Genomic Evidence for the Evolution of Streptococcus equi: Host Restriction, Increased Virulence, and Genetic Exchange with Human Pathogens
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{"title"=>"Genomic evidence for the evolution of Streptococcus equi host restriction, increased virulence, and genetic exchange with human pathogens", "type"=>"journal", "authors"=>[{"first_name"=>"Matthew T.G.", "last_name"=>"Holden", "scopus_author_id"=>"7102163449"}, {"first_name"=>"Zoe", "last_name"=>"Heather", "scopus_author_id"=>"25633580700"}, {"first_name"=>"Romain", "last_name"=>"Paillot", "scopus_author_id"=>"8591050900"}, {"first_name"=>"Karen F.", "last_name"=>"Steward", "scopus_author_id"=>"25634732300"}, {"first_name"=>"Katy", "last_name"=>"Webb", "scopus_author_id"=>"25638034300"}, {"first_name"=>"Fern", "last_name"=>"Ainslie", "scopus_author_id"=>"26425015900"}, {"first_name"=>"Thibaud", "last_name"=>"Jourdan", "scopus_author_id"=>"26425136300"}, {"first_name"=>"Nathalie C.", "last_name"=>"Bason", "scopus_author_id"=>"6505841514"}, {"first_name"=>"Nancy E.", "last_name"=>"Holroyd", "scopus_author_id"=>"15047970900"}, {"first_name"=>"Karen", "last_name"=>"Mungall", "scopus_author_id"=>"6603464538"}, {"first_name"=>"Michael A.", "last_name"=>"Quail", "scopus_author_id"=>"35380885000"}, {"first_name"=>"Mandy", "last_name"=>"Sanders", "scopus_author_id"=>"7401468482"}, {"first_name"=>"Mark", "last_name"=>"Simmonds", "scopus_author_id"=>"7103093779"}, {"first_name"=>"David", "last_name"=>"Willey", "scopus_author_id"=>"7006214811"}, {"first_name"=>"Karen", "last_name"=>"Brooks", "scopus_author_id"=>"7102727650"}, {"first_name"=>"David M.", "last_name"=>"Aanensen", "scopus_author_id"=>"6507460526"}, {"first_name"=>"Brian G.", "last_name"=>"Spratt", "scopus_author_id"=>"7006187882"}, {"first_name"=>"Keith A.", "last_name"=>"Jolley", "scopus_author_id"=>"7003265292"}, {"first_name"=>"Martin C.J.", "last_name"=>"Maiden", "scopus_author_id"=>"7006019693"}, {"first_name"=>"Michael", "last_name"=>"Kehoe", "scopus_author_id"=>"25943481900"}, {"first_name"=>"Neil", "last_name"=>"Chanter", "scopus_author_id"=>"7003316935"}, {"first_name"=>"Stephen D.", "last_name"=>"Bentley", "scopus_author_id"=>"7102548116"}, {"first_name"=>"Carl", "last_name"=>"Robinson", "scopus_author_id"=>"12241536000"}, {"first_name"=>"Duncan J.", "last_name"=>"Maskell", "scopus_author_id"=>"7005495784"}, {"first_name"=>"Julian", "last_name"=>"Parkhill", "scopus_author_id"=>"7005397039"}, {"first_name"=>"Andrew S.", "last_name"=>"Waller", "scopus_author_id"=>"8202214400"}], "year"=>2009, "source"=>"PLoS Pathogens", "identifiers"=>{"scopus"=>"2-s2.0-63449097053", "doi"=>"10.1371/journal.ppat.1000346", "sgr"=>"63449097053", "isbn"=>"1553-7374 (Electronic)", "pmid"=>"19325880", "issn"=>"15537366", "pui"=>"354404894"}, "id"=>"564d40bd-6b3a-39c2-8bbe-64c1015c6f76", "abstract"=>"The continued evolution of bacterial pathogens has major implications for both human and animal disease, but the exchange of genetic material between host-restricted pathogens is rarely considered. Streptococcus equi subspecies equi (S. equi) is a host-restricted pathogen of horses that has evolved from the zoonotic pathogen Streptococcus equi subspecies zooepidemicus (S. zooepidemicus). These pathogens share approximately 80% genome sequence identity with the important human pathogen Streptococcus pyogenes. We sequenced and compared the genomes of S. equi 4047 and S. zooepidemicus H70 and screened S. equi and S. zooepidemicus strains from around the world to uncover evidence of the genetic events that have shaped the evolution of the S. equi genome and led to its emergence as a host-restricted pathogen. Our analysis provides evidence of functional loss due to mutation and deletion, coupled with pathogenic specialization