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Ecological and temporal constraints in the evolution of bacterial genomes.

Boto L, Martínez JL - Genes (Basel) (2011)

Bottom Line: In the present article we review the differential contribution to the evolution of bacterial genomes that processes such as gene modification, gene acquisition and gene loss may have when bacteria colonize different habitats that present characteristic ecological features.In particular, we review how the different processes contribute to evolution in microbial communities, in free-living bacteria or in bacteria living in isolation.In addition, we discuss the temporal constraints in the evolution of bacterial genomes, considering bacterial evolution from the perspective of processes of short-sighted evolution and punctual acquisition of evolutionary novelties followed by long stasis periods.

View Article: PubMed Central - PubMed

Affiliation: Dpto Biodiversidad y Biología Evolutiva. Museo Nacional Ciencias Naturales. CSIC. C/JoseGutierrez Abascal 2. Madrid 28006, Spain. mcnb119@mncn.csic.es.

ABSTRACT
Studies on the experimental evolution of microorganisms, on their in vivo evolution (mainly in the case of bacteria producing chronic infections), as well as the availability of multiple full genomic sequences, are placing bacteria in the playground of evolutionary studies. In the present article we review the differential contribution to the evolution of bacterial genomes that processes such as gene modification, gene acquisition and gene loss may have when bacteria colonize different habitats that present characteristic ecological features. In particular, we review how the different processes contribute to evolution in microbial communities, in free-living bacteria or in bacteria living in isolation. In addition, we discuss the temporal constraints in the evolution of bacterial genomes, considering bacterial evolution from the perspective of processes of short-sighted evolution and punctual acquisition of evolutionary novelties followed by long stasis periods.

No MeSH data available.


Related in: MedlinePlus

Open and closed bacterial genomes. By sequencing different isolates from the same bacterial species, it is possible to distinguish between open and closed genomes. The Figure shows models of open and closed genomes based on data from [99,100]. For instance, panel a shows that after sequencing four Buchnera aphidicola isolates, sequencing a new more only provide repeated (already sequenced) genes (dotted line), indicating that this species harbors a closed genome. However, the sequence of more isolates from P. aeruginosa or from E. coli allows the increase in the number of genes. This increase is higher for E. coli (black line) than for P. aeruginosa indicating that the genome of E. coli is more open than for P. aeruginosa. As shown in panel b, presenting a very open genome might mean that the core genome is small. Black: the core genome of E. coli; Grey: the core genome of P. aeruginosa; Dotted line: the core genome of B. aphidicola. The Figure was drawn to represent the concept of open and closed genomes and is based on the data presented in [99].
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f2-genes-02-00804: Open and closed bacterial genomes. By sequencing different isolates from the same bacterial species, it is possible to distinguish between open and closed genomes. The Figure shows models of open and closed genomes based on data from [99,100]. For instance, panel a shows that after sequencing four Buchnera aphidicola isolates, sequencing a new more only provide repeated (already sequenced) genes (dotted line), indicating that this species harbors a closed genome. However, the sequence of more isolates from P. aeruginosa or from E. coli allows the increase in the number of genes. This increase is higher for E. coli (black line) than for P. aeruginosa indicating that the genome of E. coli is more open than for P. aeruginosa. As shown in panel b, presenting a very open genome might mean that the core genome is small. Black: the core genome of E. coli; Grey: the core genome of P. aeruginosa; Dotted line: the core genome of B. aphidicola. The Figure was drawn to represent the concept of open and closed genomes and is based on the data presented in [99].

Mentions: To determine the complexity of the pan-genomes, the results are analyzed using rarefaction curves (Figure 2). These curves allow the distinction between closed and open genomes [94-98]. The former are those presenting a non-asymptotic curve, which means that upon sequencing a given number of genomes, the number of novel genes does not increase. One example of closed genome is the endosymbiont Buchnera aphidicola (see the next section for a discussion of evolution in endosymbiotic bacteria). This bacterial species occupies an isolated and restricted niche that hampers its possibilities of acquiring new genes and the sequence of four strains has shown that any novel isolate to be sequenced would not contain any different gene to those that have already been found in analyed genomes.


