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Background   Chloroflexus aurantiacus  is a thermophilic filamentous anoxygenic phototrophic (FAP) bacterium, and can grow phototrophically under anaerobic conditions or chemotrophically under aerobic and dark conditions. According to 16S rRNA analysis,  Chloroflexi  species are the earliest branching bacteria capable of photosynthesis, and  Cfl. aurantiacus  has been long regarded as a key organism to resolve the obscurity of the origin and early evolution of photosynthesis.  Cfl. aurantiacus  contains a chimeric photosystem that comprises some characters of green sulfur bacteria and purple photosynthetic bacteria, and also has some unique electron transport proteins compared to other photosynthetic bacteria.    Methods  The complete genomic sequence of  Cfl. aurantiacus  has been determined, analyzed and compared to the genomes of other photosynthetic bacteria.    Results  Abundant genomic evidence suggests that there have been numerous gene adaptations/replacements in  Cfl. aurantiacus  to facilitate life under both anaerobic and aerobic conditions, including duplicate genes and gene clusters for the alternative complex III (ACIII), auracyanin and NADH:quinone oxidoreductase; and several aerobic/anaerobic enzyme pairs in central carbon metabolism and tetrapyrroles and nucleic acids biosynthesis. Overall, genomic information is consistent with a high tolerance for oxygen that has been reported in the growth of  Cfl. aurantiacus . Genes for the chimeric photosystem, photosynthetic electron transport chain, the 3-hydroxypropionate autotrophic carbon fixation cycle, CO 2 -anaplerotic pathways, glyoxylate cycle, and sulfur reduction pathway are present. The central carbon metabolism and sulfur assimilation pathways in  Cfl. aurantiacus  are discussed. Some features of the  Cfl. aurantiacus  genome are compared with those of the  Roseiflexus castenholzii  genome.  Roseiflexus castenholzii  is a recently characterized FAP bacterium and phylogenetically closely related to  Cfl. aurantiacus . According to previous reports and the genomic information, perspectives of  Cfl. aurantiacus  in the evolution of photosynthesis are also discussed.    Conclusions  The genomic analyses presented in this report, along with previous physiological, ecological and biochemical studies, indicate that the anoxygenic phototroph  Cfl. aurantiacus  has many interesting and certain unique features in its metabolic pathways. The complete genome may also shed light on possible evolutionary connections of photosynthesis.

Complete genome sequence of the filamentous anoxygenic phototrophic bacterium Chloroflexus aurantiacus