through the acquisition of bacteriophage encoding a phospholipase A(2) toxin, and four superantigens, and an integrative conjugative element carrying a novel iron acquisition system with similarity to the high pathogenicity island of Yersinia pestis. We also highlight that S. equi, S. zooepidemicus, and S. pyogenes share a common phage pool that enhances cross-species pathogen evolution. We conclude that the complex interplay of functional loss, pathogenic specialization, and genetic exchange between S. equi, S. zooepidemicus, and S. pyogenes continues to influence the evolution of these important streptococci.", "link"=>"http://www.mendeley.com/research/genomic-evidence-evolution-streptococcus-equi-host-restriction-increased-virulence-genetic-exchange", "reader_count"=>68, "reader_count_by_academic_status"=>{"Unspecified"=>5, "Professor > Associate Professor"=>7, "Researcher"=>17, "Student > Ph. D. Student"=>11, "Student > Postgraduate"=>1, "Student > Master"=>2, "Student > Bachelor"=>16, "Lecturer"=>2, "Lecturer > Senior Lecturer"=>1, "Professor"=>6}, "reader_count_by_user_role"=>{"Unspecified"=>5, "Professor > Associate Professor"=>7, "Researcher"=>17, "Student > Ph. D. Student"=>11, "Student > Postgraduate"=>1, "Student > Master"=>2, "Student > Bachelor"=>16, "Lecturer"=>2, "Lecturer > Senior Lecturer"=>1, "Professor"=>6}, "reader_count_by_subject_area"=>{"Unspecified"=>5, "Engineering"=>1, "Environmental Science"=>2, "Biochemistry, Genetics and Molecular Biology"=>5, "Materials Science"=>1, "Agricultural and Biological Sciences"=>39, "Medicine and Dentistry"=>6, "Arts and Humanities"=>1, "Veterinary Science and Veterinary Medicine"=>4, "Business, Management and Accounting"=>1, "Immunology and Microbiology"=>3}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>1}, "Materials Science"=>{"Materials Science"=>1}, "Medicine and Dentistry"=>{"Medicine and Dentistry"=>6}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>3}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>39}, "Business, Management and Accounting"=>{"Business, Management and Accounting"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>5}, "Unspecified"=>{"Unspecified"=>5}, "Environmental Science"=>{"Environmental Science"=>2}, "Arts and Humanities"=>{"Arts and Humanities"=>1}, "Veterinary Science and Veterinary Medicine"=>{"Veterinary Science and Veterinary Medicine"=>4}}, "reader_count_by_country"=>{"Canada"=>1, "United States"=>2, "Brazil"=>1, "Mexico"=>1, "United Kingdom"=>1}, "group_count"=>3}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/903921"], "description"=>"<p>The sequences have been aligned from the predicted replication origins (<i>oriC</i>; right). The colored bars separating each genome (red and blue) represent similarity matches identified by reciprocal TBLASTX analysis <a href=\"http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1000346#ppat.1000346-Altschul1\" target=\"_blank\">[71]</a>, with a score cutoff of 100. Red lines link matches in the same orientation; blue lines link matches in the reverse orientation. The prophage (pink) and ICE (purple) are highlighted as colored boxes.</p>", "links"=>[], "tags"=>["chromosomes"], "article_id"=>574348, "categories"=>["Genetics", "Microbiology", "Infectious Diseases", "Evolutionary Biology", "Medicine"], "users"=>["Matthew T. G. Holden", "Zoe Heather", "Romain Paillot", "Karen F. Steward", "Katy Webb", "Fern Ainslie", "Thibaud Jourdan", "Nathalie C. Bason", "Nancy E. Holroyd", "Karen Mungall", "Michael A. Quail", "Mandy Sanders", "Mark Simmonds", "David Willey", "Karen Brooks", "David M. Aanensen", "Brian G. Spratt", "Keith A. Jolley", "Martin C. J. Maiden", "Michael Kehoe", "Neil Chanter", "Stephen D. Bentley", "Carl Robinson", "Duncan J. Maskell", "Julian Parkhill", "Andrew S. Waller"], "doi"=>"https://dx.doi.org/10.1371/journal.ppat.1000346.g002", "stats"=>{"downloads"=>0, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Pairwise_comparison_of_the_chromosomes_of_Se_4047_and_Sz_H70_using_ACT_/574348", "title"=>"Pairwise comparison of the chromosomes of <i>Se</i>4047 and <i>Sz</i>H70 using ACT.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-03-27 01:12:28"}
