Haloquadratum walsbyi : Limited Diversity in a Global Pond
Publication Date
June 20, 2011
Journal
PLOS ONE
Authors
Mike L. Dyall Smith, Friedhelm Pfeiffer, Kathrin Klee, Peter Palm, et al
Volume
6
Issue
6
Pages
e20968
DOI
http://doi.org/10.1371/journal.pone.0020968
Publisher URL
http://journals.plos.org/plosone/article?id=10.1371%2Fjournal.pone.0020968
PubMed
http://www.ncbi.nlm.nih.gov/pubmed/21701686
PubMed Central
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3119063
Europe PMC
http://europepmc.org/abstract/MED/21701686
Web of Science
000291983800016
Scopus
79959307357
Mendeley
http://www.mendeley.com/research/haloquadratum-walsbyi-limited-diversity-global-pond
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Mendeley | Further Information

{"title"=>"Haloquadratum walsbyi: Limited Diversity in a Global Pond", "type"=>"journal", "authors"=>[{"first_name"=>"Mike L.", "last_name"=>"Dyall-Smith", "scopus_author_id"=>"7003783303"}, {"first_name"=>"Friedhelm", "last_name"=>"Pfeiffer", "scopus_author_id"=>"7102420609"}, {"first_name"=>"Kathrin", "last_name"=>"Klee", "scopus_author_id"=>"15760523400"}, {"first_name"=>"Peter", "last_name"=>"Palm", "scopus_author_id"=>"55296803100"}, {"first_name"=>"Karin", "last_name"=>"Gross", "scopus_author_id"=>"43161264900"}, {"first_name"=>"Stephan C.", "last_name"=>"Schuster", "scopus_author_id"=>"7202029217"}, {"first_name"=>"Markus", "last_name"=>"Rampp", "scopus_author_id"=>"6603136039"}, {"first_name"=>"Dieter", "last_name"=>"Oesterhelt", "scopus_author_id"=>"7101607962"}], "year"=>2011, "source"=>"PLoS ONE", "identifiers"=>{"scopus"=>"2-s2.0-79959307357", "doi"=>"10.1371/journal.pone.0020968", "isbn"=>"1932-6203 (Electronic)\\r1932-6203 (Linking)", "sgr"=>"79959307357", "issn"=>"19326203", "pui"=>"361974865", "pmid"=>"21701686"}, "id"=>"7f02e6c6-3e8e-3cab-9c76-cc2f8b12174a", "abstract"=>"BACKGROUND: Haloquadratum walsbyi commonly dominates the microbial flora of hypersaline waters. Its cells are extremely fragile squares requiring >14%(w/v) salt for growth, properties that should limit its dispersal and promote geographical isolation and divergence. To assess this, the genome sequences of two isolates recovered from sites at near maximum distance on Earth, were compared.\\n\\nPRINCIPAL FINDINGS: Both chromosomes are 3.1 MB in size, and 84% of each sequence was highly similar to the other (98.6% identity), comprising the core sequence. ORFs of this shared sequence were completely synteneic (conserved in genomic orientation and order), without inversion or rearrangement. Strain-specific insertions/deletions could be precisely mapped, often allowing the genetic events to be inferred. Many inferred deletions were associated with short direct repeats (4-20 bp). Deletion-coupled insertions are frequent, producing different sequences at identical positions. In cases where the inserted and deleted sequences are homologous, this leads to variant genes in a common synteneic background (as already described by others). Cas/CRISPR systems are present in C23(T) but have been lost in HBSQ001 except for a few spacer remnants. Numerous types of mobile genetic elements occur in both strains, most of which appear to be active, and with some specifically targetting others. Strain C23(T) carries two ∼6 kb plasmids that show similarity to halovirus His1 and to sequences nearby halovirus/plasmid gene clusters commonly found in haloarchaea.\\n\\nCONCLUSIONS: Deletion-coupled insertions show that Hqr. walsbyi evolves by uptake and precise integration of foreign DNA, probably originating from close relatives. Change is also driven by mobile genetic elements but these do not by themselves explain the atypically low gene coding density found in this species. The remarkable genome conservation despite the presence of active systems for genome rearrangement implies both an efficient global dispersal system, and a high selective fitness for this species.", "link"=>"http://www.mendeley.com/research/haloquadratum-walsbyi-limited-diversity-global-pond", "reader_count"=>49, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>1, "Librarian"=>1, "Researcher"=>10, "Student > Doctoral Student"=>3, "Student > Ph. D. Student"=>11, "Student > Postgraduate"=>2, "Student > Master"=>10, "Other"=>3, "Student > Bachelor"=>5, "Lecturer"=>1, "Professor"=>2}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>1, "Librarian"=>1, "Researcher"=>10, "Student > Doctoral Student"=>3, "Student > Ph. D. Student"=>11, "Student > Postgraduate"=>2, "Student > Master"=>10, "Other"=>3, "Student > Bachelor"=>5, "Lecturer"=>1, "Professor"=>2}, "reader_count_by_subject_area"=>{"Biochemistry, Genetics and Molecular Biology"=>7, "Agricultural and Biological Sciences"=>37, "Medicine and Dentistry"=>1, "Social Sciences"=>1, "Computer Science"=>1, "Immunology and Microbiology"=>1, "Business, Management and Accounting"=>1}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>1}, "Social Sciences"=>{"Social Sciences"=>1}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>37}, "Computer Science"=>{"Computer Science"=>1}, "Business, Management and Accounting"=>{"Business, Management and Accounting"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>7}}, "reader_count_by_country"=>{"New Zealand"=>1, "United States"=>1, "United Kingdom"=>1, "Mexico"=>1, "France"=>1, "Germany"=>2}, "group_count"=>0}

CrossRef

Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/764567"], "description"=>"a<p>Canonical transposons (TP-B), and A-/B-type Small Mobile Repeats (SMR) show a high sequence conservation between elements classified into the same type (commonly >95% sequence identity). PATEs and IS605-type transposons are much more divergent, except for a few types of homogeneous PATEs. MGE types classified into the same family show sequence homology of the element itself or of the encoded transposase. The total number of elements and the number of SSEIs (total/SSEI) is given for strains C23<sup>T</sup> and HBSQ001. For TP-A and PATE, a distinction is made between SSEIs of complete elements (first value) and SSEIs of terminal-only elements that have suffered core deletions (second value in parenthesis, prefixed with a plus sign). Terminal-only TP-As have lost their transposase genes and so have degenerated to PATEs.</p>", "links"=>[], "tags"=>["properties", "categories"], "article_id"=>434939, "categories"=>["Biochemistry", "Genetics", "Microbiology"], "users"=>["Mike L. Dyall-Smith", "Friedhelm Pfeiffer", "Kathrin Klee", "Peter Palm", "Karin Gross", "Stephan C. Schuster", "Markus Rampp", "Dieter Oesterhelt"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0020968.t004", "stats"=>{"downloads"=>2, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_General_properties_of_the_six_categories_of_Haloquadratum_MGEs_/434939", "title"=>"General properties of the six categories of <i>Haloquadratum</i> MGEs.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2011-06-20 01:22:19"}
  • {"files"=>["https://ndownloader.figshare.com/files/383874", "https://ndownloader.figshare.com/files/383911", "https://ndownloader.figshare.com/files/383961", "https://ndownloader.figshare.com/files/384010", "https://ndownloader.figshare.com/files/384051", "https://ndownloader.figshare.com/files/384110", "https://ndownloader.figshare.com/files/384275", "https://ndownloader.figshare.com/files/384343", "https://ndownloader.figshare.com/files/384426", "https://ndownloader.figshare.com/files/384543", "https://ndownloader.figshare.com/files/384584"], "description"=>"<div><h3>Background</h3><p><em>Haloquadratum walsbyi</em> commonly dominates the microbial flora of hypersaline waters. Its cells are extremely fragile squares requiring >14%(w/v) salt for growth, properties that should limit its dispersal and promote geographical isolation and divergence. To assess this, the genome sequences of two isolates recovered from sites at near maximum distance on Earth, were compared.