Comparative Genomic Analysis of Mannheimia haemolytica from Bovine Sources
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{"title"=>"Comparative genomic analysis of mannheimia haemolytica from bovine sources", "type"=>"journal", "authors"=>[{"first_name"=>"Cassidy L.", "last_name"=>"Klima", "scopus_author_id"=>"36096774700"}, {"first_name"=>"Shaun R.", "last_name"=>"Cook", "scopus_author_id"=>"9436377700"}, {"first_name"=>"Rahat", "last_name"=>"Zaheer", "scopus_author_id"=>"57028058900"}, {"first_name"=>"Chad", "last_name"=>"Laing", "scopus_author_id"=>"16506751500"}, {"first_name"=>"Vick P.", "last_name"=>"Gannon", "scopus_author_id"=>"6701704193"}, {"first_name"=>"Yong", "last_name"=>"Xu", "scopus_author_id"=>"55856444300"}, {"first_name"=>"Jay", "last_name"=>"Rasmussen", "scopus_author_id"=>"36768059600"}, {"first_name"=>"Andrew", "last_name"=>"Potter", "scopus_author_id"=>"35461198600"}, {"first_name"=>"Steve", "last_name"=>"Hendrick", "scopus_author_id"=>"7004331193"}, {"first_name"=>"Trevor W.", "last_name"=>"Alexander", "scopus_author_id"=>"7101893824"}, {"first_name"=>"Tim A.", "last_name"=>"McAllister", "scopus_author_id"=>"7102068695"}], "year"=>2016, "source"=>"PLoS ONE", "identifiers"=>{"scopus"=>"2-s2.0-84960539672", "sgr"=>"84960539672", "issn"=>"19326203", "doi"=>"10.1371/journal.pone.0149520", "pmid"=>"26926339", "pui"=>"608858431"}, "id"=>"1eb7978b-12de-3fac-9697-28aa5d7a19b2", "abstract"=>"Bovine respiratory disease is a common health problem in beef production. The primary bac-terial agent involved, Mannheimia haemolytica, is a target for antimicrobial therapy and at risk for associated antimicrobial resistance development. The role of M. haemolytica in pathogen-esis is linked to serotype with serotypes 1 (S1) and 6 (S6) isolated from pneumonic lesions and serotype 2 (S2) found in the upper respiratory tract of healthy animals. Here, we sequenced the genomes of 11 strains of M. haemolytica, representing all three serotypes and performed comparative genomics analysis to identify genetic features that may contribute to pathogenesis. Possible virulence associated genes were identified within 14 distinct pro-phage, including a periplasmic chaperone, a lipoprotein, peptidoglycan glycosyltransferase and a stress response protein. Prophage content ranged from 2–8 per genome, but was higher in S1 and S6 strains. A type I-C CRISPR-Cas system was identified in each strain with spacer diversity and organization conserved among serotypes. The majority of spacers occur in S1 and S6 strains and originate from phage suggesting that serotypes 1 and 6 may be more resistant to phage predation. However, two spacers complementary to the host chromo-some targeting a UDP-N-acetylglucosamine 2-epimerase and a glycosyl transferases group 1 gene are present in S1 and S6 strains only indicating these serotypes may employ CRISPR-Cas to regulate gene expression to avoid host immune responses or enhance adhe-sion during infection. Integrative conjugative elements are present in nine of the eleven genomes. Three of these harbor extensive multi-drug resistance cassettes encoding resis-tance against the majority of drugs used to combat infection in beef cattle, including macro-lides and tetracyclines used in human medicine. The findings here identify key features that are likely contributing to serotype related pathogenesis and specific targets for vaccine design intended to reduce the dependency on antibiotics to treat respiratory infection in cattle.", "link"=>"http://www.mendeley.com/research/comparative-genomic-analysis-mannheimia-haemolytica-bovine-sources", "reader_count"=>29, "reader_count_by_academic_status"=>{"Unspecified"=>3, "Librarian"=>1, "Researcher"=>8, "Student > Doctoral Student"=>2, "Student > Ph. D. Student"=>4, "Student > Postgraduate"=>2, "Other"=>2, "Student > Bachelor"=>4, "Professor"=>2, "Student > Master"=>1}, "reader_count_by_user_role"=>{"Unspecified"=>3, "Librarian"=>1, "Researcher"=>8, "Student > Doctoral