Construction of a Phylogenetic Tree of Photosynthetic Prokaryotes Based on Average Similarities of Whole Genome Sequences
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{"title"=>"Construction of a Phylogenetic Tree of Photosynthetic Prokaryotes Based on Average Similarities of Whole Genome Sequences", "type"=>"journal", "authors"=>[{"first_name"=>"Soichirou", "last_name"=>"Satoh", "scopus_author_id"=>"7403082647"}, {"first_name"=>"Mamoru", "last_name"=>"Mimuro", "scopus_author_id"=>"7006461138"}, {"first_name"=>"Ayumi", "last_name"=>"Tanaka", "scopus_author_id"=>"7404667898"}], "year"=>2013, "source"=>"PLoS ONE", "identifiers"=>{"pmid"=>"23922968", "issn"=>"19326203", "doi"=>"10.1371/journal.pone.0070290", "pui"=>"369439137", "isbn"=>"1932-6203 (Electronic)\\r1932-6203 (Linking)", "scopus"=>"2-s2.0-84880800678", "sgr"=>"84880800678"}, "id"=>"e3cff516-914d-3125-84ec-3c8ac0d909aa", "abstract"=>"Phylogenetic trees have been constructed for a wide range of organisms using gene sequence information, especially through the identification of orthologous genes that have been vertically inherited. The number of available complete genome sequences is rapidly increasing, and many tools for construction of genome trees based on whole genome sequences have been proposed. However, development of a reasonable method of using complete genome sequences for construction of phylogenetic trees has not been established. We have developed a method for construction of phylogenetic trees based on the average sequence similarities of whole genome sequences. We used this method to examine the phylogeny of 115 photosynthetic prokaryotes, i.e., cyanobacteria, Chlorobi, proteobacteria, Chloroflexi, Firmicutes and nonphotosynthetic organisms including Archaea. Although the bootstrap values for the branching order of phyla were low, probably due to lateral gene transfer and saturated mutation, the obtained tree was largely consistent with the previously reported phylogenetic trees, indicating that this method is a robust alternative to traditional phylogenetic methods.", "link"=>"http://www.mendeley.com/research/construction-phylogenetic-tree-photosynthetic-prokaryotes-based-average-similarities-whole-genome-se", "reader_count"=>45, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>2, "Researcher"=>8, "Student > Doctoral Student"=>3, "Student > Ph. D. Student"=>11, "Student > Postgraduate"=>1, "Other"=>3, "Student > Master"=>9, "Student > Bachelor"=>6, "Lecturer > Senior Lecturer"=>1, "Professor"=>1}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>2, "Researcher"=>8, "Student > Doctoral Student"=>3, "Student > Ph. D. Student"=>11, "Student > Postgraduate"=>1, "Other"=>3, "Student > Master"=>9, "Student > Bachelor"=>6, "Lecturer > Senior Lecturer"=>1, "Professor"=>1}, "reader_count_by_subject_area"=>{"Unspecified"=>2, "Environmental Science"=>2, "Biochemistry, Genetics and Molecular Biology"=>12, "Agricultural and Biological Sciences"=>25, "Design"=>1, "Earth and Planetary Sciences"=>3}, "reader_count_by_subdiscipline"=>{"Design"=>{"Design"=>1}, "Earth and Planetary Sciences"=>{"Earth and Planetary Sciences"=>3}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>25}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>12}, "Unspecified"=>{"Unspecified"=>2}, "Environmental Science"=>{"Environmental Science"=>2}}, "reader_count_by_country"=>{"Canada"=>1, "United States"=>1, "Japan"=>1, "United Kingdom"=>1}, "group_count"=>1}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/1132607"], "description"=>"<p>Ten independent databases of <i>Synechococcus</i> sp. CC9311 were artificially formed with 289 randomly selected genes (10% of the total gene number). Ten independent phylogenetic trees using five <i>Prochlorococcus</i> species and four <i>Synechococcus</i> species containing artificially formed <i>Synechococcus</i> sp. CC9311 databases were constructed using each of the distance indices used to generate <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0070290#pone-0070290-g002\" target=\"_blank\">Figs. 2B to 2F</a>. A consensus tree for the ten independent trees was generated with the use of the CONSENSE program for each of the five distance indices, F<sub>Av</sub>, F<sub>XY</sub>, F<sub>YX</sub>, F<sub>H</sub>, and F<sub>L</sub>. Numbers on the branch points represent the number of identical branching patterns in ten independent trees. Branching points without numbers indicate that the number of identical branching patterns is ten. <i>S. elongatus</i> PCC 6301 was used as an out-group.</p>", "links"=>[], "tags"=>["Biochemistry", "Plant biochemistry", "photosynthesis", "Evolutionary biology", "Evolutionary systematics", "phylogenetics", "Evolutionary genetics", "Genomic evolution", "genomics", "Comparative genomics", "Plant science", "Plant evolution", "constructed", "reduced", "cc9311"], "article_id"=>756256, "categories"=>["Biological Sciences"], "users"=>["Soichirou Satoh", "Mamoru Mimuro", "Ayumi Tanaka"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0070290.g003", "stats"=>{"downloads"=>2, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Phylogenetic_tree_constructed_using_a_reduced_gene_number_for_the_Synechococcus_sp_CC9311_genome_/756256", "title"=>"Phylogenetic tree constructed using a reduced gene number for the <i>Synechococcus</i> sp. CC9311 genome.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-07-26 01:39:06"}
