The Complete Genome Sequence of Haloferax volcanii DS2, a Model Archaeon
Publication Date
March 19, 2010
Journal
PLOS ONE
Authors
Amber L. Hartman, Cédric Norais, Jonathan H. Badger, Stéphane Delmas, et al
Volume
5
Issue
3
Pages
e9605
DOI
https://dx.plos.org/10.1371/journal.pone.0009605
Publisher URL
http://journals.plos.org/plosone/article?id=10.1371%2Fjournal.pone.0009605
PubMed
http://www.ncbi.nlm.nih.gov/pubmed/20333302
PubMed Central
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2841640
Europe PMC
http://europepmc.org/abstract/MED/20333302
Web of Science
000275809700003
Scopus
77954362415
Mendeley
http://www.mendeley.com/research/complete-genome-sequence-haloferax-volcanii-ds2-model-archaeon
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{"title"=>"The complete genome sequence of Haloferax volcanii DS2, a model archaeon", "type"=>"journal", "authors"=>[{"first_name"=>"Amber L.", "last_name"=>"Hartman", "scopus_author_id"=>"24722563600"}, {"first_name"=>"Cédric", "last_name"=>"Norais", "scopus_author_id"=>"6504312728"}, {"first_name"=>"Jonathan H.", "last_name"=>"Badger", "scopus_author_id"=>"35232327400"}, {"first_name"=>"Stéphane", "last_name"=>"Delmas", "scopus_author_id"=>"12791910400"}, {"first_name"=>"Sam", "last_name"=>"Haldenby", "scopus_author_id"=>"57199183883"}, {"first_name"=>"Ramana", "last_name"=>"Madupu", "scopus_author_id"=>"6603189606"}, {"first_name"=>"Jeffrey", "last_name"=>"Robinson", "scopus_author_id"=>"55480349600"}, {"first_name"=>"Hoda", "last_name"=>"Khouri", "scopus_author_id"=>"7003806458"}, {"first_name"=>"Qinghu", "last_name"=>"Ren", "scopus_author_id"=>"7101800116"}, {"first_name"=>"Todd M.", "last_name"=>"Lowe", "scopus_author_id"=>"7102566933"}, {"first_name"=>"Julie", "last_name"=>"Maupin-Furlow", "scopus_author_id"=>"6701793262"}, {"first_name"=>"Mecky", "last_name"=>"Pohlschroder", "scopus_author_id"=>"6603487964"}, {"first_name"=>"Charles", "last_name"=>"Daniels", "scopus_author_id"=>"7102745306"}, {"first_name"=>"Friedhelm", "last_name"=>"Pfeiffer", "scopus_author_id"=>"7102420609"}, {"first_name"=>"Thorsten", "last_name"=>"Allers", "scopus_author_id"=>"6603145025"}, {"first_name"=>"Jonathan A.", "last_name"=>"Eisen", "scopus_author_id"=>"35247902700"}], "year"=>2010, "source"=>"PLoS ONE", "identifiers"=>{"sgr"=>"77954362415", "doi"=>"10.1371/journal.pone.0009605", "pui"=>"368279742", "pmid"=>"20333302", "scopus"=>"2-s2.0-77954362415", "issn"=>"19326203", "isbn"=>"1932-6203 (Electronic)\\n1932-6203 (Linking)"}, "id"=>"09dd3558-a0f7-3af3-abb6-3ca726d658ec", "abstract"=>"BACKGROUND Haloferax volcanii is an easily culturable moderate halophile that grows on simple defined media, is readily transformable, and has a relatively stable genome. This, in combination with its biochemical and genetic tractability, has made Hfx. volcanii a key model organism, not only for the study of halophilicity, but also for archaeal biology in general. METHODOLOGY/PRINCIPAL FINDINGS We report here the sequencing and analysis of the genome of Hfx. volcanii DS2, the type strain of this species. The genome contains a main 2.848 Mb chromosome, three smaller chromosomes pHV1, 3, 4 (85, 438, 636 kb, respectively) and the pHV2 plasmid (6.4 kb). CONCLUSIONS/SIGNIFICANCE The completed genome sequence, presented here, provides an invaluable tool for further in vivo and in vitro studies of Hfx. volcanii.", "link"=>"http://www.mendeley.com/research/complete-genome-sequence-haloferax-volcanii-ds2-model-archaeon", "reader_count"=>176, "reader_count_by_academic_status"=>{"Unspecified"=>4, "Professor > Associate Professor"=>8, "Student > Doctoral