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{"title"=>"Cultivation and Complete Genome Sequencing of Gloeobacter kilaueensis sp. nov., from a Lava Cave in Kīlauea Caldera, Hawai'i", "type"=>"journal", "authors"=>[{"first_name"=>"Jimmy H.W.", "last_name"=>"Saw", "scopus_author_id"=>"6701444863"}, {"first_name"=>"Michael", "last_name"=>"Schatz", "scopus_author_id"=>"7102406086"}, {"first_name"=>"Mark V.", "last_name"=>"Brown", "scopus_author_id"=>"56072457900"}, {"first_name"=>"Dennis D.", "last_name"=>"Kunkel", "scopus_author_id"=>"35577437000"}, {"first_name"=>"Jamie S.", "last_name"=>"Foster", "scopus_author_id"=>"7403380625"}, {"first_name"=>"Harry", "last_name"=>"Shick", "scopus_author_id"=>"56625259900"}, {"first_name"=>"Stephanie", "last_name"=>"Christensen", "scopus_author_id"=>"7201719103"}, {"first_name"=>"Shaobin", "last_name"=>"Hou", "scopus_author_id"=>"7201471819"}, {"first_name"=>"Xuehua", "last_name"=>"Wan", "scopus_author_id"=>"8841869300"}, {"first_name"=>"Stuart P.", "last_name"=>"Donachie", "scopus_author_id"=>"6701425730"}], "year"=>2013, "source"=>"PLoS ONE", "identifiers"=>{"sgr"=>"84886039107", "doi"=>"10.1371/journal.pone.0076376", "pui"=>"370091168", "pmid"=>"24194836", "scopus"=>"2-s2.0-84886039107", "issn"=>"19326203", "isbn"=>"1932-6203"}, "id"=>"0dc5b5fd-69e1-3286-9e9f-9b91d48e4a0a", "abstract"=>"The ancestor of Gloeobacter violaceus PCC 7421(T) is believed to have diverged from that of all known cyanobacteria before the evolution of thylakoid membranes and plant plastids. The long and largely independent evolutionary history of G. violaceus presents an organism retaining ancestral features of early oxygenic photoautotrophs, and in whom cyanobacteria evolution can be investigated. No other Gloeobacter species has been described since the genus was established in 1974 (Rippka et al., Arch Microbiol 100:435). Gloeobacter affiliated ribosomal gene sequences have been reported in environmental DNA libraries, but only the type strain's genome has been sequenced. However, we report here the cultivation of a new Gloeobacter species, G. kilaueensis JS1(T), from an epilithic biofilm in a lava cave in Kīlauea Caldera, Hawai'i. The strain's genome was sequenced from an enriched culture resembling a low-complexity metagenomic sample, using 9 kb paired-end 454 pyrosequences and 400 bp paired-end Illumina reads. The JS1(T) and G. violaceus PCC 7421(T) genomes have little gene synteny despite sharing 2842 orthologous genes; comparing the genomes shows they do not belong to the same species. Our results support establishing a new species to accommodate JS1(T), for which we propose the name Gloeobacter kilaueensis sp. nov. Strain JS1(T) has been deposited in the American Type Culture Collection (BAA-2537), the Scottish Marine Institute's Culture Collection of Algae and Protozoa (CCAP 1431/1), and the Belgian Coordinated Collections of Microorganisms (ULC0316). The G. kilaueensis holotype has been deposited in the Algal Collection of the US National Herbarium (US# 217948). The JS1(T) genome sequence has been deposited in GenBank under accession number CP003587. The G+C content of the genome is 60.54 mol%. The complete genome sequence of G. kilaueensis JS1(T) may further understanding of cyanobacteria evolution, and the shift from anoxygenic to oxygenic photosynthesis.", "link"=>"http://www.mendeley.com/research/cultivation-complete-genome-sequencing-gloeobacter-kilaueensis-sp-nov-lava-cave-k%C4%ABlauea-caldera-hawa", "reader_count"=>65, "reader_count_by_academic_status"=>{"Unspecified"=>2, "Professor > Associate Professor"=>1, "Researcher"=>13, "Student > Doctoral Student"=>4, "Student > Ph. D. Student"=>22, "Student > Postgraduate"=>3, "Student > Master"=>12, "Other"=>2, "Student > Bachelor"=>4, "Professor"=>2}, "reader_count_by_user_role"=>{"Unspecified"=>2, "Professor > Associate Professor"=>1, "Researcher"=>13, "Student > Doctoral Student"=>4, "Student > Ph. D. 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• http://doi.org/10.1007/s00239-020-09965-x
