Comparative and Phylogenomic Evidence That the Alphaproteobacterium HIMB59 Is Not a Member of the Oceanic SAR11 Clade
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{"title"=>"Comparative and phylogenomic evidence that the alphaproteobacterium HIMB59 is not a member of the oceanic SAR11 clade", "type"=>"journal", "authors"=>[{"first_name"=>"Johan", "last_name"=>"Viklund", "scopus_author_id"=>"16029885000"}, {"first_name"=>"Joran", "last_name"=>"Martijn", "scopus_author_id"=>"55574602000"}, {"first_name"=>"Thijs J.G.", "last_name"=>"Ettema", "scopus_author_id"=>"6602489896"}, {"first_name"=>"Siv G.E.", "last_name"=>"Andersson", "scopus_author_id"=>"55584724700"}], "year"=>2013, "source"=>"PLoS ONE", "identifiers"=>{"scopus"=>"2-s2.0-84891442169", "pmid"=>"24223857", "sgr"=>"84891442169", "doi"=>"10.1371/journal.pone.0078858", "isbn"=>"1932-6203", "issn"=>"19326203", "pui"=>"372022013"}, "id"=>"9a3513ff-de46-3ace-b0ea-c790163a28cb", "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.", "link"=>"http://www.mendeley.com/research/comparative-phylogenomic-evidence-alphaproteobacterium-himb59-not-member-oceanic-sar11-clade", "reader_count"=>23, "reader_count_by_academic_status"=>{"Unspecified"=>2, "Professor > Associate Professor"=>1, "Student > Doctoral Student"=>1, "Researcher"=>6, "Student > Ph. D. Student"=>10, "Student > Master"=>1, "Student > Bachelor"=>2}, "reader_count_by_user_role"=>{"Unspecified"=>2, "Professor > Associate Professor"=>1, "Student > Doctoral Student"=>1, "Researcher"=>6, "Student > Ph. D. Student"=>10, "Student > Master"=>1, "Student > Bachelor"=>2}, "reader_count_by_subject_area"=>{"Unspecified"=>2, "Environmental Science"=>2, "Biochemistry, Genetics and Molecular Biology"=>1, "Agricultural and Biological Sciences"=>16, "Computer Science"=>1, "Earth and Planetary Sciences"=>1}, "reader_count_by_subdiscipline"=>{"Earth and Planetary Sciences"=>{"Earth and Planetary Sciences"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>16}, "Computer Science"=>{"Computer Science"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>1}, "Unspecified"=>{"Unspecified"=>2}, "Environmental Science"=>{"Environmental Science"=>2}}, "reader_count_by_country"=>{"Sweden"=>1, "Hong Kong"=>1, "Germany"=>1}, "group_count"=>0}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/1265149"], "description"=>"<p>Bayesian tree inferred with the CAT model applied to an alignment of 150 concatenated pan-orthologous proteins. HIMB59 (marked in red) clusters with the Rickettsiales. The SAR11 clade (marked in blue) is placed within a broad group of free-living alphaproteobacterial species that includes the Spingomonadales, Rhodobacterales, Rhizobiales, and Caulobacterales. Numbers at nodes show PP values. </p>", "links"=>[], "tags"=>[], "article_id"=>840263, "categories"=>["Biological Sciences"], "users"=>["Johan Viklund", "Joran Martijn", "Thijs J. G. Ettema", "Siv G. E. Andersson"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0078858.g001"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Phylogenetic_analysis_of_the_Alphaproteobacteria_/840263", "title"=>"Phylogenetic analysis of the Alphaproteobacteria.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-11-01 03:10:23"}
  • {"files"=>["https://ndownloader.figshare.com/files/1265150"], "description"=>"<p>Bayesian tree inferred with the CAT model applied to an alignment of 13 concatenated pan-orthologous proteins. HIMB59 (marked in red) is placed within the Rhodospirillales. The SAR11 clade (marked in blue) is placed within a broad group of free-living alphaproteobacterial species that includes the Sphingomonadales, Rhodobacterales, Rhizobiales, and Caulobacterales. Numbers at nodes show PP values. </p>", "links"=>[], "tags"=>["alphaproteobacteria"], "article_id"=>840264, "categories"=>["Biological Sciences"], "users"=>["Johan Viklund", "Joran Martijn", "Thijs J. G. Ettema", "Siv G. E. Andersson"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0078858.g002"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Phylogenetic_analysis_of_the_Alphaproteobacteria_and_mitochondria_/840264", "title"=>"Phylogenetic analysis of the Alphaproteobacteria and mitochondria.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-11-01 03:10:23"}
