DNA sequence duplication in Rhodobacter sphaeroides 2.4.1: evidence of an ancient partnership between chromosomes I and II

Abstract

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 approximately 2.7% 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 approximately 80% 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.

FIG. 1.

Schematic representation of chromosomal duplications within and between CI and CII. CI and CII are depicted as horizontal bars from left (5′ DNA end) to right (3′ DNA end). Connecting vertical lines represent the locations on the chromosome(s) where the sequence matches perfectly. Genes involved in flagellum biosynthesis (fl-), electron transport (nuo), chemotaxis (che), and carbon assimilation (cbb) are duplicated as gene clusters, and they are indicated by different colors.

FIG. 2.

Frequency distribution of the number of intra- and interchromosomal DNA sequence duplications. The two panels have different scales for the x and y axes.

FIG. 3.

Phylogenetic relationships of duplicated gene paralogues of R. sphaeroides and the orthologous sequences from closely related species or genera. As examples, consensus phylogenetic trees representing four gene pairs, rdxA/rdxB, hemA/hemT, pucB1/pucB2, and flhB1/flhB2, and their orthologous sequences are shown. The relationships reflect the two types of topology (type A and type B), and the strength of branching support is indicated by the bootstrap values at the nodes. Scale bars represent genetic distances.