Student"=>8, "Researcher"=>36, "Student > Ph. D. Student"=>35, "Student > Postgraduate"=>6, "Student > Master"=>33, "Other"=>2, "Student > Bachelor"=>33, "Lecturer"=>1, "Professor"=>10}, "reader_count_by_user_role"=>{"Unspecified"=>4, "Professor > Associate Professor"=>8, "Student > Doctoral Student"=>8, "Researcher"=>36, "Student > Ph. D. Student"=>35, "Student > Postgraduate"=>6, "Student > Master"=>33, "Other"=>2, "Student > Bachelor"=>33, "Lecturer"=>1, "Professor"=>10}, "reader_count_by_subject_area"=>{"Unspecified"=>7, "Environmental Science"=>6, "Biochemistry, Genetics and Molecular Biology"=>38, "Materials Science"=>1, "Mathematics"=>1, "Agricultural and Biological Sciences"=>102, "Neuroscience"=>1, "Physics and Astronomy"=>1, "Chemistry"=>10, "Computer Science"=>3, "Immunology and Microbiology"=>3, "Earth and Planetary Sciences"=>3}, "reader_count_by_subdiscipline"=>{"Materials Science"=>{"Materials Science"=>1}, "Neuroscience"=>{"Neuroscience"=>1}, "Chemistry"=>{"Chemistry"=>10}, "Physics and Astronomy"=>{"Physics and Astronomy"=>1}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>3}, "Earth and Planetary Sciences"=>{"Earth and Planetary Sciences"=>3}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>102}, "Computer Science"=>{"Computer Science"=>3}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>38}, "Mathematics"=>{"Mathematics"=>1}, "Unspecified"=>{"Unspecified"=>7}, "Environmental Science"=>{"Environmental Science"=>6}}, "reader_count_by_country"=>{"United States"=>6, "United Kingdom"=>1, "Spain"=>2, "Saudi Arabia"=>1, "Canada"=>1, "Brazil"=>1, "Poland"=>1, "Italy"=>1, "Australia"=>1, "France"=>1, "Tunisia"=>1, "Germany"=>3, "Indonesia"=>1}, "group_count"=>4}

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  • {"month"=>"2", "year"=>"2020", "pdf_views"=>"3", "xml_views"=>"1", "html_views"=>"22"}
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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/858837"], "description"=>"<p>(Top): a schematic diagram of the PTS system which is responsible for the concomitant transport and phosphorylation of sugar substrates and is highly regulatable (Bottom). The <i>Hfx. volcanii</i> genome contains a larger repertoire of the PTS system than previously reported in the archaea. * represents genes with homologs in the <i>Hqr. walsbyi genome</i>, <i><sup>∧</sup></i> represents genes with homologs in the <i>Har. marismortui</i> genome, the only other PTS genes described in archaea.</p>", "links"=>[], "tags"=>["biotechnology/applied microbiology", "computational biology/comparative sequence analysis", "computational biology/genomics", "genetics and genomics/genome projects", "genetics and genomics/microbial evolution and genomics", "microbiology/environmental microbiology", "microbiology/microbial evolution and genomics", "microbiology/microbial physiology and metabolism", "molecular biology/bioinformatics", "molecular biology/chromosome structure", "molecular biology/dna repair", "molecular biology/molecular evolution"], "article_id"=>529261, "categories"=>["Medicine", "Molecular Biology", "Microbiology", "Biotechnology", "Genetics", "Infectious Diseases"], "users"=>["Amber L. Hartman", "Cédric Norais", "Jonathan H. Badger", "Stéphane Delmas", "Sam Haldenby", "Ramana Madupu", "Jeffrey Robinson", "Hoda Khouri", "Qinghu Ren", "Todd M. Lowe", "Julie Maupin-Furlow", "Mecky Pohlschroder", "Charles Daniels", "Friedhelm Pfeiffer", "Thorsten Allers", "Jonathan A. Eisen"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0009605.g007", "stats"=>{"downloads"=>1, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_PTS_system_in_Hfx_volcanii_/529261", "title"=>"PTS system in <i>Hfx. volcanii</i>.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2010-03-19 02:34:21"}