Student"=>2, "Student > Ph. D. Student"=>4, "Student > Postgraduate"=>2, "Other"=>2, "Student > Bachelor"=>4, "Professor"=>2, "Student > Master"=>1}, "reader_count_by_subject_area"=>{"Unspecified"=>4, "Biochemistry, Genetics and Molecular Biology"=>6, "Agricultural and Biological Sciences"=>9, "Medicine and Dentistry"=>1, "Arts and Humanities"=>1, "Pharmacology, Toxicology and Pharmaceutical Science"=>1, "Veterinary Science and Veterinary Medicine"=>4, "Psychology"=>1, "Immunology and Microbiology"=>2}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>1}, "Psychology"=>{"Psychology"=>1}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>2}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>9}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>6}, "Unspecified"=>{"Unspecified"=>4}, "Pharmacology, Toxicology and Pharmaceutical Science"=>{"Pharmacology, Toxicology and Pharmaceutical Science"=>1}, "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"=>1, "Brazil"=>1}, "group_count"=>1}

Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/4785679"], "description"=>"<p>Petals contain number of unique CDS per strain. Petals a-h represent the serotype 1 strains <i>M</i>. <i>haemolytica</i> L024A, <i>M</i>. <i>haemolytica</i> 157-4-1, <i>M</i>. <i>haemolytica</i> L044A, <i>M</i>. <i>haemolytica</i> 535A, <i>M</i>. <i>haemolytica</i> D153, <i>M</i>. <i>haemolytica</i> MhBrain2012, <i>M</i>. <i>haemolytica</i> D193, and <i>M</i>. <i>haemolytica</i> USDA-ARS-USMARC-183 respectively. Petals i-o represent the serotype 6 strains <i>M</i>. <i>haemolytica</i> T14, <i>M</i>. <i>haemolytica</i> H23, <i>M</i>. <i>haemolytica</i> 3927A, <i>M</i>. <i>haemolytica</i> L038A, <i>M</i>. <i>haemolytica</i> D174, D38, and <i>M</i>. <i>haemolytica</i> USDA-ARS-USMARC-185 respectively. Petals p-u represent the serotype 2 strains <i>M</i>. <i>haemolytica</i> 587A, <i>M</i>. <i>haemolytica</i> L033A, <i>M</i>. <i>haemolytica</i> T2, <i>M</i>. <i>haemolytica</i> D171, <i>M</i>. <i>haemolytica</i> D35 and <i>M</i>. <i>haemolytica</i> Bovine A2, respectively. Analysis based on 85% sequence identity across 90% length.</p>", "links"=>[], "tags"=>["spacer", "S 6 strains", "Bovine Sources Bovine", "Integrative conjugative elements", "S 1", "pathogenesis", "antimicrobial resistance development", "glycosyl transferases group 1 gene", "Comparative Genomic Analysis", "stress response protein", "infection", "serotypes 1", "genome", "Mannheimia haemolytica"], "article_id"=>3079264, "categories"=>["Medicine", "Microbiology", "Genetics", "Pharmacology", "Biotechnology", "Environmental Sciences not elsewhere classified", "Ecology", "Immunology", "Biological Sciences not elsewhere classified", "Cancer", "Infectious Diseases", "Virology"], "users"=>["Cassidy L. Klima", "Shaun R. Cook", "Rahat Zaheer", "Chad Laing", "Vick P. Gannon", "Yong Xu", "Jay Rasmussen", "Andrew Potter", "Steve Hendrick", "Trevor W. Alexander", "Tim A. McAllister"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0149520.g002", "stats"=>{"downloads"=>0, "page_views"=>12, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Size_of_the_core_genome_and_dispensable_genome_and_number_of_strain_unique_CDS_in_21_i_Mannheimia_haemolytica_i_genomes_/3079264", "title"=>"Size of the core genome and dispensable genome and number of strain unique CDS in 21 <i>Mannheimia haemolytica</i> genomes.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2016-02-29 07:41:57"}