</p> <h3>Principal Findings</h3><p>Both chromosomes are 3.1 MB in size, and 84% of each sequence was highly similar to the other (98.6% identity), comprising the core sequence. ORFs of this shared sequence were completely synteneic (conserved in genomic orientation and order), without inversion or rearrangement. Strain-specific insertions/deletions could be precisely mapped, often allowing the genetic events to be inferred. Many inferred deletions were associated with short direct repeats (4–20 bp). Deletion-coupled insertions are frequent, producing different sequences at identical positions. In cases where the inserted and deleted sequences are homologous, this leads to variant genes in a common synteneic background (as already described by others). Cas/CRISPR systems are present in C23<sup>T</sup> but have been lost in HBSQ001 except for a few spacer remnants. Numerous types of mobile genetic elements occur in both strains, most of which appear to be active, and with some specifically targetting others. Strain C23<sup>T</sup> carries two ∼6 kb plasmids that show similarity to halovirus His1 and to sequences nearby halovirus/plasmid gene clusters commonly found in haloarchaea.</p> <h3>Conclusions</h3><p>Deletion-coupled insertions show that <em>Hqr. walsbyi</em> evolves by uptake and precise integration of foreign DNA, probably originating from close relatives. Change is also driven by mobile genetic elements but these do not by themselves explain the atypically low gene coding density found in this species. The remarkable genome conservation despite the presence of active systems for genome rearrangement implies both an efficient global dispersal system, and a high selective fitness for this species.</p> </div>", "links"=>[], "tags"=>[], "article_id"=>135818, "categories"=>["Biochemistry", "Genetics", "Microbiology"], "users"=>["Mike L. Dyall-Smith", "Friedhelm Pfeiffer", "Kathrin Klee", "Peter Palm", "Karin Gross", "Stephan C. Schuster", "Markus Rampp", "Dieter Oesterhelt"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0020968.s001", "https://dx.doi.org/10.1371/journal.pone.0020968.s002", "https://dx.doi.org/10.1371/journal.pone.0020968.s003", "https://dx.doi.org/10.1371/journal.pone.0020968.s004", "https://dx.doi.org/10.1371/journal.pone.0020968.s005", "https://dx.doi.org/10.1371/journal.pone.0020968.s006", "https://dx.doi.org/10.1371/journal.pone.0020968.s007", "https://dx.doi.org/10.1371/journal.pone.0020968.s008", "https://dx.doi.org/10.1371/journal.pone.0020968.s009", "https://dx.doi.org/10.1371/journal.pone.0020968.s010", "https://dx.doi.org/10.1371/journal.pone.0020968.s011"], "stats"=>{"downloads"=>25, "page_views"=>12, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Haloquadratum_walsbyi_Limited_Diversity_in_a_Global_Pond/135818", "title"=>"<em>Haloquadratum walsbyi</em> : Limited Diversity in a Global Pond", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2011-06-20 01:36:58"}
  • {"files"=>["https://ndownloader.figshare.com/files/764050"], "description"=>"<p>Panel A: Mummer nucleotide alignment, where dots indicate similar sequences in the same orientation (red), or reverse orientation (blue), shared by the two strains. Panels B and D: Tetra-nucleotide variation (TETRA) along the chromosomal sequences of each strain (labeled). Several divergent regions in each plot are labeled in both panels (see text). The %G+C deviation (if a 1 kb window is more than 2.5 SD from the average) is given for HBSQ001 immediately below the panel TETRA plot of panel D. Panel C: comparison of the chromosomal sequences using the Artemis comparison tool (ACT). Red lines indicate regions of high nucleotide similarity; white regions indicate lack of similarity. Above this plot regions of major divergence (DV 1-12) are indicated (and also on the Mummer plot in panel A), while below the previously described genomic islands (GI 1-4 <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0020968#pone.0020968-CuadrosOrellana1\" target=\"_blank\">[13]</a>) are indicated. Panel E: Cumulative GC-skew plots for the chromosomes of C23<sup>T</sup> (red) and HBSQ001 (black). The boxed region extending upwards to panel D outlines the major drop in the cumulative skew plot of HBSQ001.</p>", "links"=>[], "tags"=>["chromosomes", "strains"], "article_id"=>434421, "categories"=>["Biochemistry", "Genetics", "Microbiology"], "users"=>["Mike L. Dyall-Smith", "Friedhelm Pfeiffer", "Kathrin Klee", "Peter Palm", "Karin Gross", "Stephan C. Schuster", "Markus Rampp", "Dieter Oesterhelt"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0020968.g005", "stats"=>{"downloads"=>1, "page_views"=>15, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Comparison_of_the_chromosomes_of_Hqr_walsbyi_strains_C23_T_and_HBSQ001_/434421", "title"=>"Comparison of the chromosomes of <i>Hqr. walsbyi</i> strains C23<sup>T</sup> and HBSQ001.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-06-20 01:13:41"}