  • {"files"=>["https://ndownloader.figshare.com/files/1132609"], "description"=>"<p>Procedures for construction of the phylogenetic tree are the same as in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0070290#pone-0070290-g002\" target=\"_blank\">Figs. 2B</a> and <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0070290#pone.0070290.s002\" target=\"_blank\">S2</a>. Bootstrap values ≥50 are shown on the branch points. Bootstrap values were obtained from 100 reproduced trees of 1,000 randomly selected E-values as all genomes contain more than 1000 genes. Archaea were used as an out-group.</p>", "links"=>[], "tags"=>["Biochemistry", "Plant biochemistry", "photosynthesis", "Evolutionary biology", "Evolutionary systematics", "phylogenetics", "Evolutionary genetics", "Genomic evolution", "genomics", "Comparative genomics", "Plant science", "Plant evolution", "photosynthetic", "prokaryotes"], "article_id"=>756258, "categories"=>["Biological Sciences"], "users"=>["Soichirou Satoh", "Mamoru Mimuro", "Ayumi Tanaka"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0070290.g004", "stats"=>{"downloads"=>2, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Phylogenetic_tree_of_photosynthetic_prokaryotes_based_on_the_average_sequence_similarity_/756258", "title"=>"Phylogenetic tree of photosynthetic prokaryotes based on the average sequence similarity.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-07-26 01:39:06"}
  • {"files"=>["https://ndownloader.figshare.com/files/1132615"], "description"=>"<p>The bootstrap values of the nodes were determined using 100 reproduced trees with various amounts of best-matched pairs. Alphabetical characters of the branch points were represented in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0070290#pone.0070290.s002\" target=\"_blank\">Fig. S2</a>. Blue diamond, 100 E-values; red square, 200 E-values; yellow-green triangle, 500 E-values; purple square, 1,000 E-values; light-blue square, 3,000 E-values.</p>", "links"=>[], "tags"=>["Biochemistry", "Plant biochemistry", "photosynthesis", "Evolutionary biology", "Evolutionary systematics", "phylogenetics", "Evolutionary genetics", "Genomic evolution", "genomics", "Comparative genomics", "Plant science", "Plant evolution", "bootstrap", "numbers", "best-matched"], "article_id"=>756264, "categories"=>["Biological Sciences"], "users"=>["Soichirou Satoh", "Mamoru Mimuro", "Ayumi Tanaka"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0070290.g005", "stats"=>{"downloads"=>0, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Relationship_between_the_bootstrap_values_and_the_numbers_of_best_matched_pairs_/756264", "title"=>"Relationship between the bootstrap values and the numbers of best-matched pairs.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-07-26 01:39:06"}
  • {"files"=>["https://ndownloader.figshare.com/files/1132621", "https://ndownloader.figshare.com/files/1132627", "https://ndownloader.figshare.com/files/1132629", "https://ndownloader.figshare.com/files/1132636", "https://ndownloader.figshare.com/files/1132660", "https://ndownloader.figshare.com/files/1132661", "https://ndownloader.figshare.com/files/1132662", "https://ndownloader.figshare.com/files/1132663"], "description"=>"<div><p>Phylogenetic trees have been constructed for a wide range of organisms using gene sequence information, especially through the identification of orthologous genes that have been vertically inherited. The number of available complete genome sequences is rapidly increasing, and many tools for construction of genome trees based on whole genome sequences have been proposed. However, development of a reasonable method of using complete genome sequences for construction of phylogenetic trees has not been established. We have developed a method for construction of phylogenetic trees based on the average sequence similarities of whole genome sequences. We used this method to examine the phylogeny of 115 photosynthetic prokaryotes, i.e., cyanobacteria, Chlorobi, proteobacteria, Chloroflexi, Firmicutes and nonphotosynthetic organisms including Archaea. Although the bootstrap values for the branching order of phyla were low, probably due to lateral gene transfer and saturated mutation, the obtained tree was largely consistent with the previously reported phylogenetic trees, indicating that this method is a robust alternative to traditional phylogenetic methods.