  • {"files"=>["https://ndownloader.figshare.com/files/4785892"], "description"=>"<p>Spacer sequences identified in CRISPR arrays from 11 <i>Mannheimia haemolytica</i> genomes.</p>", "links"=>[], "tags"=>["spacer", "S 6 strains", "Bovine Sources Bovine", "Integrative conjugative elements", "S 1", "pathogenesis", "antimicrobial resistance development", "glycosyl transferases group 1 gene", "Comparative Genomic Analysis", "stress response protein", "infection", "serotypes 1", "genome", "Mannheimia haemolytica"], "article_id"=>3079456, "categories"=>["Medicine", "Microbiology", "Genetics", "Pharmacology", "Biotechnology", "Environmental Sciences not elsewhere classified", "Ecology", "Immunology", "Biological Sciences not elsewhere classified", "Cancer", "Infectious Diseases", "Virology"], "users"=>["Cassidy L. Klima", "Shaun R. Cook", "Rahat Zaheer", "Chad Laing", "Vick P. Gannon", "Yong Xu", "Jay Rasmussen", "Andrew Potter", "Steve Hendrick", "Trevor W. Alexander", "Tim A. McAllister"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0149520.t003", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Spacer_sequences_identified_in_CRISPR_arrays_from_11_i_Mannheimia_haemolytica_i_genomes_/3079456", "title"=>"Spacer sequences identified in CRISPR arrays from 11 <i>Mannheimia haemolytica</i> genomes.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2016-02-29 07:41:57"}
  • {"files"=>["https://ndownloader.figshare.com/files/4785757"], "description"=>"<p>Bars represent the number of new genes as the function of the number n or strains sequentially added. The curve represents the least-squares fit for the function y = Ax<sup>B</sup> with the best fit obtained with a correlation r<sup>2</sup> = 0.875 for A = 566.17 ± 3.16, B = -0.22. The extrapolated number of new genes expected after the number of genomes increases to 100 is 123 new genes.</p>", "links"=>[], "tags"=>["spacer", "S 6 strains", "Bovine Sources Bovine", "Integrative conjugative elements", "S 1", "pathogenesis", "antimicrobial resistance development", "glycosyl transferases group 1 gene", "Comparative Genomic Analysis", "stress response protein", "infection", "serotypes 1", "genome", "Mannheimia haemolytica"], "article_id"=>3079339, "categories"=>["Medicine", "Microbiology", "Genetics", "Pharmacology", "Biotechnology", "Environmental Sciences not elsewhere classified", "Ecology", "Immunology", "Biological Sciences not elsewhere classified", "Cancer", "Infectious Diseases", "Virology"], "users"=>["Cassidy L. Klima", "Shaun R. Cook", "Rahat Zaheer", "Chad Laing", "Vick P. Gannon", "Yong Xu", "Jay Rasmussen", "Andrew Potter", "Steve Hendrick", "Trevor W. Alexander", "Tim A. McAllister"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0149520.g004", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/New_gene_discovery_plot_for_pan_genome_analysis_of_21_i_Mannheimia_haemolytica_i_genomes_/3079339", "title"=>"New gene discovery plot for pan-genome analysis of 21 <i>Mannheimia haemolytica</i> genomes.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2016-02-29 07:41:57"}
  • {"files"=>["https://ndownloader.figshare.com/files/4785808"], "description"=>"<p>The tree was constructed by neighbour-joining method with the MAFFT program. Bootstrap values (>50) representing 100 sampling replicates are in grey located below branches with the phage cluster numbers adjacent to corresponding nodes above the branches. The scale length is equal to 0.1 nucleotide substitutions per site.</p>", "links"=>[], "tags"=>["spacer", "S 6 strains", "Bovine Sources Bovine", "Integrative conjugative elements", "S 1", "pathogenesis", "antimicrobial resistance development", "glycosyl transferases group 1 gene", "Comparative Genomic Analysis", "stress response protein", "infection", "serotypes 1", "genome", "Mannheimia haemolytica"], "article_id"=>3079396, "categories"=>["Medicine", "Microbiology", "Genetics", "Pharmacology", "Biotechnology", "Environmental Sciences not elsewhere classified", "Ecology", "Immunology", "Biological Sciences not elsewhere classified", "Cancer", "Infectious Diseases", "Virology"], "users"=>["Cassidy L. Klima", "Shaun R. Cook", "Rahat Zaheer", "Chad Laing", "Vick P. Gannon", "Yong Xu", "Jay Rasmussen", "Andrew Potter", "Steve Hendrick", "Trevor W. Alexander", "Tim A. McAllister"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0149520.g006", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Phylogenetic_analysis_of_prophage_found_in_i_M_i_i_haemolytica_i_/3079396", "title"=>"Phylogenetic analysis of prophage found in <i>M</i>. <i>haemolytica</i>.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2016-02-29 07:41:57"}