  • {"files"=>["https://ndownloader.figshare.com/files/764422"], "description"=>"a<p>CAMERA database, <a href=\"http://camera.calit2.net/about-camera/full-datasets\" target=\"_blank\">http://camera.calit2.net/about-camera/full-datasets</a>.</p>b<p>matches with expect values better than 10<sup>−10</sup>.</p>c<p>All six matching sequences were to Hqrw_6005/Hqrw_7005.</p>d<p>JCVI, J. Craig Venter Institute, USA. Data to be released in 2011 (personal communication, Matt Lewis, JCVI).</p>", "links"=>[], "tags"=>["plasmid", "sequences", "metagenomic"], "article_id"=>434787, "categories"=>["Biochemistry", "Genetics", "Microbiology"], "users"=>["Mike L. Dyall-Smith", "Friedhelm Pfeiffer", "Kathrin Klee", "Peter Palm", "Karin Gross", "Stephan C. Schuster", "Markus Rampp", "Dieter Oesterhelt"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0020968.t002", "stats"=>{"downloads"=>1, "page_views"=>17, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_PL6_plasmid_related_sequences_in_metagenomic_data_/434787", "title"=>"PL6 plasmid related sequences in metagenomic data.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2011-06-20 01:19:47"}
  • {"files"=>["https://ndownloader.figshare.com/files/763759"], "description"=>"<p>Plasmid preparations from the three strains of <i>Haloquadratum</i> were separated by electrophoresis on 1% agarose gels and stained with ethidium bromide. Panel A: the plasmid bands labeled PL6 are super-coiled (sc), open-circular (oc) and dimeric forms of two, closely related, ∼6 kb plasmids (see text for details). The Bajool9 isolate of <i>Haloquadratum </i><a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0020968#pone.0020968-Oh1\" target=\"_blank\">[16]</a> is also seen to carry a similarly sized plasmid as well as a much smaller one, running near the bottom of the gel. The position of contaminating, sheared chromosomal DNA is indicated at the right of each panel (chr). Panel B: more of the plasmid preparation from isolate C23<sup>T</sup> has been loaded, revealing the large plasmid, PL100. In both panels, MW indicates the 1 kb DNA size ladder (Invitrogen), with lengths indicated in kb at the left.</p>", "links"=>[], "tags"=>["strains"], "article_id"=>434129, "categories"=>["Biochemistry", "Genetics", "Microbiology"], "users"=>["Mike L. Dyall-Smith", "Friedhelm Pfeiffer", "Kathrin Klee", "Peter Palm", "Karin Gross", "Stephan C. Schuster", "Markus Rampp", "Dieter Oesterhelt"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0020968.g002", "stats"=>{"downloads"=>1, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Plasmids_of_strains_C23_T_HBSQ001_and_Bajool9_/434129", "title"=>"Plasmids of strains C23<sup>T</sup>, HBSQ001, and Bajool9.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-06-20 01:08:49"}
  • {"files"=>["https://ndownloader.figshare.com/files/764302"], "description"=>"<p>Three CRISPR loci are present in C23<sup>T</sup>, associated with two separate groups of Cas genes (coloured yellow and pink). No Cas genes, and only one, residual CRISPR with 5 spacers, are found in HBSQ001. The DR (direct repeat) sequences are shown beneath the CRISPRs. Shading between the leader sequence of CRISPR-2 of C23<sup>T</sup> and CRISPR-1 of HBSQ001 indicate that they are nearly identical in sequence. The relative position and orientation of ORF HB2151A is shown along with an arrow indicating where it matches (exactly) a spacer sequence in CRISPR-3 of C23<sup>T</sup>. Similarly, the spacer sequences in HBSQ001 that are closely similar to sequences in C23<sup>T</sup> are indicated by arrows, labeled spacer-related sequences, which point to their matching locations in the C23<sup>T</sup> genome. Nucleotide positions are given beneath the CRISPRs and details of the matching spacer sequences are given in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0020968#pone.0020968.s008\" target=\"_blank\">Table S7</a>.