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

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 (ATCC 17019 and ATCC 17025) 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 among their chromosome-specific DNA sequences. In addition, the exact intra- and interchromosomal DNA duplications were analyzed using Mummer. Genome analyses employing these two independent approaches revealed that strain ATCC 17025 diverged considerably from the other two strains, 2.4.1 and ATCC 17029, and that the 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 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 suggest the involvement of CII in the evolution of strain-specific genomic rearrangements, perhaps requiring strains to adapt in specialized niches.

FIG. 1.

Mauve representation of the total of 382 LCBs observed between concatenated chromosomal sequences of the three strains of Rhodobacter sphaeroides, 2.4.1, ATCC 17029, and ATCC 17025, at a minimum weight of 45. Black vertical bars indicate concatenated chromosomal boundaries. The R. sphaeroides 2.4.1 DNA sequence given on the forward strand is the reference against which the sequences of the other two strains were aligned and compared. LCBs placed under the vertical bars represent the reverse complement of the reference DNA sequence. The Mauve display window provides viewers the ability to zoom in on regions of interest and examine the local rearrangements of DNA sequences, where connecting lines between genomes identify the locations of each orthologous LCB in all three genomes. Unmatched regions within an LCB indicate the presence of strain-specific sequence. Each sequential colored block represents homologous backbone DNA sequence without rearrangements. ATCC 17025 has undergone more chromosomal rearrangements than the other two strains.