• http://doi.org/10.1007/s10750-017-3373-2
• http://doi.org/10.1007/s00248-018-1203-3
• http://doi.org/10.1099/ijsem.0.001510
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• http://doi.org/10.1007/s13213-019-01471-w
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• http://doi.org/10.1016/j.algal.2019.101541
• http://doi.org/10.1007/s00203-016-1281-x
• http://doi.org/10.1088/1361-6455/aa9c3c
• http://doi.org/10.1093/femsec/fiv143
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• http://doi.org/10.3389/fmicb.2020.572131
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• http://doi.org/10.1007/s10531-015-0890-z

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{"EMBL"=>1, "UNIPROT"=>4462}

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• {"id"=>"393133163901222912", "text"=>"Cultivation, Complete Genome Sequencing of Gloeobacter kilaueensis from a Lava Cave in Hawaii http://t.co/Q1ue91YqFf http://t.co/zzV9kqypRA", "created_at"=>"2013-10-23T21:53:45Z", "user"=>"PLOSONE", "user_name"=>"PLOS ONE", "user_profile_image"=>"http://pbs.twimg.com/profile_images/2429958559/mzjl6as5u2m09r2erof6_normal.jpeg"}
• {"id"=>"393133379098791937", "text"=>"RT @PLOSONE: Cultivation, Complete Genome Sequencing of Gloeobacter kilaueensis from a Lava Cave in Hawaii http://t.co/Q1ue91YqFf http://t.…", "created_at"=>"2013-10-23T21:54:36Z", "user"=>"svetasvet5", "user_name"=>"Svetlana Aminovna", "user_profile_image"=>"http://a0.twimg.com/profile_images/378800000497108816/52dbfe685bd6276d9d8b20c83e7d6f89_normal.jpeg"}
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• {"title"=>"Gloeomargarita lithophora", "url"=>"http://en.wikipedia.org/wiki/Gloeomargarita_lithophora", "timestamp"=>"2019-02-04T22:54:06Z"}
• {"title"=>"Gloeobacter", "url"=>"http://en.wikipedia.org/wiki/Gloeobacter", "timestamp"=>"2018-05-15T21:28:08Z"}
• {"title"=>"Gloeobacter", "url"=>"http://nl.wikipedia.org/wiki/Gloeobacter", "timestamp"=>"2018-07-11T21:51:33Z"}
• {"title"=>"Gloeobacter", "url"=>"http://pt.wikipedia.org/wiki/Gloeobacter", "timestamp"=>"2017-07-21T15:35:50Z"}

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Figshare

• {"files"=>["https://ndownloader.figshare.com/files/1256386"], "description"=>"<p>The 13,655×41 matrix was imported into the R program, and Pearson correlation coefficients were calculated using the ‘gplots’ package. Colors represent correlation values ranging from 0 to 1, with green representing lowest correlation and white representing highest correlation.</p>", "links"=>[], "tags"=>["clustered", "heatmap", "sequenced", "cyanobacteria", "genomes", "matrix", "orthologous", "groups", "41"], "article_id"=>831245, "categories"=>["Biological Sciences"], "users"=>["Jimmy H. W. Saw", "Michael Schatz", "Mark V. Brown", "Dennis D. Kunkel", "Jamie S. Foster", "Harry Shick", "Stephanie Christensen", "Shaobin Hou", "Xuehua Wan", "Stuart P. Donachie"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0076376.g005", "stats"=>{"downloads"=>5, "page_views"=>106, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Hierarchical_clustered_heatmap_representation_of_completely_sequenced_cyanobacteria_genomes_based_on_a_correlation_matrix_of_the_presence_or_absence_of_13_655_orthologous_groups_identified_in_41_cyanobacteria_/831245", "title"=>"Hierarchical clustered heatmap representation of completely sequenced cyanobacteria genomes based on a correlation matrix of the presence or absence of 13,655 orthologous groups identified in 41 cyanobacteria.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-10-23 03:31:42"}