</p>", "links"=>[], "tags"=>["systems", "strains"], "article_id"=>434672, "categories"=>["Biochemistry", "Genetics", "Microbiology"], "users"=>["Mike L. Dyall-Smith", "Friedhelm Pfeiffer", "Kathrin Klee", "Peter Palm", "Karin Gross", "Stephan C. Schuster", "Markus Rampp", "Dieter Oesterhelt"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0020968.g007", "stats"=>{"downloads"=>1, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_CRISPR_systems_of_Hqr_walsbyi_strains_C23_T_and_HBSQ001_/434672", "title"=>"CRISPR systems of <i>Hqr. walsbyi</i> strains C23<sup>T</sup> and HBSQ001.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-06-20 01:17:52"}
  • {"files"=>["https://ndownloader.figshare.com/files/763841"], "description"=>"<p>Predicted ORFs are labeled with their locus tags, and arrows represent their orientations and lengths. Nucleotide positions are given above each plasmid. Nucleotide similarity is indicated by the bar chart below the alignment (bar height and darkness of colour indicate the level of nucleotide identity, with solid black indicating 100% identity). The vertically oriented arrowhead at around 3.2 kb indicates a sharp break in homology. Percentage identity values of the corresponding protein sequences (in red) are given between ORFs in the alignment. H-T-H, helix-turn-helix protein domain. TM, transmembrane domain. Solid black arrowheads represent short repeat sequences (see text). The lowest panel shows the cumulative CT-skew plots of both sequences.</p>", "links"=>[], "tags"=>["circular", "plasmids", "pl6a", "pl6b"], "article_id"=>434205, "categories"=>["Biochemistry", "Genetics", "Microbiology"], "users"=>["Mike L. Dyall-Smith", "Friedhelm Pfeiffer", "Kathrin Klee", "Peter Palm", "Karin Gross", "Stephan C. Schuster", "Markus Rampp", "Dieter Oesterhelt"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0020968.g003", "stats"=>{"downloads"=>0, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Comparison_of_circular_plasmids_PL6A_6_129_bp_and_PL6B_6_056_bp_/434205", "title"=>"Comparison of circular plasmids PL6A (6,129 bp) and PL6B (6,056 bp).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-06-20 01:10:05"}
  • {"files"=>["https://ndownloader.figshare.com/files/764380"], "description"=>"a<p><b>DV</b>, major divergent regions between the strains are numbered 1–12 and the corresponding positions in both strains given.</p>b<p><b>GI</b>, genomic islands, as assigned by <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0020968#pone.0020968-CuadrosOrellana1\" target=\"_blank\">[13]</a>. Positions are according to the strain comparison analysis. In the cases of assigned genomic islands, the positions for HBSQ001 from <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0020968#pone.0020968-CuadrosOrellana1\" target=\"_blank\">[13]</a> are also included in parentheses.</p>c<p>Region # refers to the numbered common and strain-strain specific sequences listed in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0020968#pone.0020968.s006\" target=\"_blank\">Table S5</a>.</p>d<p><b>DCI</b>, deletion-coupled insertion.</p>", "links"=>[], "tags"=>["strain-specific", "chromosomal", "regions", "strains"], "article_id"=>434748, "categories"=>["Biochemistry", "Genetics", "Microbiology"], "users"=>["Mike L. Dyall-Smith", "Friedhelm Pfeiffer", "Kathrin Klee", "Peter Palm", "Karin Gross", "Stephan C. Schuster", "Markus Rampp", "Dieter Oesterhelt"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0020968.t003", "stats"=>{"downloads"=>1, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Prominent_strain_specific_chromosomal_regions_of_strains_C23_T_and_HBSQ001_/434748", "title"=>"Prominent strain-specific chromosomal regions of strains C23<sup>T</sup> and HBSQ001.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2011-06-20 01:19:08"}
