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Comparative and phylogenomic evidence that the alphaproteobacterium HIMB59 is not a member of the oceanic SAR11 clade.

Viklund J, Martijn J, Ettema TJ, Andersson SG - PLoS ONE (2013)

Bottom Line: By placing the comparison in the context of the evolution of the Alphaproteobacteria, we found that none of the measures of genomic similarity supports a clustering of HIMB59 and SAR11 to the exclusion of other Alphaproteobacteria.Finally, in contrast to earlier reports, we observed no sequence similarity between the hypervariable region HVR2 in the SAR11 genomes and the region located at the corresponding position in the HIMB59 genome.Based on these observations, we conclude that the alphaproteobacterium HIMB59 is not monophyletic with the SAR11 strains and that genome streamlining has evolved multiple times independently in Alphaproteobacteria adapted to the upper surface waters of the oceans.

View Article: PubMed Central - PubMed

Affiliation: Department of Molecular Evolution, Biomedical Centre, Science for Life Laboratory, Uppsala, Sweden.

ABSTRACT
SAR11 is a globally abundant group of Alphaproteobacteria in the oceans that is taxonomically not well defined. It has been suggested SAR11 should be classified into the novel order Pelagibacterales. Features such as conservation of gene content and synteny have been taken as evidence that also the divergent member HIMB59 should be included in the order. However, this proposition is controversial since phylogenetic analyses have questioned the monophyly of this grouping. Here, we performed phylogenetic analyses and reinvestigated the genomic similarity of SAR11 and HIMB59. Our phylogenetic analysis confirmed that HIMB59 is not a sister group to the other SAR11 strains. By placing the comparison in the context of the evolution of the Alphaproteobacteria, we found that none of the measures of genomic similarity supports a clustering of HIMB59 and SAR11 to the exclusion of other Alphaproteobacteria. First, pairwise sequence similarity measures for the SAR11 and HIMB59 genomes were within the range observed for unrelated pairs of Alphaproteobacteria. Second, pairwise comparisons of gene contents revealed a higher similarity of SAR11 to several other alphaproteobacterial genomes than to HIMB59. Third, the SAR11 genomes are not more similar in gene order to the HIMB59 genome than what they are to several other alphaproteobacterial genomes. Finally, in contrast to earlier reports, we observed no sequence similarity between the hypervariable region HVR2 in the SAR11 genomes and the region located at the corresponding position in the HIMB59 genome. Based on these observations, we conclude that the alphaproteobacterium HIMB59 is not monophyletic with the SAR11 strains and that genome streamlining has evolved multiple times independently in Alphaproteobacteria adapted to the upper surface waters of the oceans.

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Influence of compositional bias.Box plots of aminoGC distribution among genes estimated from the concatenated alignments used to infer the phylogenies of the Alphaproteobacteria presented in Figures 1 and 2. A shows the distribution of the 150 proteins used in Figure 1 and B shows the 13 proteins used in Figure 2.
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pone-0078858-g003: Influence of compositional bias.Box plots of aminoGC distribution among genes estimated from the concatenated alignments used to infer the phylogenies of the Alphaproteobacteria presented in Figures 1 and 2. A shows the distribution of the 150 proteins used in Figure 1 and B shows the 13 proteins used in Figure 2.

Mentions: There are extreme variations in G + C contents exist within the genomes of Alphaproteobacteria, ranging from 28% to 70%. In cases of strong heterogeneity in base composition patterns, non-phylogenetic signals in the data may override the true phylogenetic signal, resulting in different tree topologies for different data sets. To test the influence of AT/GC bias, we calculated the frequencies of amino acids coded by codons with GC in the first two positions (aminoGC) for both of the two concatenated data sets. The results showed that the concatenated alignment of the larger data set of 150 proteins was more strongly influenced by AT/GC bias than the smaller data set consisting of 13 proteins (Figure 3). The clustering of HIMB59 with the SAR11 genomes in the maximum likelihood analysis of the 150 proteins may thus represent such a nonphylogenetic signal, while the separation of HIMB59 from the SAR11 group of bacteria, as suggested from the smaller data set is more likely to represent the true phylogenetic signal.


