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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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Phylogenetic relationship and protein clusters of 12 genomes from the order Legionellales. (A) The phylogenetic tree was inferred using maximum likelihood from a concatenated alignment of 285 single copy orthologous genes. The numbers on each node represent the support of 1,000 bootstrap replicates. (B) Venn diagram depicting numbers of protein clusters in five specified groups or genomes, Rg, Rickettsiella grylli; 5 Cb, All 5 C. burnetii genomes; 4 Lb, all four Legionella genomes. *includes both clusters and single proteins not found in any cluster. (C) A comparison between COG assignment for coding genes (green) and pseudogenes (blue) found in CRt. A: RNA processing and modification; J: translation, ribosomal structure and biogenesis; K: transcription; L: replication, recombination, and repair; C: energy production and conversion; M: cell wall/membrane biogenesis; D: cell cycle control, cell division; F: nucleotide transport and metabolism; H: coenzyme transport and metabolism; G: carbohydrate transport and metabolism; O: posttranslational modification, protein turnover, and chaperones; U: intracellular trafficking; T: signal transduction mechanisms; I: lipid transport and metabolism; V: defense mechanisms; P: inorganic ion transport and metabolism; Q: secondary metabolites biosynthesis, transport, and catabolism; N: cell motility; R: general function predicted only; S: function unknown; X: not assigned.
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evv108-F1: Phylogenetic relationship and protein clusters of 12 genomes from the order Legionellales. (A) The phylogenetic tree was inferred using maximum likelihood from a concatenated alignment of 285 single copy orthologous genes. The numbers on each node represent the support of 1,000 bootstrap replicates. (B) Venn diagram depicting numbers of protein clusters in five specified groups or genomes, Rg, Rickettsiella grylli; 5 Cb, All 5 C. burnetii genomes; 4 Lb, all four Legionella genomes. *includes both clusters and single proteins not found in any cluster. (C) A comparison between COG assignment for coding genes (green) and pseudogenes (blue) found in CRt. A: RNA processing and modification; J: translation, ribosomal structure and biogenesis; K: transcription; L: replication, recombination, and repair; C: energy production and conversion; M: cell wall/membrane biogenesis; D: cell cycle control, cell division; F: nucleotide transport and metabolism; H: coenzyme transport and metabolism; G: carbohydrate transport and metabolism; O: posttranslational modification, protein turnover, and chaperones; U: intracellular trafficking; T: signal transduction mechanisms; I: lipid transport and metabolism; V: defense mechanisms; P: inorganic ion transport and metabolism; Q: secondary metabolites biosynthesis, transport, and catabolism; N: cell motility; R: general function predicted only; S: function unknown; X: not assigned.

Mentions: To investigate the dynamics of gene loss and gain in the CRt genome, clustering of orthologous proteins was performed using the proteomes of CRt and 11 other Legionellales and 7 outgroup species. A robust phylogeny created based on the 285 single copy orthologs found in all the species clearly shows the monophyletic relationship between CRt, CLEAA, and C. burnetii, to the exclusion of Rickettsiella (fig. 1A) and confirms that CRt is indeed a species in the genus Coxiella. The two tick symbionts, CRt and CLEAA, group together to form a monophyletic clade, although with CLEAA on a much longer branch than CRt indicating a faster rate of evolution in this symbiont.Fig. 1.—


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)

Phylogenetic relationship and protein clusters of 12 genomes from the order Legionellales. (A) The phylogenetic tree was inferred using maximum likelihood from a concatenated alignment of 285 single copy orthologous genes. The numbers on each node represent the support of 1,000 bootstrap replicates. (B) Venn diagram depicting numbers of protein clusters in five specified groups or genomes, Rg, Rickettsiella grylli; 5 Cb, All 5 C. burnetii genomes; 4 Lb, all four Legionella genomes. *includes both clusters and single proteins not found in any cluster. (C) A comparison between COG assignment for coding genes (green) and pseudogenes (blue) found in CRt. A: RNA processing and modification; J: translation, ribosomal structure and biogenesis; K: transcription; L: replication, recombination, and repair; C: energy production and conversion; M: cell wall/membrane biogenesis; D: cell cycle control, cell division; F: nucleotide transport and metabolism; H: coenzyme transport and metabolism; G: carbohydrate transport and metabolism; O: posttranslational modification, protein turnover, and chaperones; U: intracellular trafficking; T: signal transduction mechanisms; I: lipid transport and metabolism; V: defense mechanisms; P: inorganic ion transport and metabolism; Q: secondary metabolites biosynthesis, transport, and catabolism; N: cell motility; R: general function predicted only; S: function unknown; X: not assigned.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

evv108-F1: Phylogenetic relationship and protein clusters of 12 genomes from the order Legionellales. (A) The phylogenetic tree was inferred using maximum likelihood from a concatenated alignment of 285 single copy orthologous genes. The numbers on each node represent the support of 1,000 bootstrap replicates. (B) Venn diagram depicting numbers of protein clusters in five specified groups or genomes, Rg, Rickettsiella grylli; 5 Cb, All 5 C. burnetii genomes; 4 Lb, all four Legionella genomes. *includes both clusters and single proteins not found in any cluster. (C) A comparison between COG assignment for coding genes (green) and pseudogenes (blue) found in CRt. A: RNA processing and modification; J: translation, ribosomal structure and biogenesis; K: transcription; L: replication, recombination, and repair; C: energy production and conversion; M: cell wall/membrane biogenesis; D: cell cycle control, cell division; F: nucleotide transport and metabolism; H: coenzyme transport and metabolism; G: carbohydrate transport and metabolism; O: posttranslational modification, protein turnover, and chaperones; U: intracellular trafficking; T: signal transduction mechanisms; I: lipid transport and metabolism; V: defense mechanisms; P: inorganic ion transport and metabolism; Q: secondary metabolites biosynthesis, transport, and catabolism; N: cell motility; R: general function predicted only; S: function unknown; X: not assigned.
Mentions: To investigate the dynamics of gene loss and gain in the CRt genome, clustering of orthologous proteins was performed using the proteomes of CRt and 11 other Legionellales and 7 outgroup species. A robust phylogeny created based on the 285 single copy orthologs found in all the species clearly shows the monophyletic relationship between CRt, CLEAA, and C. burnetii, to the exclusion of Rickettsiella (fig. 1A) and confirms that CRt is indeed a species in the genus Coxiella. The two tick symbionts, CRt and CLEAA, group together to form a monophyletic clade, although with CLEAA on a much longer branch than CRt indicating a faster rate of evolution in this symbiont.Fig. 1.—

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