  • {"files"=>["https://ndownloader.figshare.com/files/859106"], "description"=>"1<p><i>H.v.</i>, <i>Haloferax volcanii</i>, <i>H.m.</i>, <i>Haloarcula marismortui</i>, <i>H.s.</i>, <i>Halobacterium</i> sp. NRC-1, <i>N.p.</i>, <i>Natronomonas pharaonis</i>, <i>H.w.</i>, <i>Haloquadratum walsbyi</i>.</p>", "links"=>[], "tags"=>["abc", "cog", "haloarchaeal"], "article_id"=>529545, "categories"=>["Medicine", "Molecular Biology", "Microbiology", "Biotechnology", "Genetics", "Infectious Diseases"], "users"=>["Amber L. Hartman", "Cédric Norais", "Jonathan H. Badger", "Stéphane Delmas", "Sam Haldenby", "Ramana Madupu", "Jeffrey Robinson", "Hoda Khouri", "Qinghu Ren", "Todd M. Lowe", "Julie Maupin-Furlow", "Mecky Pohlschroder", "Charles Daniels", "Friedhelm Pfeiffer", "Thorsten Allers", "Jonathan A. Eisen"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0009605.t003", "stats"=>{"downloads"=>5, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Homologs_of_ABC_transporters_by_COG_category_number_in_selected_haloarchaeal_genomes_1_/529545", "title"=>"Homologs of ABC transporters, by COG category number, in selected haloarchaeal genomes.<sup>1</sup>", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2010-03-19 02:39:05"}
  • {"files"=>["https://ndownloader.figshare.com/files/858957"], "description"=>"1<p>Evidence codes - TAS: Traceable Author Statement (<i>i.e.</i>, a direct report exists in the literature); NAS: Non-traceable Author Statement (<i>i.e.</i>, not directly observed for the living, isolated sample, but based on a generally accepted property for the species, or anecdotal evidence).</p>2<p><i>Hfx. volcanii</i>, which was long considered to be non-motile, has recently been shown to exhibit flagella-dependent motility (Pohlschroder, submitted), consistent with the presence of the <i>fla</i> genes in its genome.</p>", "links"=>[], "tags"=>["ds2", "genome", "sequencing", "specifications"], "article_id"=>529397, "categories"=>["Medicine", "Molecular Biology", "Microbiology", "Biotechnology", "Genetics", "Infectious Diseases"], "users"=>["Amber L. Hartman", "Cédric Norais", "Jonathan H. Badger", "Stéphane Delmas", "Sam Haldenby", "Ramana Madupu", "Jeffrey Robinson", "Hoda Khouri", "Qinghu Ren", "Todd M. Lowe", "Julie Maupin-Furlow", "Mecky Pohlschroder", "Charles Daniels", "Friedhelm Pfeiffer", "Thorsten Allers", "Jonathan A. Eisen"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0009605.t005", "stats"=>{"downloads"=>5, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Classification_and_general_features_of_Hfx_volcanii_DS2_and_this_genome_sequencing_project_according_to_the_Minimum_information_about_a_genome_sequence_MIGS_specifications_163_/529397", "title"=>"Classification and general features of <i>Hfx. volcanii</i> DS2 and this genome sequencing project according to the “Minimum information about a genome sequence (MIGS)” specifications [163].", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2010-03-19 02:36:37"}