Ecological and temporal constraints in the evolution of bacterial genomes.

Boto L, Martínez JL - Genes (Basel) (2011)

Open and closed bacterial genomes. By sequencing different isolates from the same bacterial species, it is possible to distinguish between open and closed genomes. The Figure shows models of open and closed genomes based on data from [99,100]. For instance, panel a shows that after sequencing four Buchnera aphidicola isolates, sequencing a new more only provide repeated (already sequenced) genes (dotted line), indicating that this species harbors a closed genome. However, the sequence of more isolates from P. aeruginosa or from E. coli allows the increase in the number of genes. This increase is higher for E. coli (black line) than for P. aeruginosa indicating that the genome of E. coli is more open than for P. aeruginosa. As shown in panel b, presenting a very open genome might mean that the core genome is small. Black: the core genome of E. coli; Grey: the core genome of P. aeruginosa; Dotted line: the core genome of B. aphidicola. The Figure was drawn to represent the concept of open and closed genomes and is based on the data presented in [99].
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3927597&req=5

f2-genes-02-00804: Open and closed bacterial genomes. By sequencing different isolates from the same bacterial species, it is possible to distinguish between open and closed genomes. The Figure shows models of open and closed genomes based on data from [99,100]. For instance, panel a shows that after sequencing four Buchnera aphidicola isolates, sequencing a new more only provide repeated (already sequenced) genes (dotted line), indicating that this species harbors a closed genome. However, the sequence of more isolates from P. aeruginosa or from E. coli allows the increase in the number of genes. This increase is higher for E. coli (black line) than for P. aeruginosa indicating that the genome of E. coli is more open than for P. aeruginosa. As shown in panel b, presenting a very open genome might mean that the core genome is small. Black: the core genome of E. coli; Grey: the core genome of P. aeruginosa; Dotted line: the core genome of B. aphidicola. The Figure was drawn to represent the concept of open and closed genomes and is based on the data presented in [99].
Mentions: To determine the complexity of the pan-genomes, the results are analyzed using rarefaction curves (Figure 2). These curves allow the distinction between closed and open genomes [94-98]. The former are those presenting a non-asymptotic curve, which means that upon sequencing a given number of genomes, the number of novel genes does not increase. One example of closed genome is the endosymbiont Buchnera aphidicola (see the next section for a discussion of evolution in endosymbiotic bacteria). This bacterial species occupies an isolated and restricted niche that hampers its possibilities of acquiring new genes and the sequence of four strains has shown that any novel isolate to be sequenced would not contain any different gene to those that have already been found in analyed genomes.

Bottom Line: In the present article we review the differential contribution to the evolution of bacterial genomes that processes such as gene modification, gene acquisition and gene loss may have when bacteria colonize different habitats that present characteristic ecological features.In particular, we review how the different processes contribute to evolution in microbial communities, in free-living bacteria or in bacteria living in isolation.In addition, we discuss the temporal constraints in the evolution of bacterial genomes, considering bacterial evolution from the perspective of processes of short-sighted evolution and punctual acquisition of evolutionary novelties followed by long stasis periods.

View Article: PubMed Central - PubMed

Affiliation: Dpto Biodiversidad y Biología Evolutiva. Museo Nacional Ciencias Naturales. CSIC. C/JoseGutierrez Abascal 2. Madrid 28006, Spain. mcnb119@mncn.csic.es.

ABSTRACT
Studies on the experimental evolution of microorganisms, on their in vivo evolution (mainly in the case of bacteria producing chronic infections), as well as the availability of multiple full genomic sequences, are placing bacteria in the playground of evolutionary studies. In the present article we review the differential contribution to the evolution of bacterial genomes that processes such as gene modification, gene acquisition and gene loss may have when bacteria colonize different habitats that present characteristic ecological features. In particular, we review how the different processes contribute to evolution in microbial communities, in free-living bacteria or in bacteria living in isolation. In addition, we discuss the temporal constraints in the evolution of bacterial genomes, considering bacterial evolution from the perspective of processes of short-sighted evolution and punctual acquisition of evolutionary novelties followed by long stasis periods.

No MeSH data available.


Related in: MedlinePlus