The Candidate Phylum Poribacteria by Single-Cell Genomics: New Insights into Phylogeny, Cell-Compartmentation, Eukaryote-Like Repeat Proteins, and Other Genomic Features
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{"title"=>"The candidate phylum Poribacteria by single-cell genomics: New insights into phylogeny, cell-compartmentation, eukaryote-like repeat proteins, and other genomic features", "type"=>"journal", "authors"=>[{"first_name"=>"Janine", "last_name"=>"Kamke", "scopus_author_id"=>"36126373500"}, {"first_name"=>"Christian", "last_name"=>"Rinke", "scopus_author_id"=>"56154340600"}, {"first_name"=>"Patrick", "last_name"=>"Schwientek", "scopus_author_id"=>"37027185700"}, {"first_name"=>"Kostas", "last_name"=>"Mavromatis", "scopus_author_id"=>"16039719300"}, {"first_name"=>"Natalia", "last_name"=>"Ivanova", "scopus_author_id"=>"35601137500"}, {"first_name"=>"Alexander", "last_name"=>"Sczyrba", "scopus_author_id"=>"6602804180"}, {"first_name"=>"Tanja", "last_name"=>"Woyke", "scopus_author_id"=>"6602417287"}, {"first_name"=>"Ute", "last_name"=>"Hentschel", "scopus_author_id"=>"7006077939"}], "year"=>2014, "source"=>"PLoS ONE", "identifiers"=>{"pmid"=>"24498082", "doi"=>"10.1371/journal.pone.0087353", "sgr"=>"84900313954", "isbn"=>"1932-6203 (Electronic)\\r1932-6203 (Linking)", "scopus"=>"2-s2.0-84900313954", "issn"=>"19326203", "pui"=>"373059518"}, "id"=>"b767d2d3-c4fc-3f19-abbe-3fa9be28fbc7", "abstract"=>"The candidate phylum Poribacteria is one of the most dominant and widespread members of the microbial communities residing within marine sponges. Cell compartmentalization had been postulated along with their discovery about a decade ago and their phylogenetic association to the Planctomycetes, Verrucomicrobia, Chlamydiae superphylum was proposed soon thereafter. In the present study we revised these features based on genomic data obtained from six poribacterial single cells. We propose that Poribacteria form a distinct monophyletic phylum contiguous to the PVC superphylum together with other candidate phyla. Our genomic analyses supported the possibility of cell compartmentalization in form of bacterial microcompartments. Further analyses of eukaryote-like protein domains stressed the importance of such proteins with features including tetratricopeptide repeats, leucin rich repeats as well as low density lipoproteins receptor repeats, the latter of which are reported here for the first time from a sponge symbiont. Finally, examining the most abundant protein domain family on poribacterial genomes revealed diverse phyH family proteins, some of which may be related to dissolved organic posphorus uptake.", "link"=>"http://www.mendeley.com/research/candidate-phylum-poribacteria-singlecell-genomics-new-insights-phylogeny-cellcompartmentation-eukary", "reader_count"=>80, "reader_count_by_academic_status"=>{"Unspecified"=>1, "Professor > Associate Professor"=>4, "Student > Doctoral Student"=>3, "Researcher"=>17, "Student > Ph. D. Student"=>29, "Student > Postgraduate"=>2, "Student > Master"=>9, "Other"=>1, "Student > Bachelor"=>9, "Professor"=>5}, "reader_count_by_user_role"=>{"Unspecified"=>1, "Professor > Associate Professor"=>4, "Student > Doctoral Student"=>3, "Researcher"=>17, "Student > Ph. D. Student"=>29, "Student > Postgraduate"=>2, "Student > Master"=>9, "Other"=>1, "Student > Bachelor"=>9, "Professor"=>5}, "reader_count_by_subject_area"=>{"Unspecified"=>2, "Environmental Science"=>6, "Biochemistry, Genetics and Molecular Biology"=>7, "Agricultural and Biological Sciences"=>52, "Medicine and Dentistry"=>2, "Chemistry"=>1, "Computer Science"=>3, "Immunology and Microbiology"=>3, "Earth and Planetary Sciences"=>1, "Engineering"=>3}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>3}, "Medicine and Dentistry"=>{"Medicine and Dentistry"=>2}, "Chemistry"=>{"Chemistry"=>1}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>3}, "Earth and Planetary Sciences"=>{"Earth and Planetary Sciences"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>52}, "Computer Science"=>{"Computer Science"=>3}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>7}, "Unspecified"=>{"Unspecified"=>2}, "Environmental Science"=>{"Environmental Science"=>6}}, "reader_count_by_country"=>{"New Zealand"=>1, "Saudi Arabia"=>1, "Netherlands"=>1, "United States"=>3, "China"=>1, "Mexico"=>1, "United Kingdom"=>1, "Australia"=>2, "Chile"=>1, "Portugal"=>1, "Germany"=>1}, "group_count"=>5}

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Figshare