  • {"files"=>["https://ndownloader.figshare.com/files/858721"], "description"=>"<p>A synonymous codon usage (SCU) table was generated for each individual replicon. These were compared with SCU tables generated from a moving window of size of 30 protein coding sequences (CDS) along each replicon. Chi-square analysis (40 degrees of freedom, Stop, Met and Trp codons were omitted) was carried out to determine whether the SCU of each window of CDSs was statistically similar to each whole-replicon SCU. Comparisons were carried out in an automated manner using a C++ encoded program, SCUBA (Synonymous Codon Usage Bias Analysis).</p>", "links"=>[], "tags"=>["usage"], "article_id"=>529166, "categories"=>["Medicine", "Molecular Biology", "Microbiology", "Biotechnology", "Genetics", "Infectious Diseases"], "users"=>["Amber L. Hartman", "Cédric Norais", "Jonathan H. Badger", "Stéphane Delmas", "Sam Haldenby", "Ramana Madupu", "Jeffrey Robinson", "Hoda Khouri", "Qinghu Ren", "Todd M. Lowe", "Julie Maupin-Furlow", "Mecky Pohlschroder", "Charles Daniels", "Friedhelm Pfeiffer", "Thorsten Allers", "Jonathan A. Eisen"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0009605.g006", "stats"=>{"downloads"=>3, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Codon_usage_in_Hfx_volcanii_/529166", "title"=>"Codon usage in <i>Hfx. volcanii</i>.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2010-03-19 02:32:46"}
  • {"files"=>["https://ndownloader.figshare.com/files/858627"], "description"=>"<p>Both the GC-rich <i>Hfx. volcanii</i> genome and the AT-rich <i>Hqr. walsbyi</i> genome are “evolving away” from their respective IS elements. Plot of GC content (black) overlaid with GC content of IS elements (yellow) for the <i>Hfx. volcanii</i> main chromosome (A), <i>Hfx. volcanii</i> pHV4 (B), and <i>Hqr. walsbyi</i> main chromosome (C).</p>", "links"=>[], "tags"=>["genomes", "elements", "gc"], "article_id"=>529076, "categories"=>["Medicine", "Molecular Biology", "Microbiology", "Biotechnology", "Genetics", "Infectious Diseases"], "users"=>["Amber L. Hartman", "Cédric Norais", "Jonathan H. Badger", "Stéphane Delmas", "Sam Haldenby", "Ramana Madupu", "Jeffrey Robinson", "Hoda Khouri", "Qinghu Ren", "Todd M. Lowe", "Julie Maupin-Furlow", "Mecky Pohlschroder", "Charles Daniels", "Friedhelm Pfeiffer", "Thorsten Allers", "Jonathan A. Eisen"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0009605.g005", "stats"=>{"downloads"=>1, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Haloarchaeal_genomes_are_8220_evolving_away_8221_from_IS_elements_in_regard_to_GC_content_/529076", "title"=>"Haloarchaeal genomes are “evolving away” from IS elements in regard to GC content.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2010-03-19 02:31:16"}
  • {"files"=>["https://ndownloader.figshare.com/files/858916"], "description"=>"<p>Note some of these identifications are based on functional studies, some are predictions based on analysis of the genome sequence.</p>", "links"=>[], "tags"=>["replication", "genes", "ds2"], "article_id"=>529358, "categories"=>["Medicine", "Molecular Biology", "Microbiology", "Biotechnology", "Genetics", "Infectious Diseases"], "users"=>["Amber L. Hartman", "Cédric Norais", "Jonathan H. Badger", "Stéphane Delmas", "Sam Haldenby", "Ramana Madupu", "Jeffrey Robinson", "Hoda Khouri", "Qinghu Ren", "Todd M. Lowe", "Julie Maupin-Furlow", "Mecky Pohlschroder", "Charles Daniels", "Friedhelm Pfeiffer", "Thorsten Allers", "Jonathan A. Eisen"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0009605.t004", "stats"=>{"downloads"=>1, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_DNA_replication_associated_genes_in_the_Hfx_volcanii_DS2_genome_/529358", "title"=>"DNA replication associated genes in the <i>Hfx. volcanii</i> DS2 genome.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2010-03-19 02:35:58"}