  • {"files"=>["https://ndownloader.figshare.com/files/4785853"], "description"=>"<p>Features of 11 sequenced strains of <i>Mannheimia haemolytica</i>.</p>", "links"=>[], "tags"=>["spacer", "S 6 strains", "Bovine Sources Bovine", "Integrative conjugative elements", "S 1", "pathogenesis", "antimicrobial resistance development", "glycosyl transferases group 1 gene", "Comparative Genomic Analysis", "stress response protein", "infection", "serotypes 1", "genome", "Mannheimia haemolytica"], "article_id"=>3079432, "categories"=>["Medicine", "Microbiology", "Genetics", "Pharmacology", "Biotechnology", "Environmental Sciences not elsewhere classified", "Ecology", "Immunology", "Biological Sciences not elsewhere classified", "Cancer", "Infectious Diseases", "Virology"], "users"=>["Cassidy L. Klima", "Shaun R. Cook", "Rahat Zaheer", "Chad Laing", "Vick P. Gannon", "Yong Xu", "Jay Rasmussen", "Andrew Potter", "Steve Hendrick", "Trevor W. Alexander", "Tim A. McAllister"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0149520.t001", "stats"=>{"downloads"=>0, "page_views"=>13, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Features_of_11_sequenced_strains_of_i_Mannheimia_haemolytica_i_/3079432", "title"=>"Features of 11 sequenced strains of <i>Mannheimia haemolytica</i>.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2016-02-29 07:41:57"}
  • {"files"=>["https://ndownloader.figshare.com/files/4785550", "https://ndownloader.figshare.com/files/4785559", "https://ndownloader.figshare.com/files/4785577", "https://ndownloader.figshare.com/files/4785580"], "description"=>"<div><p>Bovine respiratory disease is a common health problem in beef production. The primary bacterial agent involved, <i>Mannheimia haemolytica</i>, is a target for antimicrobial therapy and at risk for associated antimicrobial resistance development. The role of <i>M</i>. <i>haemolytica</i> in pathogenesis is linked to serotype with serotypes 1 (S1) and 6 (S6) isolated from pneumonic lesions and serotype 2 (S2) found in the upper respiratory tract of healthy animals. Here, we sequenced the genomes of 11 strains of <i>M</i>. <i>haemolytica</i>, representing all three serotypes and performed comparative genomics analysis to identify genetic features that may contribute to pathogenesis. Possible virulence associated genes were identified within 14 distinct prophage, including a periplasmic chaperone, a lipoprotein, peptidoglycan glycosyltransferase and a stress response protein. Prophage content ranged from 2–8 per genome, but was higher in S1 and S6 strains. A type I-C CRISPR-Cas system was identified in each strain with spacer diversity and organization conserved among serotypes. The majority of spacers occur in S1 and S6 strains and originate from phage suggesting that serotypes 1 and 6 may be more resistant to phage predation. However, two spacers complementary to the host chromosome targeting a UDP-N-acetylglucosamine 2-epimerase and a glycosyl transferases group 1 gene are present in S1 and S6 strains only indicating these serotypes may employ CRISPR-Cas to regulate gene expression to avoid host immune responses or enhance adhesion during infection. Integrative conjugative elements are present in nine of the eleven genomes. Three of these harbor extensive multi-drug resistance cassettes encoding resistance against the majority of drugs used to combat infection in beef cattle, including macrolides and tetracyclines used in human medicine. The findings here identify key features that are likely contributing to serotype related pathogenesis and specific targets for vaccine design intended to reduce the dependency on antibiotics to treat respiratory infection in cattle.