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The Contribution of Genetic Recombination to CRISPR Array Evolution.

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

Bottom Line: CRISPR (clustered regularly interspaced short palindromic repeats) is a microbial immune system against foreign DNA.We analyze CRISPR data sets from four bacterial species: two Gammaproteobacteria species harboring CRISPR type I and two Streptococcus species harboring CRISPR type II loci.Genetic recombination has been proposed to accelerate adaptation by combining beneficial mutations that arose in independent lineages.

View Article: PubMed Central - PubMed

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

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Overview of the analysis pipeline.
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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: CRISPR (clustered regularly interspaced short palindromic repeats) is a microbial immune system against foreign DNA.We analyze CRISPR data sets from four bacterial species: two Gammaproteobacteria species harboring CRISPR type I and two Streptococcus species harboring CRISPR type II loci.Genetic recombination has been proposed to accelerate adaptation by combining beneficial mutations that arose in independent lineages.

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