  • {"files"=>["https://ndownloader.figshare.com/files/904465"], "description"=>"<p>UPGMA tree generated from tribeMCL clustering of CDSs from <i>Se</i>4047 prophage (highlighted in red) and <i>S. pyogenes</i> prophage. <i>S. pyogenes</i> prophage used in the clustering were: Manfredo (φMan.1, φMan.2, φMan.3, φMan.4, and φMan.5), SSI-1 (SPsP1, SPsP2, SPsP3, SPsP4, and SPsP5), SF370 (370.1, 370.2, 370.3, and 370.4), MGAS315 (φ315.1, φ315.2, φ315.3, φ315.4, φ315.5, and φ315.6), MGAS8232 (φspeA, φspeC, φspeL/M, φ370.3-like, and φsda), MGAS10394 (φ10394.1, φ10394.2, φ10394.3, φ10394.4, φ10394.5, φ10394.6, φ10394.7, and φ10394.8), MGAS6180 (φ6180.1, φ6180.2, φ6180.3, and φ6180.4), MGAS5005 (φ5005.1, φ5005.2, and φ5005.3), MGAS2096 (φ2096.1 and φ2096.2), MGAS9429 (φ9429.1, φ9429.2, and φ9429.3), MGAS10270 (φ10270.1, φ10270.2, φ10270.3, 10270.4, and 10270.5), and MGAS10750 (φ10270.1, φ10270.2, φ10270.3, and φ10270.4). The distribution of homologues to virulence cargo of <i>Se</i>4047 prophage are indicated on the right hand side. CDSs belonging to the same homology groups defined using TribeMCL with a cutoff of 1e−5 are indicated by colored blocks: <i>slaA</i> (yellow), <i>seeM</i> (green), <i>seeL</i> (dark blue), <i>seeH</i> (light blue), and <i>seeI</i> (pink).</p>", "links"=>[], "tags"=>["prophage"], "article_id"=>574892, "categories"=>["Genetics", "Microbiology", "Infectious Diseases", "Evolutionary Biology", "Medicine"], "users"=>["Matthew T. G. Holden", "Zoe Heather", "Romain Paillot", "Karen F. Steward", "Katy Webb", "Fern Ainslie", "Thibaud Jourdan", "Nathalie C. Bason", "Nancy E. Holroyd", "Karen Mungall", "Michael A. Quail", "Mandy Sanders", "Mark Simmonds", "David Willey", "Karen Brooks", "David M. Aanensen", "Brian G. Spratt", "Keith A. Jolley", "Martin C. J. Maiden", "Michael Kehoe", "Neil Chanter", "Stephen D. Bentley", "Carl Robinson", "Duncan J. Maskell", "Julian Parkhill", "Andrew S. Waller"], "doi"=>"https://dx.doi.org/10.1371/journal.ppat.1000346.g006", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Clustering_of_Se_4047_prophage_with_S_pyogenes_prophage_/574892", "title"=>"Clustering of <i>Se</i>4047 prophage with <i>S. pyogenes</i> prophage.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-03-27 01:21:32"}
  • {"files"=>["https://ndownloader.figshare.com/files/447549", "https://ndownloader.figshare.com/files/447728", "https://ndownloader.figshare.com/files/447779", "https://ndownloader.figshare.com/files/447864", "https://ndownloader.figshare.com/files/447912", "https://ndownloader.figshare.com/files/447955", "https://ndownloader.figshare.com/files/447987"], "description"=>"<div><p>The continued evolution of bacterial pathogens has major implications for both human and animal disease, but the exchange of genetic material between host-restricted pathogens is rarely considered. <em>Streptococcus equi</em> subspecies <em>equi</em> (<em>S. equi</em>) is a host-restricted pathogen of horses that has evolved from the zoonotic pathogen <em>Streptococcus equi</em> subspecies <em>zooepidemicus</em> (<em>S. zooepidemicus</em>). These pathogens share approximately 80% genome sequence identity with the important human pathogen <em>Streptococcus pyogenes</em>. We sequenced and compared the genomes of <em>S. equi</em> 4047 and <em>S. zooepidemicus</em> H70 and screened <em>S. equi</em> and <em>S. zooepidemicus</em> strains from around the world to uncover evidence