Comparative and phylogenomic evidence that the alphaproteobacterium HIMB59 is not a member of the oceanic SAR11 clade.

Viklund J, Martijn J, Ettema TJ, Andersson SG - PLoS ONE (2013)

Influence of compositional bias.Box plots of aminoGC distribution among genes estimated from the concatenated alignments used to infer the phylogenies of the Alphaproteobacteria presented in Figures 1 and 2. A shows the distribution of the 150 proteins used in Figure 1 and B shows the 13 proteins used in Figure 2.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3815206&req=5

pone-0078858-g003: Influence of compositional bias.Box plots of aminoGC distribution among genes estimated from the concatenated alignments used to infer the phylogenies of the Alphaproteobacteria presented in Figures 1 and 2. A shows the distribution of the 150 proteins used in Figure 1 and B shows the 13 proteins used in Figure 2.
Mentions: There are extreme variations in G + C contents exist within the genomes of Alphaproteobacteria, ranging from 28% to 70%. In cases of strong heterogeneity in base composition patterns, non-phylogenetic signals in the data may override the true phylogenetic signal, resulting in different tree topologies for different data sets. To test the influence of AT/GC bias, we calculated the frequencies of amino acids coded by codons with GC in the first two positions (aminoGC) for both of the two concatenated data sets. The results showed that the concatenated alignment of the larger data set of 150 proteins was more strongly influenced by AT/GC bias than the smaller data set consisting of 13 proteins (Figure 3). The clustering of HIMB59 with the SAR11 genomes in the maximum likelihood analysis of the 150 proteins may thus represent such a nonphylogenetic signal, while the separation of HIMB59 from the SAR11 group of bacteria, as suggested from the smaller data set is more likely to represent the true phylogenetic signal.

Bottom Line: By placing the comparison in the context of the evolution of the Alphaproteobacteria, we found that none of the measures of genomic similarity supports a clustering of HIMB59 and SAR11 to the exclusion of other Alphaproteobacteria.Finally, in contrast to earlier reports, we observed no sequence similarity between the hypervariable region HVR2 in the SAR11 genomes and the region located at the corresponding position in the HIMB59 genome.Based on these observations, we conclude that the alphaproteobacterium HIMB59 is not monophyletic with the SAR11 strains and that genome streamlining has evolved multiple times independently in Alphaproteobacteria adapted to the upper surface waters of the oceans.

View Article: PubMed Central - PubMed

Affiliation: Department of Molecular Evolution, Biomedical Centre, Science for Life Laboratory, Uppsala, Sweden.

ABSTRACT
SAR11 is a globally abundant group of Alphaproteobacteria in the oceans that is taxonomically not well defined. It has been suggested SAR11 should be classified into the novel order Pelagibacterales. Features such as conservation of gene content and synteny have been taken as evidence that also the divergent member HIMB59 should be included in the order. However, this proposition is controversial since phylogenetic analyses have questioned the monophyly of this grouping. Here, we performed phylogenetic analyses and reinvestigated the genomic similarity of SAR11 and HIMB59. Our phylogenetic analysis confirmed that HIMB59 is not a sister group to the other SAR11 strains. By placing the comparison in the context of the evolution of the Alphaproteobacteria, we found that none of the measures of genomic similarity supports a clustering of HIMB59 and SAR11 to the exclusion of other Alphaproteobacteria. First, pairwise sequence similarity measures for the SAR11 and HIMB59 genomes were within the range observed for unrelated pairs of Alphaproteobacteria. Second, pairwise comparisons of gene contents revealed a higher similarity of SAR11 to several other alphaproteobacterial genomes than to HIMB59. Third, the SAR11 genomes are not more similar in gene order to the HIMB59 genome than what they are to several other alphaproteobacterial genomes. Finally, in contrast to earlier reports, we observed no sequence similarity between the hypervariable region HVR2 in the SAR11 genomes and the region located at the corresponding position in the HIMB59 genome. Based on these observations, we conclude that the alphaproteobacterium HIMB59 is not monophyletic with the SAR11 strains and that genome streamlining has evolved multiple times independently in Alphaproteobacteria adapted to the upper surface waters of the oceans.

Show MeSH