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Evolutionary relationships among Chlamydophila abortus variant strains inferred by rRNA secondary structure-based phylogeny.

Siarkou VI, Stamatakis A, Kappas I, Hadweh P, Laroucau K - PLoS ONE (2011)

Bottom Line: Secondary structure analysis revealed the presence of transitional single nucleotide variations (SNVs), two of which occurred in loops, while seven in stem regions that did not result in compensatory substitutions.Both lineages were found to be descendants of a common ancestor with the Prk/Daruma C. psittaci variant.The current rRNA secondary structure-based analysis and phylogenetic inference reveal new insights into how these two C. abortus lineages have differentiated during their evolution.

View Article: PubMed Central - PubMed

Affiliation: Laboratory of Microbiology and Infectious Diseases, Faculty of Veterinary Medicine, Aristotle University of Thessaloniki, Thessaloniki, Greece. vickysi@vet.auth.gr

ABSTRACT
The evolutionary relationships among known Chlamydophila abortus variant strains including the LLG and POS, previously identified as being highly distinct, were investigated based on rRNA secondary structure information. PCR-amplified overlapping fragments of the 16S, 16S-23S intergenic spacer (IS), and 23S domain I rRNAs were subjected to cloning and sequencing. Secondary structure analysis revealed the presence of transitional single nucleotide variations (SNVs), two of which occurred in loops, while seven in stem regions that did not result in compensatory substitutions. Notably, only two SNVs, in 16S and 23S, occurred within evolutionary variable regions. Maximum likelihood and Bayesian phylogeny reconstructions revealed that C. abortus strains could be regarded as representing two distinct lineages, one including the "classical" C. abortus strains and the other the "LLG/POS variant", with the type strain B577(T) possibly representing an intermediate of the two lineages. The two C. abortus lineages shared three unique (apomorphic) characters in the 23S domain I and 16S-23S IS, but interestingly lacked synapomorphies in the 16S rRNA. The two lineages could be distinguished on the basis of eight positions; four of these comprised residues that appeared to be signature or unique for the "classical" lineage, while three were unique for the "LLG/POS variant". The U277 (E. coli numbering) signature character, corresponding to a highly conserved residue of the 16S molecule, and the unique G681 residue, conserved in a functionally strategic region also of 16S, are the most pronounced attributes (autapomorphies) of the "classical" and the "LLG/POS variant" lineages, respectively. Both lineages were found to be descendants of a common ancestor with the Prk/Daruma C. psittaci variant. Compared with the "classical", the "LLG/POS variant" lineage has retained more ancestral features. The current rRNA secondary structure-based analysis and phylogenetic inference reveal new insights into how these two C. abortus lineages have differentiated during their evolution.

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Best-scoring maximum likelihood trees based on 16S (A), 23S domain I (B), and 16S-23S IS (C) rRNA chlamydial sequences.Full-length sequences of C. abortus variant strains and representatives from other Chlamydiaceae species were used. The type strains of other families within the order Chlamydiales were included as outgroups in the 16S and 23S rRNA trees. The trees were reconstructed using RAxML 7.2.6 [38]. The 16S and 23S rRNA trees were generated on the basis of secondary structure alignments created by SINA (SILVA SSU and LSU rRNA database project; [33]) while the 16S-23S IS tree was based on primary structure alignment computed using CLUSTAL X 1.83 [32]. Numbers on branches are support values to clusters on the right of them. Maximum likelihood bootstrap percentages and Bayesian posterior probabilities are included for clades that were consistently recovered using both phylogenetic methods (otherwise only bootstrap values are shown). Bayesian consensus trees are available as supporting material (Figure S5). Accession numbers for sequences retrieved from GenBank as well as for the sequences generated in this study are shown in parentheses. The mark//indicates that branches were shortened for visualization purposes.
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pone-0019813-g001: Best-scoring maximum likelihood trees based on 16S (A), 23S domain I (B), and 16S-23S IS (C) rRNA chlamydial sequences.Full-length sequences of C. abortus variant strains and representatives from other Chlamydiaceae species were used. The type strains of other families within the order Chlamydiales were included as outgroups in the 16S and 23S rRNA trees. The trees were reconstructed using RAxML 7.2.6 [38]. The 16S and 23S rRNA trees were generated on the basis of secondary structure alignments created by SINA (SILVA SSU and LSU rRNA database project; [33]) while the 16S-23S IS tree was based on primary structure alignment computed using CLUSTAL X 1.83 [32]. Numbers on branches are support values to clusters on the right of them. Maximum likelihood bootstrap percentages and Bayesian posterior probabilities are included for clades that were consistently recovered using both phylogenetic methods (otherwise only bootstrap values are shown). Bayesian consensus trees are available as supporting material (Figure S5). Accession numbers for sequences retrieved from GenBank as well as for the sequences generated in this study are shown in parentheses. The mark//indicates that branches were shortened for visualization purposes.