  • {"files"=>["https://ndownloader.figshare.com/files/1265151"], "description"=>"<p>Box plots of aminoGC distribution among genes estimated from the concatenated alignments used to infer the phylogenies of the Alphaproteobacteria presented in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0078858#pone-0078858-g001\" target=\"_blank\">Figures 1</a> and <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0078858#pone-0078858-g002\" target=\"_blank\">2</a>. A shows the distribution of the 150 proteins used in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0078858#pone-0078858-g001\" target=\"_blank\">Figure 1</a> and B shows the 13 proteins used in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0078858#pone-0078858-g002\" target=\"_blank\">Figure 2</a>. </p>", "links"=>[], "tags"=>["compositional"], "article_id"=>840265, "categories"=>["Biological Sciences"], "users"=>["Johan Viklund", "Joran Martijn", "Thijs J. G. Ettema", "Siv G. E. Andersson"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0078858.g003"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Influence_of_compositional_bias_/840265", "title"=>"Influence of compositional bias.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-11-01 03:10:23"}
  • {"files"=>["https://ndownloader.figshare.com/files/1265152"], "description"=>"<p>The analyses of the SAR11 genomes highlighted as in [<a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0078858#B5\" target=\"_blank\">5</a>]. The color-coding corresponds to the taxonomic assignments, with orange dots representing all pairwise comparisons of HIMB59 with all other taxa. Protein sequence similarity is defined as average normalized bit scores and gene order conservation as the fraction of syntenic genes. </p>", "links"=>[], "tags"=>["plotted", "pairs"], "article_id"=>840266, "categories"=>["Biological Sciences"], "users"=>["Johan Viklund", "Joran Martijn", "Thijs J. G. Ettema", "Siv G. E. Andersson"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0078858.g004"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Gene_order_conservation_plotted_against_protein_sequence_similarity_for_all_possible_pairs_of_the_Alphaproteobacteria_/840266", "title"=>"Gene order conservation plotted against protein sequence similarity for all possible pairs of the Alphaproteobacteria.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-11-01 03:10:23"}
  • {"files"=>["https://ndownloader.figshare.com/files/1265159"], "description"=>"<p>For all species except HIMB59 the region is located between 23S rRNA and 5S rRNA and includes 20kb on either side. For HIMB59, we extracted the region specified in [<a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0078858#B5\" target=\"_blank\">5</a>] as the homologous region to HVR2 and included and an extra 20 kb on either side. The sequence similarity between any two regions is based on tblastx comparisons with an e-value threshold of E<10<sup>−10</sup>.</p>", "links"=>[], "tags"=>[], "article_id"=>840268, "categories"=>["Biological Sciences"], "users"=>["Johan Viklund", "Joran Martijn", "Thijs J. G. Ettema", "Siv G. E. Andersson"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0078858.g005"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Visual_representation_of_sequence_similarity_of_HVR2_/840268", "title"=>"Visual representation of sequence similarity of HVR2.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-11-01 03:10:23"}
  • {"files"=>["https://ndownloader.figshare.com/files/1265162", "https://ndownloader.figshare.com/files/1265163", "https://ndownloader.figshare.com/files/1265164", "https://ndownloader.figshare.com/files/1265165", "https://ndownloader.figshare.com/files/1265166"], "description"=>"<div><p>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.</p> </div>", "links"=>[], "tags"=>["phylogenomic", "alphaproteobacterium", "himb59", "oceanic", "sar11", "clade"], "article_id"=>840270, "categories"=>["Biological Sciences"], "users"=>["Johan Viklund", "Joran Martijn", "Thijs J. G. Ettema", "Siv G. E. Andersson"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0078858.s001", "https://dx.doi.org/10.1371/journal.pone.0078858.s002", "https://dx.doi.org/10.1371/journal.pone.0078858.s003", "https://dx.doi.org/10.1371/journal.pone.0078858.s004", "https://dx.doi.org/10.1371/journal.pone.0078858.s005"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Comparative_and_Phylogenomic_Evidence_That_the_Alphaproteobacterium_HIMB59_Is_Not_a_Member_of_the_Oceanic_SAR11_Clade_/840270", "title"=>"Comparative and Phylogenomic Evidence That the Alphaproteobacterium HIMB59 Is Not a Member of the Oceanic SAR11 Clade", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2013-11-01 03:10:23"}

PMC Usage Stats | Further Information

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Relative Metric

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