of the genetic events that have shaped the evolution of the <em>S. equi</em> genome and led to its emergence as a host-restricted pathogen. Our analysis provides evidence of functional loss due to mutation and deletion, coupled with pathogenic specialization through the acquisition of bacteriophage encoding a phospholipase A<sub>2</sub> toxin, and four superantigens, and an integrative conjugative element carrying a novel iron acquisition system with similarity to the high pathogenicity island of <em>Yersinia pestis</em>. We also highlight that <em>S. equi</em>, <em>S. zooepidemicus</em>, and <em>S. pyogenes</em> share a common phage pool that enhances cross-species pathogen evolution. We conclude that the complex interplay of functional loss, pathogenic specialization, and genetic exchange between <em>S. equi</em>, <em>S. zooepidemicus</em>, and <em>S. pyogenes</em> continues to influence the evolution of these important streptococci.</p></div>", "links"=>[], "tags"=>["genomic", "pathogens"], "article_id"=>148195, "categories"=>["Genetics", "Microbiology", "Cancer", "Evolutionary Biology", "Medicine"], "users"=>["Matthew T. G. Holden", "Zoe Heather", "Romain Paillot", "Karen F. Steward", "Katy Webb", "Fern Ainslie", "Thibaud Jourdan", "Nathalie C. Bason", "Nancy E. Holroyd", "Karen Mungall", "Michael A. Quail", "Mandy Sanders", "Mark Simmonds", "David Willey", "Karen Brooks", "David M. Aanensen", "Brian G. Spratt", "Keith A. Jolley", "Martin C. J. Maiden", "Michael Kehoe", "Neil Chanter", "Stephen D. Bentley", "Carl Robinson", "Duncan J. Maskell", "Julian Parkhill", "Andrew S. Waller"], "doi"=>["https://dx.doi.org/10.1371/journal.ppat.1000346.s001", "https://dx.doi.org/10.1371/journal.ppat.1000346.s002", "https://dx.doi.org/10.1371/journal.ppat.1000346.s003", "https://dx.doi.org/10.1371/journal.ppat.1000346.s004", "https://dx.doi.org/10.1371/journal.ppat.1000346.s005", "https://dx.doi.org/10.1371/journal.ppat.1000346.s006", "https://dx.doi.org/10.1371/journal.ppat.1000346.s007"], "stats"=>{"downloads"=>36, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Genomic_Evidence_for_the_Evolution_of_Streptococcus_equi_Host_Restriction_Increased_Virulence_and_Genetic_Exchange_with_Human_Pathogens/148195", "title"=>"Genomic Evidence for the Evolution of <em>Streptococcus equi</em>: Host Restriction, Increased Virulence, and Genetic Exchange with Human Pathogens", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2009-03-27 02:16:35"}
  • {"files"=>["https://ndownloader.figshare.com/files/904234"], "description"=>"<p>Genes examined were <i>lacE</i>, <i>rbsD</i>, <i>sorD</i>, SZO06680 (encoding a putative hyaluronate lyase and specific to the 4 bp missing from SEQ1479), <i>srtC</i>, <i>srtD</i>, SZO08560 (encoding a <i>Listeria-Bacteroides</i> repeat domain containing surface-anchored protein), <i>esaA</i>, SZO14370 (within the CRISPR locus), <i>slaA</i>, <i>slaB</i>, <i>seeL</i>, <i>seeM</i>, <i>seeH</i>, <i>seeI</i>, <i>eqbE</i> (within the equibactin locus), SEQ0235 (encoding Se18.9), and <i>gyrA</i>. Functional assays determined the ability of different isolates to ferment lactose, ribose, and sorbitol and to induce mitogenic responses in equine peripheral blood mononuclear cells. The number of isolates representing each ST is indicated. STs where all isolates contained the gene or possessed functional activity are shown in red, STs where all isolates lacked the gene or functionality are shown in blue, and STs containing some isolates containing the gene or functionality and some that did not are colored in yellow. The position of <i>S. equi</i> isolates and <i>Sz</i>H70 are indicated. <i>Sz</i>MGCS10565 is a single locus variant of ST-10 (ST-72; not shown), and had an identical gene prevalence profile to the ST-10 isolates based on <i>in silico</i> analysis of its genome sequence <a href=\"http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1000346#ppat.1000346-Beres1\" target=\"_blank\">[12]</a>.