Prochlorothrix), SELONG (Synechococcus elongatus), and PS (Prochlorococcus/Synechococcus). Encircled numbers indicate clades/branches that were analyzed by single-gene analyses, and by NJ using the LogDet+I-model (see text and Additional File 1).