The complex genome of Rhodobacter sphaeroides 2.4.1, composed of chromosomes I (CI) and II (CII), has been sequenced and assembled. We present data demonstrating that the R. sphaeroides genome possesses an extensive amount of exact DNA sequence duplication, 111 kb or ϳ2.7% of the total chromosomal DNA. The chromosomal DNA sequence duplications were aligned to each other by using MUMmer. Frequency and size distribution analyses of the exact DNA duplications revealed that the interchromosomal duplications occurred prior to the intrachromosomal duplications. Most of the DNA sequence duplications in the R. sphaeroides genome occurred early in species history, whereas more recent sequence duplications are rarely found. To uncover the history of gene duplications in the R. sphaeroides genome, 44 gene duplications were sampled and then analyzed for DNA sequence similarity against orthologous DNA sequences. Phylogenetic analysis revealed that ϳ80% of the total gene duplications examined displayed type A phylogenetic relationships; i.e., one copy of each member of a duplicate pair was more similar to its orthologue, found in a species closely related to R. sphaeroides, than to its duplicate, counterpart allele. The data reported here demonstrate that a massive level of gene duplications occurred prior to the origin of the R. sphaeroides 2.4.1 lineage. These findings lead to the conclusion that there is an ancient partnership between CI and CII of R. sphaeroides 2.4.1.Rhodobacter sphaeroides 2.4.1, a purple nonsulfur photosynthetic eubacterium, belongs to the ␣-3 subgroup of the Proteobacteria (40,41). This species, along with other members of the class Proteobacteria, represents one of the largest divisions within the prokaryotes (41) and comprises a large number of gram-negative bacteria. R. sphaeroides is also one of the most metabolically versatile and diverse subgroups of the ␣-3 subgroup of the Proteobacteria, which includes Rhizobium, Agrobacterium, Caulobacter, Brucella, and Rickettsia (40,41). A few examples of the metabolic diversity are the diversity in assembly and regulation of the light-harvesting apparatus, in nitrogen fixation, in carbon dioxide fixation, in hydrogen metabolism, in electron transport, in oxyanion reduction, and in tetrapyrrole biosynthesis (9,19).R. sphaeroides 2.4.1 contains one of the most complex genomes found in members of the Proteobacteria (4,18,21). This species was the first bacterial species shown to possess a complex genome consisting of two circular chromosomes, one ϳ3.0 Mbp long (chromosome I [CI]) and one ϳ0.9 Mbp long (chromosome II [CII]), and five additional endogenous replicons (36, 37). The existence of multiple chromosomes in bacteria is now no longer an exception and has been instrumental in setting aside the long-held dogma that all bacterial species have a single circular chromosome.Currently there is an extensive list of prokaryotic genomes that have been sequenced, including that of R. sphaeroides 2.4.1. As a result, R. sphaeroides is an ideal system for the study o...