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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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Genome comparison of CLEAA, CRt, and C. burnetii. Blue boxes depict protein-coding genes, green boxes represent pseudogenes, and yellow boxes indicate transposases. The regions framed in black indicate the position of the large duplicated region in CRt. Similarity between genome is shown by the gray lines, where a darker shade indicates higher similar.
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evv108-F2: Genome comparison of CLEAA, CRt, and C. burnetii. Blue boxes depict protein-coding genes, green boxes represent pseudogenes, and yellow boxes indicate transposases. The regions framed in black indicate the position of the large duplicated region in CRt. Similarity between genome is shown by the gray lines, where a darker shade indicates higher similar.

Mentions: The CRt, CLEAA, and C. burnetii RSA493 genomes were searched against each other using tBLASTx and increasing –max_hsps_per_subject to 5,000, in order to visualize most of the homologous regions between them. The output from tBLASTx was then used to generate the genome comparison maps (fig. 2 and supplementary fig. S1, Supplementary Material online) with the genoPlotR package (Guy et al. 2010). Whole-genome alignments were done using Mauve (Darling et al. 2004) with one of the copies of the large duplication in CRt masked, and the resulting permutations file was used as input for MGR (Multiple Genome Rearrangements) (Bourque and Pevzner 2002), with the circular genome setting, to infer the ancestral gene order and phylogenetic tree.


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)

Genome comparison of CLEAA, CRt, and C. burnetii. Blue boxes depict protein-coding genes, green boxes represent pseudogenes, and yellow boxes indicate transposases. The regions framed in black indicate the position of the large duplicated region in CRt. Similarity between genome is shown by the gray lines, where a darker shade indicates higher similar.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

evv108-F2: Genome comparison of CLEAA, CRt, and C. burnetii. Blue boxes depict protein-coding genes, green boxes represent pseudogenes, and yellow boxes indicate transposases. The regions framed in black indicate the position of the large duplicated region in CRt. Similarity between genome is shown by the gray lines, where a darker shade indicates higher similar.
Mentions: The CRt, CLEAA, and C. burnetii RSA493 genomes were searched against each other using tBLASTx and increasing –max_hsps_per_subject to 5,000, in order to visualize most of the homologous regions between them. The output from tBLASTx was then used to generate the genome comparison maps (fig. 2 and supplementary fig. S1, Supplementary Material online) with the genoPlotR package (Guy et al. 2010). Whole-genome alignments were done using Mauve (Darling et al. 2004) with one of the copies of the large duplication in CRt masked, and the resulting permutations file was used as input for MGR (Multiple Genome Rearrangements) (Bourque and Pevzner 2002), with the circular genome setting, to infer the ancestral gene order and phylogenetic tree.

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