Mentions: Phylogenetic trees were constructed using a subset of 27 or 26 full-length sequence alignments of the 16S, 23S domain I, and 16S-23S IS rRNAs. In particular, all available C. abortus sequences as well as representatives (type or reference strains) from all other hitherto defined species within Chlamydiaceae, including intraspecific variants, were employed to elucidate the evolutionary relationships of the C. abortus variants. The type strains of the families Parachlamydiaceae, Waddliaceae, and Simkaniaceae, phylogenetically positioned in the order Chlamydiales, were used as outgroups in the 16S and 23S rRNA trees. These outgroups were not used in 16S-23S IS tree due to their limited sequence identity with Chlamydiaceae and therefore the difficulty to align (Figure S4A). The best-scoring likelihood trees for 16S, 23S, and 16S-23S IS inferred by RAxML under the GTR+Gamma substitution model, are shown in Figure 1 (A, B and C). Branch support values (in congruent arrangements) for each of the two different approaches used (bootstrap support values from ML analyses, BS; Bayesian posterior probabilities, PP) are also indicated.


Evolutionary relationships among Chlamydophila abortus variant strains inferred by rRNA secondary structure-based phylogeny.

Siarkou VI, Stamatakis A, Kappas I, Hadweh P, Laroucau K - PLoS ONE (2011)

Best-scoring maximum likelihood trees based on 16S (A), 23S domain I (B), and 16S-23S IS (C) rRNA chlamydial sequences.Full-length sequences of C. abortus variant strains and representatives from other Chlamydiaceae species were used. The type strains of other families within the order Chlamydiales were included as outgroups in the 16S and 23S rRNA trees. The trees were reconstructed using RAxML 7.2.6 [38]. The 16S and 23S rRNA trees were generated on the basis of secondary structure alignments created by SINA (SILVA SSU and LSU rRNA database project; [33]) while the 16S-23S IS tree was based on primary structure alignment computed using CLUSTAL X 1.83 [32]. Numbers on branches are support values to clusters on the right of them. Maximum likelihood bootstrap percentages and Bayesian posterior probabilities are included for clades that were consistently recovered using both phylogenetic methods (otherwise only bootstrap values are shown). Bayesian consensus trees are available as supporting material (Figure S5). Accession numbers for sequences retrieved from GenBank as well as for the sequences generated in this study are shown in parentheses. The mark//indicates that branches were shortened for visualization purposes.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3101216&req=5