  • {"files"=>["https://ndownloader.figshare.com/files/764459"], "description"=>"a<p>The data for HBSQ001 have been updated from the previous publication. The number of ORFs is reduced because pseudogenes are now counted as a single ORF even if they consist of several fragments.</p>", "links"=>[], "tags"=>["compared"], "article_id"=>434826, "categories"=>["Biochemistry", "Genetics", "Microbiology"], "users"=>["Mike L. Dyall-Smith", "Friedhelm Pfeiffer", "Kathrin Klee", "Peter Palm", "Karin Gross", "Stephan C. Schuster", "Markus Rampp", "Dieter Oesterhelt"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0020968.t001", "stats"=>{"downloads"=>1, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_General_features_of_Hqr_walsbyi_C23_T_compared_with_those_of_strain_HBSQ001_/434826", "title"=>"General features of <i>Hqr. walsbyi</i> C23<sup>T</sup> compared with those of strain HBSQ001.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2011-06-20 01:20:26"}
  • {"files"=>["https://ndownloader.figshare.com/files/763612"], "description"=>"<p>The constant horizontal axis in all cases is the genome from left to right (first to last base of deposited sequence), with a scale given in Mbp. From top to bottom are plots of: (a) %G+C if the deviation for a 1 kb window is more than 2.5 SD from the average, (b) protein-coding pseudogenes (vertical triangles), excluding those of transposases, (c) variation in tetramer nucleotide composition (TETRA), where darker colors indicated more prominent deviation, (d) GC-profile, (e) cumulative GC-skew, (f) positions and orientations of the following gene categories: CDC6, <i>orc1</i>/<i>cdc6</i> homologues; tRNA, transfer RNA genes; rRNA, ribosomal RNA operons; r-Prot, ribosomal protein genes; RNAP, RNA polymerase subunit genes; CRISPR, loci of clustered regularly interspersed short palindromic repeats. Smaller, unfilled arrowheads in the CDC6 line represent the positions of <i>cdc6</i> pseudogenes. DV6 (divergent region 6, see <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0020968#pone-0020968-g005\" target=\"_blank\">Figure 5</a>) is indicated below the cumulative GC-skew plot. Vertical grey-shaded stripes mark correlating features.</p>", "links"=>[], "tags"=>["genetics and genomics", "microbiology", "Biochemistry"], "article_id"=>433980, "categories"=>["Biochemistry", "Genetics", "Microbiology"], "users"=>["Mike L. Dyall-Smith", "Friedhelm Pfeiffer", "Kathrin Klee", "Peter Palm", "Karin Gross", "Stephan C. Schuster", "Markus Rampp", "Dieter Oesterhelt"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0020968.g001", "stats"=>{"downloads"=>0, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Features_of_the_strain_C23_T_chromosome_/433980", "title"=>"Features of the strain C23<sup>T</sup> chromosome.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-06-20 01:06:20"}
  • {"files"=>["https://ndownloader.figshare.com/files/763928"], "description"=>"<p>Alignment of genomic regions of <i>Haloarcula marismortui</i> (Hmar), <i>Haloferax volcanii</i> (Hvol), <i>Halomicrobium mukohataei</i> (Hmuk), <i>Halorhabdus utahensis</i> (Huta), <i>Natronomonas pharaonis</i> (Napha), <i>Archaeoglobus fulgidus</i> (Archaeoglobus) and <i>Natrialba magadii</i> (Nmag) with the corresponding genes of haloviruses His2, HRPV-1 and plasmid pHK2 (top) and <i>Hqr. walsbyi</i> C23<sup>T</sup> plasmid PL6A (bottom). Locus tags or ORF numbers are given for most ORFs. Homologues of the capsid protein genes of His2 are colour coded (red, green, blue and grey). Homologues of PL6 ORF2 genes are coloured yellow. Integrase (Int) and transposase (Tnp) genes are coloured black. Dashed lines indicate related genes (other than those colour coded) that occur between two or more genomes. Asterisks within the His2 VP1 ORF and its homologues indicate a predicted signal sequence. Genomic position scales are indicated for each genome in kilobase pairs.</p>", "links"=>[], "tags"=>["pl6-associated", "genes"], "article_id"=>434294, "categories"=>["Biochemistry", "Genetics", "Microbiology"], "users"=>["Mike L. Dyall-Smith", "Friedhelm Pfeiffer", "Kathrin Klee", "Peter Palm", "Karin Gross", "Stephan C. Schuster", "Markus Rampp", "Dieter Oesterhelt"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0020968.g004", "stats"=>{"downloads"=>3, "page_views"=>14, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Plasmid_PL6_associated_virus_genes_in_haloarchaea_/434294", "title"=>"Plasmid PL6-associated virus genes in haloarchaea.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-06-20 01:11:34"}
