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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: 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.

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Estimation of deletion effects from 1,000 perturbed replicates. Left: Distribution of artificial deletions observed after introducing simulated deletions. The number of inferred deletions (left y axis) is calculated as the number of deletions inferred minus the number of deletions inferred for the original data set. The boxplot whisker range includes the outlier points. Middle: Artificial ODEs are present in the perturbed data set and not present in the original data set (see Materials and Methods for details). Absent events are present in the original data set and missing in the perturbed data set. Right: Ratio of mean number of artificial ODEs to deletion events. The median of each line is given as a thicker horizontal line. For comparison, the ratio from the original data set is shown. For the remaining E. coli data sets, see supplementary figure S3, Supplementary Material online.
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evv113-F6: Estimation of deletion effects from 1,000 perturbed replicates. Left: Distribution of artificial deletions observed after introducing simulated deletions. The number of inferred deletions (left y axis) is calculated as the number of deletions inferred minus the number of deletions inferred for the original data set. The boxplot whisker range includes the outlier points. Middle: Artificial ODEs are present in the perturbed data set and not present in the original data set (see Materials and Methods for details). Absent events are present in the original data set and missing in the perturbed data set. Right: Ratio of mean number of artificial ODEs to deletion events. The median of each line is given as a thicker horizontal line. For comparison, the ratio from the original data set is shown. For the remaining E. coli data sets, see supplementary figure S3, Supplementary Material online.

Mentions: The observed stable ratios can be the result of either a constant rate of deletions and recombination events or a constant rate of deletions and the ensuing proximal deletions. To distinguish between these two alternatives, we performed additional perturbations of the original data sets. Simulated deletions are introduced into the data sets where the number of successive spacers being deleted is randomly chosen from the observed distribution of deletion length in the respective data set (supplementary table S1, Supplementary Material online). We define artificial deletions as the deletions that are inferred in the data sets following the perturbation. This analysis reveals that increasing the number of simulated deletions in the data set results in an increased number of artificial deletions (fig. 6). However, only a minority of the simulated deletions is detectable, with a ratio of artificial to simulated deletions ranging from 0.12 (S. agalactiae) to 0.3 (S. thermophilus) (fig. 6 and table 3; supplementary fig. S3, Supplementary Material online).Fig. 6.—


The Contribution of Genetic Recombination to CRISPR Array Evolution.

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

Estimation of deletion effects from 1,000 perturbed replicates. Left: Distribution of artificial deletions observed after introducing simulated deletions. The number of inferred deletions (left y axis) is calculated as the number of deletions inferred minus the number of deletions inferred for the original data set. The boxplot whisker range includes the outlier points. Middle: Artificial ODEs are present in the perturbed data set and not present in the original data set (see Materials and Methods for details). Absent events are present in the original data set and missing in the perturbed data set. Right: Ratio of mean number of artificial ODEs to deletion events. The median of each line is given as a thicker horizontal line. For comparison, the ratio from the original data set is shown. For the remaining E. coli data sets, see supplementary figure S3, Supplementary Material online.
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Related In: Results  -  Collection

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evv113-F6: Estimation of deletion effects from 1,000 perturbed replicates. Left: Distribution of artificial deletions observed after introducing simulated deletions. The number of inferred deletions (left y axis) is calculated as the number of deletions inferred minus the number of deletions inferred for the original data set. The boxplot whisker range includes the outlier points. Middle: Artificial ODEs are present in the perturbed data set and not present in the original data set (see Materials and Methods for details). Absent events are present in the original data set and missing in the perturbed data set. Right: Ratio of mean number of artificial ODEs to deletion events. The median of each line is given as a thicker horizontal line. For comparison, the ratio from the original data set is shown. For the remaining E. coli data sets, see supplementary figure S3, Supplementary Material online.
Mentions: The observed stable ratios can be the result of either a constant rate of deletions and recombination events or a constant rate of deletions and the ensuing proximal deletions. To distinguish between these two alternatives, we performed additional perturbations of the original data sets. Simulated deletions are introduced into the data sets where the number of successive spacers being deleted is randomly chosen from the observed distribution of deletion length in the respective data set (supplementary table S1, Supplementary Material online). We define artificial deletions as the deletions that are inferred in the data sets following the perturbation. This analysis reveals that increasing the number of simulated deletions in the data set results in an increased number of artificial deletions (fig. 6). However, only a minority of the simulated deletions is detectable, with a ratio of artificial to simulated deletions ranging from 0.12 (S. agalactiae) to 0.3 (S. thermophilus) (fig. 6 and table 3; supplementary fig. S3, Supplementary Material online).Fig. 6.—

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