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  • {"files"=>["https://ndownloader.figshare.com/files/1372048", "https://ndownloader.figshare.com/files/1372049", "https://ndownloader.figshare.com/files/1372051", "https://ndownloader.figshare.com/files/1372052", "https://ndownloader.figshare.com/files/1372053", "https://ndownloader.figshare.com/files/1372054", "https://ndownloader.figshare.com/files/1372055", "https://ndownloader.figshare.com/files/1372056", "https://ndownloader.figshare.com/files/1372057", "https://ndownloader.figshare.com/files/1372058", "https://ndownloader.figshare.com/files/1372059", "https://ndownloader.figshare.com/files/1372060"], "description"=>"<div><p>The candidate phylum <i>Poribacteria</i> is one of the most dominant and widespread members of the microbial communities residing within marine sponges. Cell compartmentalization had been postulated along with their discovery about a decade ago and their phylogenetic association to the <i>Planctomycetes</i>, <i>Verrucomicrobia</i>, <i>Chlamydiae</i> superphylum was proposed soon thereafter. In the present study we revised these features based on genomic data obtained from six poribacterial single cells. We propose that <i>Poribacteria</i> form a distinct monophyletic phylum contiguous to the PVC superphylum together with other candidate phyla. Our genomic analyses supported the possibility of cell compartmentalization in form of bacterial microcompartments. Further analyses of eukaryote-like protein domains stressed the importance of such proteins with features including tetratricopeptide repeats, leucin rich repeats as well as low density lipoproteins receptor repeats, the latter of which are reported here for the first time from a sponge symbiont. Finally, examining the most abundant protein domain family on poribacterial genomes revealed diverse phyH family proteins, some of which may be related to dissolved organic posphorus uptake.</p></div>", "links"=>[], "tags"=>["Computational biology", "genomics", "Genome sequencing", "Sequence analysis", "Evolutionary biology", "Evolutionary systematics", "phylogenetics", "metagenomics", "Marine biology", "microbiology", "bacteriology", "microbial ecology", "phylum", "single-cell", "insights", "eukaryote-like", "genomic"], "article_id"=>922690, "categories"=>["Biological Sciences"], "users"=>["Janine Kamke", "Christian Rinke", "Patrick Schwientek", "Kostas Mavromatis", "Natalia Ivanova", "Alexander Sczyrba", "Tanja Woyke", "Ute Hentschel"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0087353.s001", "https://dx.doi.org/10.1371/journal.pone.0087353.s002", "https://dx.doi.org/10.1371/journal.pone.0087353.s003", "https://dx.doi.org/10.1371/journal.pone.0087353.s004", "https://dx.doi.org/10.1371/journal.pone.0087353.s005", "https://dx.doi.org/10.1371/journal.pone.0087353.s006", "https://dx.doi.org/10.1371/journal.pone.0087353.s007", "https://dx.doi.org/10.1371/journal.pone.0087353.s008", "https://dx.doi.org/10.1371/journal.pone.0087353.s009", "https://dx.doi.org/10.1371/journal.pone.0087353.s010", "https://dx.doi.org/10.1371/journal.pone.0087353.s011", "https://dx.doi.org/10.1371/journal.pone.0087353.s012"], "stats"=>{"downloads"=>8, "page_views"=>22, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/The_Candidate_Phylum_Poribacteria_by_Single_Cell_Genomics_New_Insights_into_Phylogeny_Cell_Compartmentation_Eukaryote_Like_Repeat_Proteins_and_Other_Genomic_Features/922690", "title"=>"The Candidate Phylum <i>Poribacteria</i> by Single-Cell Genomics: New Insights into Phylogeny, Cell-Compartmentation, Eukaryote-Like Repeat Proteins, and Other Genomic Features", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2014-01-31 04:05:12"}
  • {"files"=>["https://ndownloader.figshare.com/files/1372027"], "description"=>"<p>Bootstrap values (500 resamplings) ≥50% are shown on tree nodes. Numbers of sequences included per group is shown in group boxes. Outgroup consists of 80 sequences belonging to the <i>Bacteroidetes</i>. Scale bar represents 10% sequences divergence.</p>", "links"=>[], "tags"=>["Computational biology", "genomics", "Genome sequencing", "Sequence analysis", "Evolutionary biology", "Evolutionary systematics", "phylogenetics", "metagenomics", "Marine biology", "microbiology", "bacteriology", "microbial ecology", "rrna", "illustrating", "phylogenetic", "phylum"], "article_id"=>922671, "categories"=>["Biological Sciences"], "users"=>["Janine Kamke", "Christian Rinke", "Patrick Schwientek", "Kostas Mavromatis", "Natalia Ivanova", "Alexander Sczyrba", "Tanja Woyke", "Ute Hentschel"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0087353.g002", "stats"=>{"downloads"=>0, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_16S_rRNA_gene_based_maximum_likelihood_tree_illustrating_the_phylogenetic_position_of_the_candidate_phylum_Poribacteria_/922671", "title"=>"16S rRNA gene based maximum likelihood tree illustrating the phylogenetic position of the candidate phylum <i>Poribacteria</i>.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-01-31 04:05:12"}
