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Use of the Internal Transcribed Spacer (ITS) Regions to Examine Symbiont Divergence and as a Diagnostic Tool for Sodalis-Related Bacteria.

Snyder AK, Adkins KZ, Rio RV - Insects (2011)

Bottom Line: Additionally, we propose an ITS region as a diagnostic marker for the identification of additional Sodalis-allied symbionts in the field.These results expand our knowledge of informative genome regions to assess genetic divergence since splitting from the last common ancestor, of this versatile insect symbiont clade that have become increasingly recognized as valuable towards our understanding of the evolution of symbiosis.These facultative and recently associated symbionts may provide a novel source of traits adaptable to the dynamic ecologies encountered by diverse host backgrounds.

View Article: PubMed Central - PubMed

Affiliation: Department of Biology, West Virginia University, Morgantown, WV 26506, USA. asnyde19@mix.wvu.edu.

ABSTRACT
Bacteria excel in most ecological niches, including insect symbioses. A cluster of bacterial symbionts, established within a broad range of insects, share high 16S rRNA similarities with the secondary symbiont of the tsetse fly (Diptera: Glossinidae), Sodalis glossinidius. Although 16S rRNA has proven informative towards characterization of this clade, the gene is insufficient for examining recent divergence due to selective constraints. Here, we assess the application of the internal transcribed spacer (ITS) regions, specifically the ITS(glu) and ITS(ala,ile), used in conjunction with 16S rRNA to enhance the phylogenetic resolution of Sodalis-allied bacteria. The 16S rRNA + ITS regions of Sodalis and allied bacteria demonstrated significant divergence and were robust towards phylogenetic resolution. A monophyletic clade of Sodalis isolates from tsetse species, distinct from other Enterobacteriaceae, was consistently observed suggesting diversification due to host adaptation. In contrast, the phylogenetic distribution of symbionts isolated from hippoboscid flies and various Hemiptera and Coleoptera were intertwined suggesting either horizontal transfer or a recent establishment from an environmental source. Lineage splitting of Sodalis-allied bacteria into symbiotic and free-living sister groups was also observed. Additionally, we propose an ITS region as a diagnostic marker for the identification of additional Sodalis-allied symbionts in the field. These results expand our knowledge of informative genome regions to assess genetic divergence since splitting from the last common ancestor, of this versatile insect symbiont clade that have become increasingly recognized as valuable towards our understanding of the evolution of symbiosis. These facultative and recently associated symbionts may provide a novel source of traits adaptable to the dynamic ecologies encountered by diverse host backgrounds.

No MeSH data available.


Phylogenetic placement of Sodalis and related symbiotic bacteria within Gammaproteobacteria based on 16S rRNA and ITSglu concatenation. A Bayesian tree, inferred from a total of 2,467 unambiguously aligned nucleotide sites, with support values indicating Bayesian posterior probabilities (PP)/MP bootstrap (BS) is shown. PP indicated as percentage, i.e., PP = 0.95 is depicted as 95. Branches constrained with MP are shown in bold. For insect symbionts, host species are indicated. S = symbiont, SS = S-symbiont, PS = P-symbiont. Scale bar represents substitutions/site.
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f1-insects-02-00515: Phylogenetic placement of Sodalis and related symbiotic bacteria within Gammaproteobacteria based on 16S rRNA and ITSglu concatenation. A Bayesian tree, inferred from a total of 2,467 unambiguously aligned nucleotide sites, with support values indicating Bayesian posterior probabilities (PP)/MP bootstrap (BS) is shown. PP indicated as percentage, i.e., PP = 0.95 is depicted as 95. Branches constrained with MP are shown in bold. For insect symbionts, host species are indicated. S = symbiont, SS = S-symbiont, PS = P-symbiont. Scale bar represents substitutions/site.

Mentions: To determine the utility of the 16S rRNA + ITS regions as a tool for resolving relationships and understanding the degree of diversity between Sodalis and allied symbionts, NJ, MP and Bayesian phylogenetic analyses were performed. The resulting phylogenetic trees of 16S rRNA + ITSglu and 16S rRNA + ITSala,ile (Figures 1 and 2, respectively) gave substantially the same topology and were generally concordant with 16S rRNA based phylogeny [29,32], yet provided stronger resolution among the Sodalis and allied bacteria as indicated with relatively higher MP bootstrap (BS) and Bayesian posterior probability (PP) support for most nodes. Phylogenetic analyses of ITS based trees reflect the conserved nature of ITS regions within tsetse isolates (Figures 1 and 2), with both ITSglu and ITSala,ile trees containing a well-supported monophyletic nest of Sodalis isolates, distinct from other Enterobacteriaceae, and suggestive of diversification potentially attributed to tsetse host adaptation. Increased sequence divergence of ITSala,ile with Sodalis isolates from G. pallidipes and G. brevipalpis hosts was also observed, although BS and PP values were not robust at this node.