pone-0019813-g001: Best-scoring maximum likelihood trees based on 16S (A), 23S domain I (B), and 16S-23S IS (C) rRNA chlamydial sequences.Full-length sequences of C. abortus variant strains and representatives from other Chlamydiaceae species were used. The type strains of other families within the order Chlamydiales were included as outgroups in the 16S and 23S rRNA trees. The trees were reconstructed using RAxML 7.2.6 [38]. The 16S and 23S rRNA trees were generated on the basis of secondary structure alignments created by SINA (SILVA SSU and LSU rRNA database project; [33]) while the 16S-23S IS tree was based on primary structure alignment computed using CLUSTAL X 1.83 [32]. Numbers on branches are support values to clusters on the right of them. Maximum likelihood bootstrap percentages and Bayesian posterior probabilities are included for clades that were consistently recovered using both phylogenetic methods (otherwise only bootstrap values are shown). Bayesian consensus trees are available as supporting material (Figure S5). Accession numbers for sequences retrieved from GenBank as well as for the sequences generated in this study are shown in parentheses. The mark//indicates that branches were shortened for visualization purposes.
Mentions: Phylogenetic trees were constructed using a subset of 27 or 26 full-length sequence alignments of the 16S, 23S domain I, and 16S-23S IS rRNAs. In particular, all available C. abortus sequences as well as representatives (type or reference strains) from all other hitherto defined species within Chlamydiaceae, including intraspecific variants, were employed to elucidate the evolutionary relationships of the C. abortus variants. The type strains of the families Parachlamydiaceae, Waddliaceae, and Simkaniaceae, phylogenetically positioned in the order Chlamydiales, were used as outgroups in the 16S and 23S rRNA trees. These outgroups were not used in 16S-23S IS tree due to their limited sequence identity with Chlamydiaceae and therefore the difficulty to align (Figure S4A). The best-scoring likelihood trees for 16S, 23S, and 16S-23S IS inferred by RAxML under the GTR+Gamma substitution model, are shown in Figure 1 (A, B and C). Branch support values (in congruent arrangements) for each of the two different approaches used (bootstrap support values from ML analyses, BS; Bayesian posterior probabilities, PP) are also indicated.

Bottom Line: Secondary structure analysis revealed the presence of transitional single nucleotide variations (SNVs), two of which occurred in loops, while seven in stem regions that did not result in compensatory substitutions.Both lineages were found to be descendants of a common ancestor with the Prk/Daruma C. psittaci variant.The current rRNA secondary structure-based analysis and phylogenetic inference reveal new insights into how these two C. abortus lineages have differentiated during their evolution.

View Article: PubMed Central - PubMed

Affiliation: Laboratory of Microbiology and Infectious Diseases, Faculty of Veterinary Medicine, Aristotle University of Thessaloniki, Thessaloniki, Greece. vickysi@vet.auth.gr

ABSTRACT
The evolutionary relationships among known Chlamydophila abortus variant strains including the LLG and POS, previously identified as being highly distinct, were investigated based on rRNA secondary structure information. PCR-amplified overlapping fragments of the 16S, 16S-23S intergenic spacer (IS), and 23S domain I rRNAs were subjected to cloning and sequencing. Secondary structure analysis revealed the presence of transitional single nucleotide variations (SNVs), two of which occurred in loops, while seven in stem regions that did not result in compensatory substitutions. Notably, only two SNVs, in 16S and 23S, occurred within evolutionary variable regions. Maximum likelihood and Bayesian phylogeny reconstructions revealed that C. abortus strains could be regarded as representing two distinct lineages, one including the "classical" C. abortus strains and the other the "LLG/POS variant", with the type strain B577(T) possibly representing an intermediate of the two lineages. The two C. abortus lineages shared three unique (apomorphic) characters in the 23S domain I and 16S-23S IS, but interestingly lacked synapomorphies in the 16S rRNA. The two lineages could be distinguished on the basis of eight positions; four of these comprised residues that appeared to be signature or unique for the "classical" lineage, while three were unique for the "LLG/POS variant". The U277 (E. coli numbering) signature character, corresponding to a highly conserved residue of the 16S molecule, and the unique G681 residue, conserved in a functionally strategic region also of 16S, are the most pronounced attributes (autapomorphies) of the "classical" and the "LLG/POS variant" lineages, respectively. Both lineages were found to be descendants of a common ancestor with the Prk/Daruma C. psittaci variant. Compared with the "classical", the "LLG/POS variant" lineage has retained more ancestral features. The current rRNA secondary structure-based analysis and phylogenetic inference reveal new insights into how these two C. abortus lineages have differentiated during their evolution.

Show MeSH
Related in: MedlinePlus