  • {"files"=>["https://ndownloader.figshare.com/files/1372026"], "description"=>"<p>Bootstrap value (100 resamplings) are shown on tree nodes where support ≥50%. Number of genomes per group is displayed in group boxes. Outgroup consists of several species of <i>Spirochaetes</i> and <i>Gammaproteobacteria</i>. The scale bar represents 10% sequence divergence.</p>", "links"=>[], "tags"=>["Computational biology", "genomics", "Genome sequencing", "Sequence analysis", "Evolutionary biology", "Evolutionary systematics", "phylogenetics", "metagenomics", "Marine biology", "microbiology", "bacteriology", "microbial ecology", "concatenated", "alignment", "83", "genes", "illustrating", "phylogenetic", "phylum"], "article_id"=>922670, "categories"=>["Biological Sciences"], "users"=>["Janine Kamke", "Christian Rinke", "Patrick Schwientek", "Kostas Mavromatis", "Natalia Ivanova", "Alexander Sczyrba", "Tanja Woyke", "Ute Hentschel"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0087353.g001", "stats"=>{"downloads"=>0, "page_views"=>14, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Phylogenomic_tree_based_on_a_concatenated_alignment_of_up_to_83_genes_illustrating_the_phylogenetic_position_of_the_candidate_phylum_Poribacteria_/922670", "title"=>"Phylogenomic tree based on a concatenated alignment of up to 83 genes illustrating the phylogenetic position of the candidate phylum <i>Poribacteria</i>.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-01-31 04:05:12"}
  • {"files"=>["https://ndownloader.figshare.com/files/1372036"], "description"=>"1<p>Inference method, rate categories, and substitution model.</p>2<p>number of species in tree. Single sequences which did not belong to any main clades were removed before tree calculations where indicated (noS = no Singletons).</p>3<p>Bootstrap support for the phylum Poribacteria.</p>4<p>sistergroup to the phylum Poribacteria.</p>5<p>sistergroup to the phylum Poribacteria.</p>6<p>phyla added as outgroups for tree calculation.</p>", "links"=>[], "tags"=>["Computational biology", "genomics", "Genome sequencing", "Sequence analysis", "Evolutionary biology", "Evolutionary systematics", "phylogenetics", "metagenomics", "Marine biology", "microbiology", "bacteriology", "microbial ecology", "phylogenetic", "inference", "phylogenomic"], "article_id"=>922680, "categories"=>["Biological Sciences"], "users"=>["Janine Kamke", "Christian Rinke", "Patrick Schwientek", "Kostas Mavromatis", "Natalia Ivanova", "Alexander Sczyrba", "Tanja Woyke", "Ute Hentschel"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0087353.t001", "stats"=>{"downloads"=>8, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Summary_of_phylogenetic_inference_results_from_all_phylogenomic_tree_calculations_/922680", "title"=>"Summary of phylogenetic inference results from all phylogenomic tree calculations.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-01-31 04:05:12"}
  • {"files"=>["https://ndownloader.figshare.com/files/1372034"], "description"=>"_", "links"=>[], "tags"=>["Computational biology", "genomics", "Genome sequencing", "Sequence analysis", "Evolutionary biology", "Evolutionary systematics", "phylogenetics", "metagenomics", "Marine biology", "microbiology", "bacteriology", "microbial ecology", "markers", "poribacterial"], "article_id"=>922678, "categories"=>["Biological Sciences"], "users"=>["Janine Kamke", "Christian Rinke", "Patrick Schwientek", "Kostas Mavromatis", "Natalia Ivanova", "Alexander Sczyrba", "Tanja Woyke", "Ute Hentschel"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0087353.t002", "stats"=>{"downloads"=>2, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_BMC_shell_protein_markers_on_poribacterial_SAGs_/922678", "title"=>"BMC shell protein markers on poribacterial SAGs.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-01-31 04:05:12"}
  • {"files"=>["https://ndownloader.figshare.com/files/1372031"], "description"=>"<p>For a better overview all genes are displayed in 5′-3′ direction of the BMC shell protein gene. The actual strand orientation might be different and is indicated by plus or minus signs. Genes are shown with locus taq and amino acid identities based on IMG/MER homology searches are shown between genes where applicable. BMC shell protein genes are shown in white, other genes with homologies between different SAGs are shown in dark grey, other genes are shown in light grey.</p>", "links"=>[], "tags"=>["Computational biology", "genomics", "Genome sequencing", "Sequence analysis", "Evolutionary biology", "Evolutionary systematics", "phylogenetics", "metagenomics", "Marine biology", "microbiology", "bacteriology", "microbial ecology", "poribacterial", "bmc"], "article_id"=>922675, "categories"=>["Biological Sciences"], "users"=>["Janine Kamke", "Christian Rinke", "Patrick Schwientek", "Kostas Mavromatis", "Natalia Ivanova", "Alexander Sczyrba", "Tanja Woyke", "Ute Hentschel"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0087353.g003", "stats"=>{"downloads"=>0, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Schematic_view_of_poribacterial_BMC_shell_protein_groups_/922675", "title"=>"Schematic view of poribacterial BMC shell protein groups.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-01-31 04:05:12"}

PMC Usage Stats | Further Information

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