• {"files"=>["https://ndownloader.figshare.com/files/1256381"], "description"=>"<p>Sequences were aligned using Muscle, edited with Gblocks, and the tree was inferred using RAxML program with 100 bootstrap replicates and the GTR+Gamma model of rate substitution. The root of the tree was shortened to fit the figure (A). Sequences in this tree included the top 50 BLASTn matches of the <i>Gloeobacter kilaueensis</i> JS1^T 16S rDNA sequence, among others. A phylogenetic tree was also constructed on the basis of 43 ribosomal proteins found in 41 cyanobacteria and the <i>Beggiatoa</i> sp. PS outgroup (B). Amino acid sequences of the 43 such proteins in each genome were individually aligned using Muscle, trimmed with Gblocks, and concatenated. Based on 5,359 aligned characters, the maximum likelihood analysis was performed using the RAxML program with the Gamma+WAG model of amino acid substitution and 100 bootstrap replicates, and visualized in FigTree.</p>", "links"=>[], "tags"=>["phylogenetic", "16s", "rrna"], "article_id"=>831241, "categories"=>["Biological Sciences"], "users"=>["Jimmy H. W. Saw", "Michael Schatz", "Mark V. Brown", "Dennis D. Kunkel", "Jamie S. Foster", "Harry Shick", "Stephanie Christensen", "Shaobin Hou", "Xuehua Wan", "Stuart P. Donachie"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0076376.g004", "stats"=>{"downloads"=>2, "page_views"=>15, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Maximum_likelihood_phylogenetic_tree_based_on_16S_rRNA_gene_sequences_/831241", "title"=>"Maximum likelihood phylogenetic tree based on 16S rRNA gene sequences.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-10-23 03:31:42"}
• {"files"=>["https://ndownloader.figshare.com/files/1256379"], "description"=>"<p>(A) MUMMER alignment; colored rectangular blocks represent protein coding sequences according to COG functional categories. Lines represent matching DNA segments between the two genomes. Colors of connecting line segments are categorized according to % identities. (B) Shared orthologs identified between <i>Gloeobacter kilaueensis</i> JS1^T and <i>Gloeobacter violaceus</i> PCC 7421^T and their locations in the genomes. Lines connect orthologous genes and are colored according to COG functional categories. BLASTp E-values between bi-directional best hits are less than or equal to 1×10⁻⁵. Custom Python scripts were written to visualize these alignments.</p>", "links"=>[], "tags"=>["synteny", "genome", "rearrangements", "pcc"], "article_id"=>831239, "categories"=>["Biological Sciences"], "users"=>["Jimmy H. W. Saw", "Michael Schatz", "Mark V. Brown", "Dennis D. Kunkel", "Jamie S. Foster", "Harry Shick", "Stephanie Christensen", "Shaobin Hou", "Xuehua Wan", "Stuart P. Donachie"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0076376.g003", "stats"=>{"downloads"=>6, "page_views"=>33, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Comparison_of_gene_synteny_and_genome_rearrangements_between_Gloeobacter_kilaueensis_JS1_T_and_Gloeobacter_violaceus_PCC_7421_T_/831239", "title"=>"Comparison of gene synteny and genome rearrangements between <i>Gloeobacter kilaueensis</i> JS1^T and <i>Gloeobacter violaceus</i> PCC 7421^T.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-10-23 03:31:42"}
• {"files"=>["https://ndownloader.figshare.com/files/1256361"], "description"=>"<p>Dividing cells are near the top and left of the image. Note mucilaginous material among the cells. Scale bar is 1 µm.</p>", "links"=>[], "tags"=>["electron", "micrograph", "cells", "grown", "modified", "bg-11"], "article_id"=>831221, "categories"=>["Biological Sciences"], "users"=>["Jimmy H. W. Saw", "Michael Schatz", "Mark V. Brown", "Dennis D. Kunkel", "Jamie S. Foster", "Harry Shick", "Stephanie Christensen", "Shaobin Hou", "Xuehua Wan", "Stuart P. Donachie"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0076376.g001", "stats"=>{"downloads"=>3, "page_views"=>217, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Scanning_electron_micrograph_of_Gloeobacter_kilaueensis_JS1_T_cells_grown_in_modified_BG_11_liquid_medium_/831221", "title"=>"Scanning electron micrograph of <i>Gloeobacter kilaueensis</i> JS1^T cells grown in modified BG-11 liquid medium.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-10-23 03:31:42"}