Use of the Internal Transcribed Spacer (ITS) Regions to Examine Symbiont Divergence and as a Diagnostic Tool for Sodalis-Related Bacteria.

Snyder AK, Adkins KZ, Rio RV - Insects (2011)

Phylogenetic placement of Sodalis and related symbiotic bacteria within Gammaproteobacteria based on 16S rRNA and ITSglu concatenation. A Bayesian tree, inferred from a total of 2,467 unambiguously aligned nucleotide sites, with support values indicating Bayesian posterior probabilities (PP)/MP bootstrap (BS) is shown. PP indicated as percentage, i.e., PP = 0.95 is depicted as 95. Branches constrained with MP are shown in bold. For insect symbionts, host species are indicated. S = symbiont, SS = S-symbiont, PS = P-symbiont. Scale bar represents substitutions/site.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4553445&req=5

f1-insects-02-00515: Phylogenetic placement of Sodalis and related symbiotic bacteria within Gammaproteobacteria based on 16S rRNA and ITSglu concatenation. A Bayesian tree, inferred from a total of 2,467 unambiguously aligned nucleotide sites, with support values indicating Bayesian posterior probabilities (PP)/MP bootstrap (BS) is shown. PP indicated as percentage, i.e., PP = 0.95 is depicted as 95. Branches constrained with MP are shown in bold. For insect symbionts, host species are indicated. S = symbiont, SS = S-symbiont, PS = P-symbiont. Scale bar represents substitutions/site.
Mentions: To determine the utility of the 16S rRNA + ITS regions as a tool for resolving relationships and understanding the degree of diversity between Sodalis and allied symbionts, NJ, MP and Bayesian phylogenetic analyses were performed. The resulting phylogenetic trees of 16S rRNA + ITSglu and 16S rRNA + ITSala,ile (Figures 1 and 2, respectively) gave substantially the same topology and were generally concordant with 16S rRNA based phylogeny [29,32], yet provided stronger resolution among the Sodalis and allied bacteria as indicated with relatively higher MP bootstrap (BS) and Bayesian posterior probability (PP) support for most nodes. Phylogenetic analyses of ITS based trees reflect the conserved nature of ITS regions within tsetse isolates (Figures 1 and 2), with both ITSglu and ITSala,ile trees containing a well-supported monophyletic nest of Sodalis isolates, distinct from other Enterobacteriaceae, and suggestive of diversification potentially attributed to tsetse host adaptation. Increased sequence divergence of ITSala,ile with Sodalis isolates from G. pallidipes and G. brevipalpis hosts was also observed, although BS and PP values were not robust at this node.

Bottom Line: Additionally, we propose an ITS region as a diagnostic marker for the identification of additional Sodalis-allied symbionts in the field.These results expand our knowledge of informative genome regions to assess genetic divergence since splitting from the last common ancestor, of this versatile insect symbiont clade that have become increasingly recognized as valuable towards our understanding of the evolution of symbiosis.These facultative and recently associated symbionts may provide a novel source of traits adaptable to the dynamic ecologies encountered by diverse host backgrounds.

View Article: PubMed Central - PubMed

Affiliation: Department of Biology, West Virginia University, Morgantown, WV 26506, USA. asnyde19@mix.wvu.edu.

ABSTRACT
Bacteria excel in most ecological niches, including insect symbioses. A cluster of bacterial symbionts, established within a broad range of insects, share high 16S rRNA similarities with the secondary symbiont of the tsetse fly (Diptera: Glossinidae), Sodalis glossinidius. Although 16S rRNA has proven informative towards characterization of this clade, the gene is insufficient for examining recent divergence due to selective constraints. Here, we assess the application of the internal transcribed spacer (ITS) regions, specifically the ITS(glu) and ITS(ala,ile), used in conjunction with 16S rRNA to enhance the phylogenetic resolution of Sodalis-allied bacteria. The 16S rRNA + ITS regions of Sodalis and allied bacteria demonstrated significant divergence and were robust towards phylogenetic resolution. A monophyletic clade of Sodalis isolates from tsetse species, distinct from other Enterobacteriaceae, was consistently observed suggesting diversification due to host adaptation. In contrast, the phylogenetic distribution of symbionts isolated from hippoboscid flies and various Hemiptera and Coleoptera were intertwined suggesting either horizontal transfer or a recent establishment from an environmental source. Lineage splitting of Sodalis-allied bacteria into symbiotic and free-living sister groups was also observed. Additionally, we propose an ITS region as a diagnostic marker for the identification of additional Sodalis-allied symbionts in the field. These results expand our knowledge of informative genome regions to assess genetic divergence since splitting from the last common ancestor, of this versatile insect symbiont clade that have become increasingly recognized as valuable towards our understanding of the evolution of symbiosis. These facultative and recently associated symbionts may provide a novel source of traits adaptable to the dynamic ecologies encountered by diverse host backgrounds.

No MeSH data available.