</p>", "links"=>[], "tags"=>["mlst", "alleles", "26", "140", "isolates", "prevalence", "differences"], "article_id"=>574638, "categories"=>["Genetics", "Microbiology", "Infectious Diseases", "Evolutionary Biology", "Medicine"], "users"=>["Matthew T. G. Holden", "Zoe Heather", "Romain Paillot", "Karen F. Steward", "Katy Webb", "Fern Ainslie", "Thibaud Jourdan", "Nathalie C. Bason", "Nancy E. Holroyd", "Karen Mungall", "Michael A. Quail", "Mandy Sanders", "Mark Simmonds", "David Willey", "Karen Brooks", "David M. Aanensen", "Brian G. Spratt", "Keith A. Jolley", "Martin C. J. Maiden", "Michael Kehoe", "Neil Chanter", "Stephen D. Bentley", "Carl Robinson", "Duncan J. Maskell", "Julian Parkhill", "Andrew S. Waller"], "doi"=>"https://dx.doi.org/10.1371/journal.ppat.1000346.g004", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_ClonalFrame_analysis_of_MLST_alleles_of_26_S_equi_and_140_S_zooepidemicus_isolates_and_its_relationship_with_the_prevalence_of_selected_differences_between_the_Se_4047_and_Sz_H70_genomes_/574638", "title"=>"ClonalFrame analysis of MLST alleles of 26 <i>S. equi</i> and 140 <i>S. zooepidemicus</i> isolates and its relationship with the prevalence of selected differences between the <i>Se</i>4047 and <i>Sz</i>H70 genomes.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-03-27 01:17:18"}
  • {"files"=>["https://ndownloader.figshare.com/files/904820"], "description"=>"<p>Gene loss (blue): (1) <i>Se</i>4047 has lost the ability to ferment lactose, sorbitol, and ribose, which may reduce its ability to colonize the mucosal surface. (2) Hyaluronate lyase activity is predicted to be reduced in <i>Se</i>4047, which could decrease its ability to invade tissue and provide an explanation for increased levels of hyaluronate capsule. Increased levels of capsule may enhance resistance to phagocytosis, but could also reduce adhesion to the mucosal surface. (3) Truncation of fne and Shr in <i>Se</i>4047 and subsequent synthesis of secreted fibronectin products may decrease the adhesive properties of <i>Se</i>4047 and interfere with fibronectin-dependent attachment mechanisms of competing pathogens. (4) Loss of function of the <i>tetR</i> regulator may lead to constitutive production of longer collagen-binding pili by <i>S. equi</i>. (5) The putative SZO18310 pilus locus of <i>Sz</i>H70 has been deleted from the <i>Se</i>4047 genome. (6) <i>Se</i>4047 has lost a <i>Listeria-Bacteroides</i> repeat domain containing surface-anchored protein. Gene gain (red): (7) The acquisition of prophage plays an important evolutionary role through integration of cargo genes. (8) Recirculation and secretion of the integrated φSeq1 may kill susceptible competing bacteria such as <i>S. zooepidemicus</i>. (9) φSeq2 contains a gene encoding a phospholipase A<sub>2</sub> (SlaA) that may enhance virulence. (10) φSeq3 and φSeq4 encode superantigens SeeH, SeeI, SeeL, and SeeM that target the equine immune system (11). (12) The absence of prophage in <i>S. zooepidemicus</i> may be explained by the presence of CRISPR arrays and competence proteins that confer resistance to circulating phage and maintain genome integrity. (13) The ICE<i>Se</i>2 locus may enhance iron acquisition in <i>Se</i>4047 through the production of a potential siderophore, equibactin. (14) Se18.9 binds Factor H and interferes with complement activation.