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Dynamics of gene duplication in the genomes of chlorophyll d-producing cyanobacteria: implications for the ecological niche.
- Source :
-
Genome biology and evolution [Genome Biol Evol] 2011; Vol. 3, pp. 601-13. Date of Electronic Publication: 2011 Jun 21. - Publication Year :
- 2011
-
Abstract
- Gene duplication may be an important mechanism for the evolution of new functions and for the adaptive modulation of gene expression via dosage effects. Here, we analyzed the fate of gene duplicates for two strains of a novel group of cyanobacteria (genus Acaryochloris) that produces the far-red light absorbing chlorophyll d as its main photosynthetic pigment. The genomes of both strains contain an unusually high number of gene duplicates for bacteria. As has been observed for eukaryotic genomes, we find that the demography of gene duplicates can be well modeled by a birth-death process. Most duplicated Acaryochloris genes are of comparatively recent origin, are strain-specific, and tend to be located on different genetic elements. Analyses of selection on duplicates of different divergence classes suggest that a minority of paralogs exhibit near neutral evolutionary dynamics immediately following duplication but that most duplicate pairs (including those which have been retained for long periods) are under strong purifying selection against amino acid change. The likelihood of duplicate retention varied among gene functional classes, and the pronounced differences between strains in the pool of retained recent duplicates likely reflects differences in the nutrient status and other characteristics of their respective environments. We conclude that most duplicates are quickly purged from Acaryochloris genomes and that those which are retained likely make important contributions to organism ecology by conferring fitness benefits via gene dosage effects. The mechanism of enhanced duplication may involve homologous recombination between genetic elements mediated by paralogous copies of recA.
- Subjects :
- Amino Acid Sequence
Chromosomes, Bacterial genetics
Contig Mapping
Cyanobacteria classification
Cyanobacteria metabolism
DNA, Bacterial chemistry
DNA, Bacterial genetics
Ecosystem
Evolution, Molecular
Genes, Bacterial genetics
Genes, Duplicate genetics
Genetic Variation
Molecular Sequence Data
Open Reading Frames genetics
Phylogeny
Selection, Genetic
Sequence Analysis, DNA
Sequence Homology, Amino Acid
Species Specificity
Chlorophyll biosynthesis
Cyanobacteria genetics
Gene Duplication
Genome, Bacterial genetics
Subjects
Details
- Language :
- English
- ISSN :
- 1759-6653
- Volume :
- 3
- Database :
- MEDLINE
- Journal :
- Genome biology and evolution
- Publication Type :
- Academic Journal
- Accession number :
- 21697100
- Full Text :
- https://doi.org/10.1093/gbe/evr060