  • {"files"=>["https://ndownloader.figshare.com/files/859047"], "description"=>"<p>Location of CRISPR regions in selected haloarchaeal genomes.</p>", "links"=>[], "tags"=>["crispr", "regions", "haloarchaeal"], "article_id"=>529486, "categories"=>["Medicine", "Molecular Biology", "Microbiology", "Biotechnology", "Genetics", "Infectious Diseases"], "users"=>["Amber L. Hartman", "Cédric Norais", "Jonathan H. Badger", "Stéphane Delmas", "Sam Haldenby", "Ramana Madupu", "Jeffrey Robinson", "Hoda Khouri", "Qinghu Ren", "Todd M. Lowe", "Julie Maupin-Furlow", "Mecky Pohlschroder", "Charles Daniels", "Friedhelm Pfeiffer", "Thorsten Allers", "Jonathan A. Eisen"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0009605.t002", "stats"=>{"downloads"=>4, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Location_of_CRISPR_regions_in_selected_haloarchaeal_genomes_/529486", "title"=>"Location of CRISPR regions in selected haloarchaeal genomes.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2010-03-19 02:38:06"}
  • {"files"=>["https://ndownloader.figshare.com/files/426418", "https://ndownloader.figshare.com/files/426467", "https://ndownloader.figshare.com/files/426499", "https://ndownloader.figshare.com/files/426536"], "description"=>"<div><h3>Background</h3><p><em>Haloferax volcanii</em> is an easily culturable moderate halophile that grows on simple defined media, is readily transformable, and has a relatively stable genome. This, in combination with its biochemical and genetic tractability, has made <em>Hfx. volcanii</em> a key model organism, not only for the study of halophilicity, but also for archaeal biology in general.</p><h3>Methodology/Principal Findings</h3><p>We report here the sequencing and analysis of the genome of <em>Hfx. volcanii</em> DS2, the type strain of this species. The genome contains a main 2.848 Mb chromosome, three smaller chromosomes pHV1, 3, 4 (85, 438, 636 kb, respectively) and the pHV2 plasmid (6.4 kb).</p><h3>Conclusions/Significance</h3><p>The completed genome sequence, presented here, provides an invaluable tool for further <em>in vivo</em> and <em>in vitro</em> studies of <em>Hfx. volcanii</em>.</p></div>", "links"=>[], "tags"=>["genome", "archaeon"], "article_id"=>144171, "categories"=>["Medicine", "Molecular Biology", "Microbiology", "Biotechnology", "Genetics", "Cancer"], "users"=>["Amber L. Hartman", "Cédric Norais", "Jonathan H. Badger", "Stéphane Delmas", "Sam Haldenby", "Ramana Madupu", "Jeffrey Robinson", "Hoda Khouri", "Qinghu Ren", "Todd M. Lowe", "Julie Maupin-Furlow", "Mecky Pohlschroder", "Charles Daniels", "Friedhelm Pfeiffer", "Thorsten Allers", "Jonathan A. Eisen"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0009605.s001", "https://dx.doi.org/10.1371/journal.pone.0009605.s002", "https://dx.doi.org/10.1371/journal.pone.0009605.s003", "https://dx.doi.org/10.1371/journal.pone.0009605.s004"], "stats"=>{"downloads"=>5, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/The_Complete_Genome_Sequence_of_Haloferax_volcanii_DS2_a_Model_Archaeon/144171", "title"=>"The Complete Genome Sequence of <em>Haloferax volcanii</em> DS2, a Model Archaeon", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2010-03-19 01:09:31"}
  • {"files"=>["https://ndownloader.figshare.com/files/858257"], "description"=>"<p>(A) Nucleotide skews obtained using the Zcurve method <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0009605#pone.0009605-Zhang1\" target=\"_blank\">[61]</a> for the four <i>Hfx. volcanii</i> chromosomes. The * indicates the positions of replication origins identified in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0009605#pone.0009605-Norais1\" target=\"_blank\">[43]</a>. (B) Comparison of the Zcurve GC skew from the main chromosome of <i>Hfx. volcanii</i> with those of other halophiles. The curves have been offset to start at respective replication origins and show the inverted GC skews of haloarchaea versus the halophilic bacterium that is characteristic of other bacteria and non-halophilic archaea as explained in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0009605#pone.0009605-Norais1\" target=\"_blank\">[43]</a>.