</p>", "links"=>[], "tags"=>["evolutionary biology/microbial evolution and genomics", "genetics and genomics/gene discovery", "genetics and genomics/genome projects", "genetics and genomics/microbial evolution and genomics", "genetics and genomics/population genetics", "infectious diseases/bacterial infections", "infectious diseases/respiratory infections", "microbiology/microbial evolution and genomics"], "article_id"=>575228, "categories"=>["Genetics", "Microbiology", "Infectious Diseases", "Evolutionary Biology", "Medicine"], "users"=>["Matthew T. G. Holden", "Zoe Heather", "Romain Paillot", "Karen F. Steward", "Katy Webb", "Fern Ainslie", "Thibaud Jourdan", "Nathalie C. Bason", "Nancy E. Holroyd", "Karen Mungall", "Michael A. Quail", "Mandy Sanders", "Mark Simmonds", "David Willey", "Karen Brooks", "David M. Aanensen", "Brian G. Spratt", "Keith A. Jolley", "Martin C. J. Maiden", "Michael Kehoe", "Neil Chanter", "Stephen D. Bentley", "Carl Robinson", "Duncan J. Maskell", "Julian Parkhill", "Andrew S. Waller"], "doi"=>"https://dx.doi.org/10.1371/journal.ppat.1000346.g008", "stats"=>{"downloads"=>0, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Summary_of_functional_loss_and_gene_gain_by_S_equi_/575228", "title"=>"Summary of functional loss and gene gain by <i>S. equi</i>.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-03-27 01:27:08"}
  • {"files"=>["https://ndownloader.figshare.com/files/904653"], "description"=>"<p>The red bars separating each sequence represent similarity matches identified by TBLASTX analysis. The locations of <i>seeI</i>, <i>seeH</i>, <i>speI</i>, and <i>speH</i> are indicated.</p>", "links"=>[], "tags"=>["manfredo", "displayed"], "article_id"=>575064, "categories"=>["Genetics", "Microbiology", "Infectious Diseases", "Evolutionary Biology", "Medicine"], "users"=>["Matthew T. G. Holden", "Zoe Heather", "Romain Paillot", "Karen F. Steward", "Katy Webb", "Fern Ainslie", "Thibaud Jourdan", "Nathalie C. Bason", "Nancy E. Holroyd", "Karen Mungall", "Michael A. Quail", "Mandy Sanders", "Mark Simmonds", "David Willey", "Karen Brooks", "David M. Aanensen", "Brian G. Spratt", "Keith A. Jolley", "Martin C. J. Maiden", "Michael Kehoe", "Neil Chanter", "Stephen D. Bentley", "Carl Robinson", "Duncan J. Maskell", "Julian Parkhill", "Andrew S. Waller"], "doi"=>"https://dx.doi.org/10.1371/journal.ppat.1000346.g007", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Pairwise_comparison_of_Se_4047_Seq_4_and_Man_3_from_S_pyogenes_Manfredo_displayed_using_ACT_/575064", "title"=>"Pairwise comparison of <i>Se</i>4047 φSeq.4 and φMan.3 from <i>S. pyogenes</i> Manfredo displayed using ACT.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-03-27 01:24:24"}
  • {"files"=>["https://ndownloader.figshare.com/files/904369"], "description"=>"<p>The promoter region of SZO08560 (−170 bp to −55 bp) is bordered by GTAGACTTTA and TAAAGTCTAC inverted repeats that invert to switch transcription from forward to reverse orientation.</p>", "links"=>[], "tags"=>["szo08560", "invertible", "promoter"], "article_id"=>574789, "categories"=>["Genetics", "Microbiology", "Infectious Diseases", "Evolutionary Biology", "Medicine"], "users"=>["Matthew T. G. Holden", "Zoe Heather", "Romain Paillot", "Karen F. Steward", "Katy Webb", "Fern Ainslie", "Thibaud Jourdan", "Nathalie C. Bason", "Nancy E. Holroyd", "Karen Mungall", "Michael A. Quail", "Mandy Sanders", "Mark Simmonds", "David Willey", "Karen Brooks", "David M. Aanensen", "Brian G. Spratt", "Keith A. Jolley", "Martin C. J. Maiden", "Michael Kehoe", "Neil Chanter", "Stephen D. Bentley", "Carl Robinson", "Duncan J. Maskell", "Julian Parkhill", "Andrew S. Waller"], "doi"=>"https://dx.doi.org/10.1371/journal.ppat.1000346.g005", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Diagram_of_the_SZO08560_invertible_promoter_in_Sz_H70_/574789", "title"=>"Diagram of the SZO08560 invertible promoter in <i>Sz</i>H70.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-03-27 01:19:49"}
