Abstract
BackgroundRhodobacter sphaeroides 2.4.1 is a metabolically versatile organism that belongs to α-3 subdivision of Proteobacteria. The present study was to identify the extent, history, and role of gene duplications in R. sphaeroides 2.4.1, an organism that possesses two chromosomes.ResultsA protein similarity search (BLASTP) identified 1247 orfs (~29.4% of the total protein coding orfs) that are present in 2 or more copies, 37.5% (234 gene-pairs) of which exist in duplicate copies. The distribution of the duplicate gene-pairs in all Clusters of Orthologous Groups (COGs) differed significantly when compared to the COG distribution across the whole genome. Location plots revealed clusters of gene duplications that possessed the same COG classification. Phylogenetic analyses were performed to determine a tree topology predicting either a Type-A or Type-B phylogenetic relationship. A Type-A phylogenetic relationship shows that a copy of the protein-pair matches more with an ortholog from a species closely related to R. sphaeroides while a Type-B relationship predicts the highest match between both copies of the R. sphaeroides protein-pair. The results revealed that ~77% of the proteins exhibited a Type-A phylogenetic relationship demonstrating the ancient origin of these gene duplications. Additional analyses on three other strains of R. sphaeroides revealed varying levels of gene loss and retention in these strains. Also, analyses on common gene pairs among the four strains revealed that these genes experience similar functional constraints and undergo purifying selection.ConclusionsAlthough the results suggest that the level of gene duplication in organisms with complex genome structuring (more than one chromosome) seems to be not markedly different from that in organisms with only a single chromosome, these duplications may have aided in genome reorganization in this group of eubacteria prior to the formation of R. sphaeroides as gene duplications involved in specialized functions might have contributed to complex genomic development.
Highlights
Rhodobacter sphaeroides 2.4.1 is a metabolically versatile organism that belongs to a-3 subdivision of Proteobacteria
Bacterial species continue to encounter different ecological niches, and their genome size increases by acquiring habitat relevant genes by horizontal gene transfer [16,17,18] and gene duplication [19,20], which together play a major role in the evolution of both genome size and complexity
Analyses on over 100 fully sequenced eubacterial and archaeal genomes have revealed a great extent of DNA sequence duplications [25], it remains unclear whether the expansions of genome size and complexity were essential for adaptive phenotypic diversification
Summary
Rhodobacter sphaeroides 2.4.1 is a metabolically versatile organism that belongs to a-3 subdivision of Proteobacteria. The present study was to identify the extent, history, and role of gene duplications in R. sphaeroides 2.4.1, an organism that possesses two chromosomes. Rhodobacter sphaeroides 2.4.1, a purple nonsulfur photosynthetic eubacterium, belongs to the a-3 subgroup of Proteobacteria [1,2], members of which display an array of metabolic capabilities in the assembly and regulation of metabolic functions [3], electron transport [4,5,6], bioremediation [7], and tetrapyrrole biosynthesis [8,9]. Analyses on over 100 fully sequenced eubacterial and archaeal genomes have revealed a great extent of DNA sequence duplications [25], it remains unclear whether the expansions of genome size and complexity were essential for adaptive phenotypic diversification
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