title: Evolutionary constraints and expression analysis of gene duplications in Rhodobacter sphaeroides 2.4.1.
abstract: BACKGROUND
  Gene duplication is a major force that contributes to the evolution of new metabolic functions in all organisms. Rhodobacter sphaeroides 2.4.1 is a bacterium that displays a wide degree of metabolic versatility and genome complexity and therefore is a fitting model for the study of gene duplications in bacteria. A comprehensive analysis of 234 duplicate gene-pairs in R. sphaeroides was performed using structural constraint and expression analysis.
  
  
  RESULTS
  The results revealed that most gene-pairs in in-paralogs are maintained under negative selection (ω ≤  0.3), but the strength of selection differed among in-paralog gene-pairs. Although in-paralogs located on different replicons are maintained under purifying selection, the duplicated genes distributed between the primary chromosome (CI) and the second chromosome (CII) are relatively less selectively constrained than the gene-pairs located within each chromosome. The mRNA expression patterns of duplicate gene-pairs were examined through microarray analysis of this organism grown under seven different growth conditions. Results revealed that ~62% of paralogs have similar expression patterns (cosine ≥ 0.90) over all of these growth conditions, while only ~7% of paralogs are very different in their expression patterns (cosine < 0.50).
  
  
  CONCLUSIONS
  The overall findings of the study suggest that only a small proportion of paralogs contribute to the metabolic diversity and the evolution of novel metabolic functions in R. sphaeroides. In addition, the lack of relationships between structural constraints and gene-pair expression suggests that patterns of gene-pair expression are likely associated with conservation or divergence of gene-pair promoter regions and other coregulation mechanisms.
authors.affiliation: Department of Biological Sciences, Sam Houston State University, Huntsville, TX 77341, USA.
authors.forename: Anne E
authors.initials: AE
authors.lastname: Peters
authors.forename: Anish
authors.initials: A
authors.lastname: Bavishi
authors.forename: Hyuk
authors.initials: H
authors.lastname: Cho
authors.forename: Madhusudan
authors.initials: M
authors.lastname: Choudhary
mesh_terms: D005075:Biological Evolution; D002874:Chromosome Mapping; D002876:Chromosomes, Bacterial; D020440:Gene Duplication; D015870:Gene Expression; D020869:Gene Expression Profiling; D005798:Genes, Bacterial; D020131:Genes, Duplicate; D020411:Oligonucleotide Array Sequence Analysis; D011401:Promoter Regions, Genetic; D012333:RNA, Messenger / Q000235:genetics*; D012093:Replicon; D012242:Rhodobacter sphaeroides / Q000235:genetics*
chemical_list: D012333:RNA, Messenger