  • {"files"=>["https://ndownloader.figshare.com/files/764530"], "description"=>"<p>Targeting of <i>Haloquadratum</i> MGEs. This lists the 192 targeting events where one MGE was found inserted into another MGE. Rows indicate how frequently elements of the given category have targeted another element, while columns indicate how frequently an element of the given category has been affected by insertion of another element. More than half of the targeting events are caused by A-type SMRs (114, 59%), while the majority of the affected elements are from PATEs (106, 55%) or from IS605-type transposons (TP-A, 64, 33%). Thus, these related categories of elements suffered 88% of the foreign element insertions.</p>", "links"=>[], "tags"=>["lists", "192", "targeting", "events", "mge", "was", "inserted", "rows", "elements", "targeted", "columns", "been", "affected", "insertion", "caused", "a-type", "smrs", "pates", "is605-type", "transposons", "categories", "suffered"], "article_id"=>434866, "categories"=>["Biochemistry", "Genetics", "Microbiology"], "users"=>["Mike L. Dyall-Smith", "Friedhelm Pfeiffer", "Kathrin Klee", "Peter Palm", "Karin Gross", "Stephan C. Schuster", "Markus Rampp", "Dieter Oesterhelt"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0020968.t005", "stats"=>{"downloads"=>0, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Targeting_of_Haloquadratum_MGEs_This_lists_the_192_targeting_events_where_one_MGE_was_found_inserted_into_another_MGE_Rows_indicate_how_frequently_elements_of_the_given_category_have_targeted_another_element_while_columns_indicate_how_frequently_an_eleme/434866", "title"=>"Targeting of <i>Haloquadratum</i> MGEs. This lists the 192 targeting events where one MGE was found inserted into another MGE. Rows indicate how frequently elements of the given category have targeted another element, while columns indicate how frequently an element of the given category has been affected by insertion of another element. More than half of the targeting events are caused by A-type SMRs (114, 59%), while the majority of the affected elements are from PATEs (106, 55%) or from IS605-type transposons (TP-A, 64, 33%). Thus, these related categories of elements suffered 88% of the foreign element insertions.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2011-06-20 01:21:06"}
  • {"files"=>["https://ndownloader.figshare.com/files/764233"], "description"=>"<p>Pie chart showing the types of strain specific regions in both strains. Blue: mobile genetic elements, which includes transposons and transposase-free mobile elements (MITEs, PATEs, and SMRs). Green: insertions and deletions (indels). Red: Deletion-Coupled Insertions (DCI). Long indels and DCIs (> 1.5 kb) are filled colour sectors while medium (0.15–1.5 kb) or short (20–150 bp) sequences in these categories are dotted. Numbers at the outer edge of each sector are the numbers of cases in each category. Data from <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0020968#pone.0020968.s005\" target=\"_blank\">Table S4</a>.</p>", "links"=>[], "tags"=>["strain-specific", "plotted", "numbers"], "article_id"=>434601, "categories"=>["Biochemistry", "Genetics", "Microbiology"], "users"=>["Mike L. Dyall-Smith", "Friedhelm Pfeiffer", "Kathrin Klee", "Peter Palm", "Karin Gross", "Stephan C. Schuster", "Markus Rampp", "Dieter Oesterhelt"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0020968.g006", "stats"=>{"downloads"=>1, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Categories_of_strain_specific_regions_plotted_according_to_the_relative_numbers_in_each_type_/434601", "title"=>"Categories of strain-specific regions, plotted according to the relative numbers in each type.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-06-20 01:16:41"}

PMC Usage Stats | Further Information

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