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J. Bacteriol. doi:10.1128/JB.01498-06
Copyright (c) 2006, American Society for Microbiology and/or the Listed Authors/Institutions. All Rights Reserved.

Genome analyses of three strains of Rhodobacter sphaeroides: Evidence of rapid evolution of chromosome II

Department of Microbiology and Molecular Genetics; and Computational Genomic Section, Human Genetics Center, The University of Texas health science center, Houston, Texas 77030

^* To whom correspondence should be addressed. Email: Samuel.Kaplan{at}uth.tmc.edu.

	Abstract

Three strains of Rhodobacter sphaeroides of diverse origin have been under investigation in our laboratory for their genome complexities, including the presence of multiple chromosomes and the distribution of essential genes within their genomes. The genome of R. sphaeroides 2.4.1 has been completely sequenced and fully annotated, and now two additional strains (ATCC17019 and ATCC17025) of R. sphaeroides have been sequenced. Thus, genome comparisons have become a useful approach in determining the evolutionary relationships among different strains of R. sphaeroides. In this study, the concatenated chromosomal sequences from the three strains of R. sphaeroides were aligned, using Mauve, to examine the extent of shared DNA regions and the degree of relatedness amongst their chromosome-specific DNA sequences. In addition, the exact intra- and inter-chromosomal DNA duplications were analyzed using Mummer. Genome analyses employing these two independent approaches revealed that strain ATCC17025 diverged considerably from the other two strains, 2.4.1 and ATCC17029, and these two latter strains are more closely related to one another. Results further demonstrated that chromosome II (CII)-specific DNA sequences of R. sphaeroides have rapidly evolved while chromosome I (CI)-specific DNA sequences have remained highly conserved. Aside from the size-variation of CII of R. sphaeroides, variation in sequence lengths of the CII-shared DNA regions and their high sequence divergence among strains of R. sphaeroides suggests the involvement of CII in the evolution of strain-specific genomic rearrangements perhaps, requiring strains to adapt in specialized niches.