• {"files"=>["https://ndownloader.figshare.com/files/1256393", "https://ndownloader.figshare.com/files/1256394", "https://ndownloader.figshare.com/files/1256395", "https://ndownloader.figshare.com/files/1256396", "https://ndownloader.figshare.com/files/1256397", "https://ndownloader.figshare.com/files/1256398", "https://ndownloader.figshare.com/files/1256399", "https://ndownloader.figshare.com/files/1256400"], "description"=>"<div><p>The ancestor of <i>Gloeobacter violaceus</i> PCC 7421^T is believed to have diverged from that of all known cyanobacteria before the evolution of thylakoid membranes and plant plastids. The long and largely independent evolutionary history of <i>G. violaceus</i> presents an organism retaining ancestral features of early oxygenic photoautotrophs, and in whom cyanobacteria evolution can be investigated. No other <i>Gloeobacter</i> species has been described since the genus was established in 1974 (Rippka <i>et al.</i>, Arch Microbiol 100:435). <i>Gloeobacter</i> affiliated ribosomal gene sequences have been reported in environmental DNA libraries, but only the type strain's genome has been sequenced. However, we report here the cultivation of a new <i>Gloeobacter</i> species, <i>G. kilaueensis</i> JS1^T, from an epilithic biofilm in a lava cave in Kīlauea Caldera, Hawai'i. The strain's genome was sequenced from an enriched culture resembling a low-complexity metagenomic sample, using 9 kb paired-end 454 pyrosequences and 400 bp paired-end Illumina reads. The JS1^T and <i>G. violaceus</i> PCC 7421^T genomes have little gene synteny despite sharing 2842 orthologous genes; comparing the genomes shows they do not belong to the same species. Our results support establishing a new species to accommodate JS1^T, for which we propose the name <i>Gloeobacter kilaueensis</i> sp. nov. Strain JS1^T has been deposited in the American Type Culture Collection (BAA-2537), the Scottish Marine Institute's Culture Collection of Algae and Protozoa (CCAP 1431/1), and the Belgian Coordinated Collections of Microorganisms (ULC0316). The <i>G. kilaueensis</i> holotype has been deposited in the Algal Collection of the US National Herbarium (US# 217948). The JS1^T genome sequence has been deposited in GenBank under accession number CP003587. The G+C content of the genome is 60.54 mol%. The complete genome sequence of <i>G. kilaueensis</i> JS1^T may further understanding of cyanobacteria evolution, and the shift from anoxygenic to oxygenic photosynthesis.</p></div>", "links"=>[], "tags"=>["cultivation", "genome", "sequencing", "lava"], "article_id"=>831252, "categories"=>["Biological Sciences"], "users"=>["Jimmy H. W. Saw", "Michael Schatz", "Mark V. Brown", "Dennis D. Kunkel", "Jamie S. Foster", "Harry Shick", "Stephanie Christensen", "Shaobin Hou", "Xuehua Wan", "Stuart P. Donachie"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0076376.s001", "https://dx.doi.org/10.1371/journal.pone.0076376.s002", "https://dx.doi.org/10.1371/journal.pone.0076376.s003", "https://dx.doi.org/10.1371/journal.pone.0076376.s004", "https://dx.doi.org/10.1371/journal.pone.0076376.s005", "https://dx.doi.org/10.1371/journal.pone.0076376.s006", "https://dx.doi.org/10.1371/journal.pone.0076376.s007", "https://dx.doi.org/10.1371/journal.pone.0076376.s008"], "stats"=>{"downloads"=>15, "page_views"=>20, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Cultivation_and_Complete_Genome_Sequencing_of_Gloeobacter_kilaueensis_sp_nov_from_a_Lava_Cave_in_K_lauea_Caldera_Hawai_i/831252", "title"=>"Cultivation and Complete Genome Sequencing of <i>Gloeobacter kilaueensis</i> sp. nov., from a Lava Cave in Kīlauea Caldera, Hawai'i", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2013-10-23 03:31:42"}
