Limits...
The Contribution of Genetic Recombination to CRISPR Array Evolution.

Kupczok A, Landan G, Dagan T - Genome Biol Evol (2015)

Bottom Line: Genetic recombination has been proposed to accelerate adaptation by combining beneficial mutations that arose in independent lineages.However, for most species under study, we find that CRISPR evolution is shaped mainly by spacer acquisition and loss rather than recombination.Since the evolution of spacer content is characterized by a rapid turnover, it is likely that recombination is not beneficial for improving phage resistance in the strains under study, or that it cannot be detected in the resolution of intraspecies comparisons.

View Article: PubMed Central - PubMed

Affiliation: Institute of General Microbiology, Christian-Albrechts-University Kiel, Germany akupczok@ifam.uni-kiel.de.

Show MeSH

Related in: MedlinePlus

Overview of the analysis pipeline.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4524480&req=5

evv113-F2: Overview of the analysis pipeline.

Mentions: Here, we study the lateral component of CRISPR spacer evolution and estimate the frequency of recombination-mediated spacer acquisition into preexisting CRISPR loci. Lateral spacer transfer leads to changes in spacer order that can be recognized by a comparative analysis. To detect recombination events, we compare the spacer order in CRISPR arrays from multiple strains of a single species. In the absence of recombination, we expect the ordering to be conserved on the 3′ (leader-distal) end of the CRISPR array and diversified on the 5′ (leader-proximal) end. Lateral spacer transfer can introduce an additional pattern of spacer content similarity, which we term order divergence events (ODEs). These are composed of shared segments followed toward the 3′-end by diverse spacers that are termed here different segments (fig. 1). Here, we present a novel algorithm to infer ODEs in CRISPR arrays. To assess the power of our inference algorithm, we apply it to perturbations of the original data sets where additional recombination events were introduced and test its performance (fig. 2).Fig. 1.—


The Contribution of Genetic Recombination to CRISPR Array Evolution.

Kupczok A, Landan G, Dagan T - Genome Biol Evol (2015)

Overview of the analysis pipeline.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4524480&req=5

evv113-F2: Overview of the analysis pipeline.
Mentions: Here, we study the lateral component of CRISPR spacer evolution and estimate the frequency of recombination-mediated spacer acquisition into preexisting CRISPR loci. Lateral spacer transfer leads to changes in spacer order that can be recognized by a comparative analysis. To detect recombination events, we compare the spacer order in CRISPR arrays from multiple strains of a single species. In the absence of recombination, we expect the ordering to be conserved on the 3′ (leader-distal) end of the CRISPR array and diversified on the 5′ (leader-proximal) end. Lateral spacer transfer can introduce an additional pattern of spacer content similarity, which we term order divergence events (ODEs). These are composed of shared segments followed toward the 3′-end by diverse spacers that are termed here different segments (fig. 1). Here, we present a novel algorithm to infer ODEs in CRISPR arrays. To assess the power of our inference algorithm, we apply it to perturbations of the original data sets where additional recombination events were introduced and test its performance (fig. 2).Fig. 1.—

Bottom Line: Genetic recombination has been proposed to accelerate adaptation by combining beneficial mutations that arose in independent lineages.However, for most species under study, we find that CRISPR evolution is shaped mainly by spacer acquisition and loss rather than recombination.Since the evolution of spacer content is characterized by a rapid turnover, it is likely that recombination is not beneficial for improving phage resistance in the strains under study, or that it cannot be detected in the resolution of intraspecies comparisons.

View Article: PubMed Central - PubMed

Affiliation: Institute of General Microbiology, Christian-Albrechts-University Kiel, Germany akupczok@ifam.uni-kiel.de.

Show MeSH
Related in: MedlinePlus