Accelerated evolution associated with genome reduction in a free-living prokaryote

@article{Dufresne2004AcceleratedEA,
  title={Accelerated evolution associated with genome reduction in a free-living prokaryote},
  author={Alexis Dufresne and Laurence Garczarek and Fr{\'e}d{\'e}ric Partensky},
  journal={Genome Biology},
  year={2004},
  volume={6},
  pages={R14 - R14}
}
BackgroundThree complete genomes of Prochlorococcus species, the smallest and most abundant photosynthetic organism in the ocean, have recently been published. Comparative genome analyses reveal that genome shrinkage has occurred within this genus, associated with a sharp reduction in G+C content. As all examples of genome reduction characterized so far have been restricted to endosymbionts or pathogens, with a host-dependent lifestyle, the observed genome reduction in Prochlorococcus is the… 

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References

SHOWING 1-10 OF 54 REFERENCES

The process of genome shrinkage in the obligate symbiont Buchnera aphidicola

TLDR
The most plausible interpretation of this reconstruction is that Buchnera lost many genes through the fixation of large deletions soon after the acquisition of an obligate endosymbiotic lifestyle, suggesting that final genome composition may be partly the chance outcome of initial deletions and that neighboring genes influence the likelihood of loss of particular genes and pathways.

Accelerated evolution and Muller's rachet in endosymbiotic bacteria.

  • N. Moran
  • Biology
    Proceedings of the National Academy of Sciences of the United States of America
  • 1996
TLDR
Polypeptides for all Buchnera genes analyzed have accumulated amino acids with codon families rich in A+T, supporting the hypothesis that substitutions are deleterious in terms of polypeptide function, and the observation that the speedup is concentrated at nonsynonymous sites is contradicted.

The genome of a motile marine Synechococcus

TLDR
The genome of WH8102 seems to have been greatly influenced by horizontal gene transfer, partially through phages, and is more of a generalist than two related marine cyanobacteria.

Tracing the evolution of gene loss in obligate bacterial symbionts.

  • N. Moran
  • Biology
    Current opinion in microbiology
  • 2003

Genome divergence in two Prochlorococcus ecotypes reflects oceanic niche differentiation

TLDR
The genomes of two Prochlorococcus strains that span the largest evolutionary distance within the Pro chlorococcus lineage are compared and reveal dynamic genomes that are constantly changing in response to myriad selection pressures.

Genome sequence of the cyanobacterium Prochlorococcus marinus SS120, a nearly minimal oxyphototrophic genome

  • A. DufresneM. Salanoubat W. Hess
  • Biology, Environmental Science
    Proceedings of the National Academy of Sciences of the United States of America
  • 2003
TLDR
The genome of P. marinus SS120 is one of the two smallest genomes of a photosynthetic organism known to date and lacks many genes that are involved in photosynthesis, DNA repair, solute uptake, intermediary metabolism, motility, phototaxis, and other functions that are conserved among other cyanobacteria.

Reductive genome evolution in Buchnera aphidicola

TLDR
A computational study of protein folding predicts that proteins in Buchnera, as well as proteins of other intracellular bacteria, are generally characterized by smaller folding efficiency compared with proteins of free living bacteria.

Evolution in bacteria: Evidence for a universal substitution rate in cellular genomes

TLDR
A temporal scale for bacterial evolution is constructed by tying ecological events that took place at known times in the geological past to specific branch points in the genealogical tree relating the 16S ribosomal RNAs of eubacteria, mitochondria, and chloroplasts to specific branches in the bacterial tree.

Deleterious mutations destabilize ribosomal RNA in endosymbiotic bacteria.

  • J. D. LambertN. Moran
  • Biology
    Proceedings of the National Academy of Sciences of the United States of America
  • 1998
TLDR
It is shown that several independently derived insect endosymbionts, each with a long history of maternal transmission, have accumulated destabilizing base substitutions in the highly conserved 16S rRNA, and that decreased ribosomal stability has evolved separately in each endosYmbiont lineage.

Sequencing and analysis of bacterial genomes

...