  • {"files"=>["https://ndownloader.figshare.com/files/904056"], "description"=>"<p>(A) Functional CDSs and pseudogenes of <i>Se</i>4047 and <i>Sz</i>H70. (B) Partially deleted or pseudogenes in the <i>Se</i>4047 and <i>Sz</i>H70 genomes.</p>", "links"=>[], "tags"=>["cdss", "belonging", "classes"], "article_id"=>574483, "categories"=>["Genetics", "Microbiology", "Infectious Diseases", "Evolutionary Biology", "Medicine"], "users"=>["Matthew T. G. Holden", "Zoe Heather", "Romain Paillot", "Karen F. Steward", "Katy Webb", "Fern Ainslie", "Thibaud Jourdan", "Nathalie C. Bason", "Nancy E. Holroyd", "Karen Mungall", "Michael A. Quail", "Mandy Sanders", "Mark Simmonds", "David Willey", "Karen Brooks", "David M. Aanensen", "Brian G. Spratt", "Keith A. Jolley", "Martin C. J. Maiden", "Michael Kehoe", "Neil Chanter", "Stephen D. Bentley", "Carl Robinson", "Duncan J. Maskell", "Julian Parkhill", "Andrew S. Waller"], "doi"=>"https://dx.doi.org/10.1371/journal.ppat.1000346.g003", "stats"=>{"downloads"=>0, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Distribution_of_CDSs_belonging_to_different_functional_classes_in_the_Se_4047_and_Sz_H70_genomes_/574483", "title"=>"Distribution of CDSs belonging to different functional classes in the <i>Se</i>4047 and <i>Sz</i>H70 genomes.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-03-27 01:14:43"}
  • {"files"=>["https://ndownloader.figshare.com/files/903762"], "description"=>"<p>Key for the circular diagrams (outside to inside): scale (in Mb); annotated CDSs colored according to predicted function represented on a pair of concentric circles, representing both coding strands; orthologue matches shared with the Streptococcal species, <i>Se</i>4047 or <i>Sz</i>H70, <i>Sz</i>MGCS10565, <i>S. uberis</i> 0140J, <i>S. pyogenes</i> Manfredo, <i>S.</i> mutans UA159, <i>S. gordonii</i> Challis CH1, <i>S. sanguinis</i> SK36, <i>S. pneumoniae</i> TIGR4, <i>S. agalactiae</i> NEM316, <i>S. suis</i> P1/7, <i>S. thermophilus</i> CNRZ1066, blue; orthologue matches shared with <i>Lactococcus lactis</i> subspecies <i>lactis</i>, green; G+C% content plot; G+C deviation plot (>0%, olive, <0%, purple). Color coding for CDS functions: dark blue, pathogenicity/adaptation; black, energy metabolism; red, information transfer; dark green, surface-associated; cyan, degradation of large molecules; magenta, degradation of small molecules; yellow, central/intermediary metabolism; pale green, unknown; pale blue, regulators; orange, conserved hypothetical; brown, pseudogenes; pink, phage and IS elements; grey, miscellaneous. The positions of the four prophage and two ICE<i>Se</i> present in the <i>Se</i>4047 genome, and two ICE<i>Sz</i> in the <i>Sz</i>H70 genome, are indicated.</p>", "links"=>[], "tags"=>["circular", "diagrams", "genomes"], "article_id"=>574175, "categories"=>["Genetics", "Microbiology", "Infectious Diseases", "Evolutionary Biology", "Medicine"], "users"=>["Matthew T. G. Holden", "Zoe Heather", "Romain Paillot", "Karen F. Steward", "Katy Webb", "Fern Ainslie", "Thibaud Jourdan", "Nathalie C. Bason", "Nancy E. Holroyd", "Karen Mungall", "Michael A. Quail", "Mandy Sanders", "Mark Simmonds", "David Willey", "Karen Brooks", "David M. Aanensen", "Brian G. Spratt", "Keith A. Jolley", "Martin C. J. Maiden", "Michael Kehoe", "Neil Chanter", "Stephen D. Bentley", "Carl Robinson", "Duncan J. Maskell", "Julian Parkhill", "Andrew S. Waller"], "doi"=>"https://dx.doi.org/10.1371/journal.ppat.1000346.g001", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Schematic_circular_diagrams_of_the_Se_4047_A_and_Sz_H70_genomes_B_/574175", "title"=>"Schematic circular diagrams of the <i>Se</i>4047 (A) and <i>Sz</i>H70 genomes (B).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-03-27 01:09:35"}

PMC Usage Stats | Further Information

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Relative Metric

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