</p>", "links"=>[], "tags"=>["cumulative", "skews", "episomes", "halophilic"], "article_id"=>528697, "categories"=>["Medicine", "Molecular Biology", "Microbiology", "Biotechnology", "Genetics", "Infectious Diseases"], "users"=>["Amber L. Hartman", "Cédric Norais", "Jonathan H. Badger", "Stéphane Delmas", "Sam Haldenby", "Ramana Madupu", "Jeffrey Robinson", "Hoda Khouri", "Qinghu Ren", "Todd M. Lowe", "Julie Maupin-Furlow", "Mecky Pohlschroder", "Charles Daniels", "Friedhelm Pfeiffer", "Thorsten Allers", "Jonathan A. Eisen"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0009605.g002", "stats"=>{"downloads"=>1, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Nucleotide_cumulative_skews_of_Hfx_volcanii_episomes_and_other_halophilic_bacteria_and_archaea_/528697", "title"=>"Nucleotide cumulative skews of <i>Hfx. volcanii</i> episomes and other halophilic bacteria and archaea.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2010-03-19 02:24:57"}
  • {"files"=>["https://ndownloader.figshare.com/files/859006"], "description"=>"<p>General features of the <i>Hfx. volcanii</i> DS2 genome.</p>", "links"=>[], "tags"=>["ds2"], "article_id"=>529450, "categories"=>["Medicine", "Molecular Biology", "Microbiology", "Biotechnology", "Genetics", "Infectious Diseases"], "users"=>["Amber L. Hartman", "Cédric Norais", "Jonathan H. Badger", "Stéphane Delmas", "Sam Haldenby", "Ramana Madupu", "Jeffrey Robinson", "Hoda Khouri", "Qinghu Ren", "Todd M. Lowe", "Julie Maupin-Furlow", "Mecky Pohlschroder", "Charles Daniels", "Friedhelm Pfeiffer", "Thorsten Allers", "Jonathan A. Eisen"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0009605.t001", "stats"=>{"downloads"=>6, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_General_features_of_the_Hfx_volcanii_DS2_genome_/529450", "title"=>"General features of the <i>Hfx. volcanii</i> DS2 genome.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2010-03-19 02:37:30"}
  • {"files"=>["https://ndownloader.figshare.com/files/858499"], "description"=>"<p>Plot of the average %GC content of the genome vs. the average isoelectric point of the multiple chromosomes of <i>Hfx. volcanii</i> (A) and the predicted proteome for sequenced archaeal genomes (B). Groups of ORFs that show abnormal pI distribution (C). Distribution of pI of all proteins in haloarchaea compared to other archaea does not show a bimodal distribution (D).</p>", "links"=>[], "tags"=>["biotechnology/applied microbiology", "computational biology/comparative sequence analysis", "computational biology/genomics", "genetics and genomics/genome projects", "genetics and genomics/microbial evolution and genomics", "microbiology/environmental microbiology", "microbiology/microbial evolution and genomics", "microbiology/microbial physiology and metabolism", "molecular biology/bioinformatics", "molecular biology/chromosome structure", "molecular biology/dna repair", "molecular biology/molecular evolution"], "article_id"=>528933, "categories"=>["Medicine", "Molecular Biology", "Microbiology", "Biotechnology", "Genetics", "Infectious Diseases"], "users"=>["Amber L. Hartman", "Cédric Norais", "Jonathan H. Badger", "Stéphane Delmas", "Sam Haldenby", "Ramana Madupu", "Jeffrey Robinson", "Hoda Khouri", "Qinghu Ren", "Todd M. Lowe", "Julie Maupin-Furlow", "Mecky Pohlschroder", "Charles Daniels", "Friedhelm Pfeiffer", "Thorsten Allers", "Jonathan A. Eisen"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0009605.g004", "stats"=>{"downloads"=>1, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_GC_content_patterns_/528933", "title"=>"GC content patterns.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2010-03-19 02:28:53"}
