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Distinctive Genome Reduction Rates Revealed by Genomic Analyses of Two Coxiella-Like Endosymbionts in Ticks.

Gottlieb Y, Lalzar I, Klasson L - Genome Biol Evol (2015)

Bottom Line: Genome reduction is a hallmark of symbiotic genomes, and the rate and patterns of gene loss associated with this process have been investigated in several different symbiotic systems.However, in long-term host-associated coevolving symbiont clades, the genome size differences between strains are normally quite small and hence patterns of large-scale genome reduction can only be inferred from distant relatives.The CRt genome is an extreme example of a symbiont genome caught in the act of genome reduction, and the comparison between CLEAA and CRt indicates that losses of particular genes early on in this process can potentially greatly influence the speed of this process.

View Article: PubMed Central - PubMed

Affiliation: Koret School of Veterinary Medicine, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel.

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Polymorphisms in the genomic data of CRt. (A) Number and type of polymorphism found in coding and noncoding parts of the genome. Ps, pseudogenes; Ig, intergenic region; Nsyn, nonsynonymous; Syn, synonymous; Fs, frameshift. (B) Histogram of minor allele variants. (C) Mutational spectrum in different genomic regions inferred from variants with a frequency less than 0.15. (D) Ts:Tv ratio for low frequency allele variants and all allele variants, and variants at 4D sites.
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evv108-F6: Polymorphisms in the genomic data of CRt. (A) Number and type of polymorphism found in coding and noncoding parts of the genome. Ps, pseudogenes; Ig, intergenic region; Nsyn, nonsynonymous; Syn, synonymous; Fs, frameshift. (B) Histogram of minor allele variants. (C) Mutational spectrum in different genomic regions inferred from variants with a frequency less than 0.15. (D) Ts:Tv ratio for low frequency allele variants and all allele variants, and variants at 4D sites.

Mentions: As expected under selection, the majority of the polymorphisms is found in pseudogenes and intergenic regions (fig. 6A). However, a total of 407 SNPs can be found in genic sequences, with a relatively equal amount generating synonymous and nonsynonymous changes (fig. 6A). In order to investigate the number of stable variants present in the sample, the allele frequency for each SNP was calculated. The frequency of minor alleles, that is, the less common variants, varies among the SNPs, but three peaks are clearly observed in a histogram of the minor allele frequencies (MAF) (fig. 6B). Given that the sample represents a pool of bacterial DNA from nine ticks and the number of bacterial cells in each tick might not have been equal, it is not possible to determine the exact number of variants based on the MAF frequencies, but a minimum of three variants must be present to explain the data. Although the SNPs with an MAF around 0.1 could indicate the presence of even more stable variants, this peak might instead represent transient mutational variants.Fig. 6.—


Distinctive Genome Reduction Rates Revealed by Genomic Analyses of Two Coxiella-Like Endosymbionts in Ticks.

Gottlieb Y, Lalzar I, Klasson L - Genome Biol Evol (2015)

Polymorphisms in the genomic data of CRt. (A) Number and type of polymorphism found in coding and noncoding parts of the genome. Ps, pseudogenes; Ig, intergenic region; Nsyn, nonsynonymous; Syn, synonymous; Fs, frameshift. (B) Histogram of minor allele variants. (C) Mutational spectrum in different genomic regions inferred from variants with a frequency less than 0.15. (D) Ts:Tv ratio for low frequency allele variants and all allele variants, and variants at 4D sites.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4494066&req=5

evv108-F6: Polymorphisms in the genomic data of CRt. (A) Number and type of polymorphism found in coding and noncoding parts of the genome. Ps, pseudogenes; Ig, intergenic region; Nsyn, nonsynonymous; Syn, synonymous; Fs, frameshift. (B) Histogram of minor allele variants. (C) Mutational spectrum in different genomic regions inferred from variants with a frequency less than 0.15. (D) Ts:Tv ratio for low frequency allele variants and all allele variants, and variants at 4D sites.
Mentions: As expected under selection, the majority of the polymorphisms is found in pseudogenes and intergenic regions (fig. 6A). However, a total of 407 SNPs can be found in genic sequences, with a relatively equal amount generating synonymous and nonsynonymous changes (fig. 6A). In order to investigate the number of stable variants present in the sample, the allele frequency for each SNP was calculated. The frequency of minor alleles, that is, the less common variants, varies among the SNPs, but three peaks are clearly observed in a histogram of the minor allele frequencies (MAF) (fig. 6B). Given that the sample represents a pool of bacterial DNA from nine ticks and the number of bacterial cells in each tick might not have been equal, it is not possible to determine the exact number of variants based on the MAF frequencies, but a minimum of three variants must be present to explain the data. Although the SNPs with an MAF around 0.1 could indicate the presence of even more stable variants, this peak might instead represent transient mutational variants.Fig. 6.—

Bottom Line: Genome reduction is a hallmark of symbiotic genomes, and the rate and patterns of gene loss associated with this process have been investigated in several different symbiotic systems.However, in long-term host-associated coevolving symbiont clades, the genome size differences between strains are normally quite small and hence patterns of large-scale genome reduction can only be inferred from distant relatives.The CRt genome is an extreme example of a symbiont genome caught in the act of genome reduction, and the comparison between CLEAA and CRt indicates that losses of particular genes early on in this process can potentially greatly influence the speed of this process.

View Article: PubMed Central - PubMed

Affiliation: Koret School of Veterinary Medicine, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel.

Show MeSH
Related in: MedlinePlus