• {"files"=>["https://ndownloader.figshare.com/files/1256374"], "description"=>"<p>From inside out: GC skew (Yellow>0, Green<0), GC percent (Blue>50%, Red<50%), Newbler scaffold contigs, Celera contigs, Velvet contigs (Illumina reads only), read coverage (Combined 454 and Illumina reads sampled for 1,000 bp window. Highest coverage is 368×), minimal tiling clone pairs (shown in red), recruited reads from metagenome, taxonomic rank of top BLAST hit (yellow = <i>Cyanobacteria</i>, Red = others, Grey = no BLAST hit), coding regions in minus and plus strands (colored by COG functional categories). CRISPR repeat regions are highlighted in yellow in the outermost circle. Locations of genes involved in photosystems are labeled in the outermost circle.</p>", "links"=>[], "tags"=>[], "article_id"=>831234, "categories"=>["Biological Sciences"], "users"=>["Jimmy H. W. Saw", "Michael Schatz", "Mark V. Brown", "Dennis D. Kunkel", "Jamie S. Foster", "Harry Shick", "Stephanie Christensen", "Shaobin Hou", "Xuehua Wan", "Stuart P. Donachie"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0076376.g002", "stats"=>{"downloads"=>4, "page_views"=>18, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Circular_representation_of_the_Gloeobacter_kilaueensis_JS1_T_genome_/831234", "title"=>"Circular representation of the <i>Gloeobacter kilaueensis</i> JS1^T genome.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-10-23 03:31:42"}
• {"files"=>["https://ndownloader.figshare.com/files/1256389"], "description"=>"<p><i>G. kilaueensis</i> JS1^T genome assembly statistics.</p>", "links"=>[], "tags"=>["genome"], "article_id"=>831248, "categories"=>["Biological Sciences"], "users"=>["Jimmy H. W. Saw", "Michael Schatz", "Mark V. Brown", "Dennis D. Kunkel", "Jamie S. Foster", "Harry Shick", "Stephanie Christensen", "Shaobin Hou", "Xuehua Wan", "Stuart P. Donachie"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0076376.t001", "stats"=>{"downloads"=>5, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_G_kilaueensis_JS1_T_genome_assembly_statistics_/831248", "title"=>"<i>G. kilaueensis</i> JS1^T genome assembly statistics.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-10-23 03:31:42"}
• {"files"=>["https://ndownloader.figshare.com/files/1256387"], "description"=>"<p>General features of the <i>G. kilaueensis</i> JS1^T genome and comparison with that of <i>Gloeobacter violaceus</i> PCC 7421^T.</p>", "links"=>[], "tags"=>["genome", "pcc"], "article_id"=>831246, "categories"=>["Biological Sciences"], "users"=>["Jimmy H. W. Saw", "Michael Schatz", "Mark V. Brown", "Dennis D. Kunkel", "Jamie S. Foster", "Harry Shick", "Stephanie Christensen", "Shaobin Hou", "Xuehua Wan", "Stuart P. Donachie"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0076376.t002", "stats"=>{"downloads"=>1, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_General_features_of_the_G_kilaueensis_JS1_T_genome_and_comparison_with_that_of_Gloeobacter_violaceus_PCC_7421_T_/831246", "title"=>"General features of the <i>G. kilaueensis</i> JS1^T genome and comparison with that of <i>Gloeobacter violaceus</i> PCC 7421^T.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-10-23 03:31:42"}

PMC Usage Stats | Further Information

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Relative Metric

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F1000Prime