  • {"files"=>["https://ndownloader.figshare.com/files/858125"], "description"=>"<p>The circles display the following features, starting with the outermost circle: (1) forward strand CDSs; (2) reverse strand CDSs, (3) chi square deviation of local nucleotide composition from the genome average; (4) GC skew (G−C)/(G+C) (blue bars represent positive values, red bars represent negative values) (5) tRNAs (green lines); (6) rRNAs (blue lines). Gene color indicates the assigned role category. A gene can be included in the gene count for multiple role categories.</p>", "links"=>[], "tags"=>["graph", "chromosome"], "article_id"=>528564, "categories"=>["Medicine", "Molecular Biology", "Microbiology", "Biotechnology", "Genetics", "Infectious Diseases"], "users"=>["Amber L. Hartman", "Cédric Norais", "Jonathan H. Badger", "Stéphane Delmas", "Sam Haldenby", "Ramana Madupu", "Jeffrey Robinson", "Hoda Khouri", "Qinghu Ren", "Todd M. Lowe", "Julie Maupin-Furlow", "Mecky Pohlschroder", "Charles Daniels", "Friedhelm Pfeiffer", "Thorsten Allers", "Jonathan A. Eisen"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0009605.g001", "stats"=>{"downloads"=>1, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Circular_graph_of_the_chromosome_of_Hfx_volcanii_/528564", "title"=>"Circular graph of the chromosome of <i>Hfx. volcanii</i>.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2010-03-19 02:22:44"}
  • {"files"=>["https://ndownloader.figshare.com/files/858387"], "description"=>"<p>(A) 16S rRNA phylogeny of the haloarchaea that are closely related to <i>Hfx. volcanii</i> and that are discussed in the text. Organisms whose genomes are sequenced are in bold. (B and C) Genome alignments comparing the main chromosome of <i>Hfx. volcanii</i> with those of <i>Hbt.</i> sp. NRC-1 (B) and <i>Hqr. walsbyii</i> (C).</p>", "links"=>[], "tags"=>["biotechnology/applied microbiology", "computational biology/comparative sequence analysis", "computational biology/genomics", "genetics and genomics/genome projects", "genetics and genomics/microbial evolution and genomics", "microbiology/environmental microbiology", "microbiology/microbial evolution and genomics", "microbiology/microbial physiology and metabolism", "molecular biology/bioinformatics", "molecular biology/chromosome structure", "molecular biology/dna repair", "molecular biology/molecular evolution"], "article_id"=>528818, "categories"=>["Medicine", "Molecular Biology", "Microbiology", "Biotechnology", "Genetics", "Infectious Diseases"], "users"=>["Amber L. Hartman", "Cédric Norais", "Jonathan H. Badger", "Stéphane Delmas", "Sam Haldenby", "Ramana Madupu", "Jeffrey Robinson", "Hoda Khouri", "Qinghu Ren", "Todd M. Lowe", "Julie Maupin-Furlow", "Mecky Pohlschroder", "Charles Daniels", "Friedhelm Pfeiffer", "Thorsten Allers", "Jonathan A. Eisen"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0009605.g003", "stats"=>{"downloads"=>1, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Phylogenomics_of_Hfx_volcanii_/528818", "title"=>"Phylogenomics of <i>Hfx. volcanii</i>.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2010-03-19 02:26:58"}

PMC Usage Stats | Further Information

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Relative Metric

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