</p></div>", "links"=>[], "tags"=>["Biochemistry", "Plant biochemistry", "photosynthesis", "Evolutionary biology", "Evolutionary systematics", "phylogenetics", "Evolutionary genetics", "Genomic evolution", "genomics", "Comparative genomics", "Plant science", "Plant evolution", "phylogenetic", "photosynthetic", "prokaryotes", "similarities", "genome"], "article_id"=>756267, "categories"=>["Biological Sciences"], "users"=>["Soichirou Satoh", "Mamoru Mimuro", "Ayumi Tanaka"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0070290.s001", "https://dx.doi.org/10.1371/journal.pone.0070290.s002", "https://dx.doi.org/10.1371/journal.pone.0070290.s003", "https://dx.doi.org/10.1371/journal.pone.0070290.s004", "https://dx.doi.org/10.1371/journal.pone.0070290.s005", "https://dx.doi.org/10.1371/journal.pone.0070290.s006", "https://dx.doi.org/10.1371/journal.pone.0070290.s007", "https://dx.doi.org/10.1371/journal.pone.0070290.s008"], "stats"=>{"downloads"=>43, "page_views"=>21, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Construction_of_a_Phylogenetic_Tree_of_Photosynthetic_Prokaryotes_Based_on_Average_Similarities_of_Whole_Genome_Sequences_/756267", "title"=>"Construction of a Phylogenetic Tree of Photosynthetic Prokaryotes Based on Average Similarities of Whole Genome Sequences", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2013-07-26 01:39:06"}
  • {"files"=>["https://ndownloader.figshare.com/files/1132605"], "description"=>"<p>Representation of best-matched proteins on a two-dimensional display. The vertical axes represent the logarithmic E-values of the best-matched proteins of <i>Anabaena</i> sp. PCC 7120 (A) and <i>Rhodobacter sphaeroides</i> 2.4.1 (B) to the proteins of <i>Synechocystis</i> sp. PCC 6803. The horizontal axes represent the logarithmic E-values of the best-matched proteins of <i>Synechocystis</i> sp. PCC 6803 to <i>Synechocystis</i> sp. PCC 6803 (A, B). In this case, the best-matched proteins are identical to the query proteins. The green lines are linear regression lines and the red lines mark the diagonal. θ is the angle between the red and green lines. (C) Relationship between tan θ and the 16S rDNA substitution rate. Each point represents the tan θ values (vertical axis) calculated with two genomes and the substitution rates of their 16S rDNA sequences (horizontal axis). The solid line represents the regression curve.</p>", "links"=>[], "tags"=>["Biochemistry", "Plant biochemistry", "photosynthesis", "Evolutionary biology", "Evolutionary systematics", "phylogenetics", "Evolutionary genetics", "Genomic evolution", "genomics", "Comparative genomics", "Plant science", "Plant evolution", "rdna", "substitution"], "article_id"=>756254, "categories"=>["Biological Sciences"], "users"=>["Soichirou Satoh", "Mamoru Mimuro", "Ayumi Tanaka"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0070290.g001", "stats"=>{"downloads"=>0, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Evolutionary_distance_based_on_protein_similarity_and_its_relationship_to_rDNA_substitution_rate_/756254", "title"=>"Evolutionary distance based on protein similarity and its relationship to rDNA substitution rate.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-07-26 01:39:06"}
  • {"files"=>["https://ndownloader.figshare.com/files/1132606"], "description"=>"<p>Phylogenetic tree of 16S rDNA sequences (A). The lengths of the nodes represent the substitution rate, which is defined as the percentage of substitution sites per alignment length. Bootstrap values ≥50 are shown on the branch points. (B) to (F). Phylogenetic trees were constructed using F<sub>Av</sub> (B), F<sub>XY</sub> (C), F<sub>YX</sub> (D), F<sub>H</sub> (E) and F<sub>L</sub> (F) values. The lengths of the nodes in the trees (B) to (F) represent the F<sub>Av</sub>, F<sub>XY</sub>, F<sub>YX</sub>, F<sub>H</sub>, and F<sub>L</sub>, respectively. Phylogenetic trees were drawn as NJ trees using the NEIGHBOR program in the PHYLIP package 3.67. Out-group of phylogenetic trees is the same as in (A).</p>", "links"=>[], "tags"=>["Biochemistry", "Plant biochemistry", "photosynthesis", "Evolutionary biology", "Evolutionary systematics", "phylogenetics", "Evolutionary genetics", "Genomic evolution", "genomics", "Comparative genomics", "Plant science", "Plant evolution", "trees"], "article_id"=>756255, "categories"=>["Biological Sciences"], "users"=>["Soichirou Satoh", "Mamoru Mimuro", "Ayumi Tanaka"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0070290.g002", "stats"=>{"downloads"=>0, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Phylogenetic_trees_of_Prochlorococcus_and_Synechococcus_species_/756255", "title"=>"Phylogenetic trees of <i>Prochlorococcus</i> and <i>Synechococcus</i> species.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-07-26 01:39:06"}

PMC Usage Stats | Further Information

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Relative Metric

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