</p></div>", "links"=>[], "tags"=>["spacer", "S 6 strains", "Bovine Sources Bovine", "Integrative conjugative elements", "S 1", "pathogenesis", "antimicrobial resistance development", "glycosyl transferases group 1 gene", "Comparative Genomic Analysis", "stress response protein", "infection", "serotypes 1", "genome", "Mannheimia haemolytica"], "article_id"=>3079147, "categories"=>["Medicine", "Microbiology", "Genetics", "Pharmacology", "Biotechnology", "Environmental Sciences not elsewhere classified", "Ecology", "Immunology", "Biological Sciences not elsewhere classified", "Cancer", "Infectious Diseases", "Virology"], "users"=>["Cassidy L. Klima", "Shaun R. Cook", "Rahat Zaheer", "Chad Laing", "Vick P. Gannon", "Yong Xu", "Jay Rasmussen", "Andrew Potter", "Steve Hendrick", "Trevor W. Alexander", "Tim A. McAllister"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0149520.s001", "https://dx.doi.org/10.1371/journal.pone.0149520.s002", "https://dx.doi.org/10.1371/journal.pone.0149520.s003", "https://dx.doi.org/10.1371/journal.pone.0149520.s004"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Comparative_Genomic_Analysis_of_i_Mannheimia_haemolytica_i_from_Bovine_Sources/3079147", "title"=>"Comparative Genomic Analysis of <i>Mannheimia haemolytica</i> from Bovine Sources", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2016-02-29 07:41:57"}
  • {"files"=>["https://ndownloader.figshare.com/files/4785781"], "description"=>"<p>For both the pan-genome (grey) and the core genome (black), the number of genes is plotted as a function of the number <i>n</i> of strains sequentially added. Panel A: serotype 1 strains, n = 8. Panel B: serotype 6 strains, n = 7. Panel C: serotype 2 strains, n = 6. The curve for the S1 pan-genome represents the least-squares fit for the function y = Ax<sup>B</sup> + C with the best fit obtained with a correlation r<sup>2</sup> = 0.999 for A = 572.81 ± 4.45, B = 0.79, C = 2104.32 ± 19.12. The curve for the S1 core genome represents the least-squares fit for the function y = Ae<sup>Bx</sup> + C with the best fit obtained with a correlation r<sup>2</sup> = 0.976 for A = 1549.09 ± 90.55, B = -0.81, C = 1964.34 ± 14.87. The curve for the S6 pan-genome represents the least-squares fit for the function y = Ax<sup>B</sup> + C with the best fit obtained with a correlation r<sup>2</sup> = 0.999 for A = 652.62 ± 8.5, B = 0.73, C = 1942.33 ± 25.16. The curve for the S6 core genome represents the least-squares fit for the function y = Ae<sup>Bx</sup> + C with the best fit obtained with a correlation r<sup>2</sup> = 0.983 for A = 1601.51 ± 92.41, B = -0.74, C = 1806.86 ± 19.97. The curve for the S2 pan-genome represents the least-squares fit for the function y = Ax<sup>B</sup> + C with the best fit obtained with a correlation r<sup>2</sup> = 0.999 for A = 944.93 ± 10.83, B = 0.65, C = 1527.44 ± 23.12. The curve for the S2 core genome represents the least-squares fit for the function y = Ae<sup>Bx</sup> + C with the best fit obtained with a correlation r<sup>2</sup> = 0.988 for A = 2123.13 ± 68.56, B = -0.88, C = 1579.86 ± 5.88.</p>", "links"=>[], "tags"=>["spacer", "S 6 strains", "Bovine Sources Bovine", "Integrative conjugative elements", "S 1", "pathogenesis", "antimicrobial resistance development", "glycosyl transferases group 1 gene", "Comparative Genomic Analysis", "stress response protein", "infection", "serotypes 1", "genome", "Mannheimia haemolytica"], "article_id"=>3079372, "categories"=>["Medicine", "Microbiology", "Genetics", "Pharmacology", "Biotechnology", "Environmental Sciences not elsewhere classified", "Ecology", "Immunology", "Biological Sciences not elsewhere classified", "Cancer", "Infectious Diseases", "Virology"], "users"=>["Cassidy L. Klima", "Shaun R. Cook", "Rahat Zaheer", "Chad Laing", "Vick P. Gannon", "Yong Xu", "Jay Rasmussen", "Andrew Potter", "Steve Hendrick", "Trevor W. Alexander", "Tim A. McAllister"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0149520.g005", "stats"=>{"downloads"=>0, "page_views"=>13, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Pan_genome_and_core_genome_of_21_i_M_i_i_haemolytica_i_isolates_/3079372", "title"=>"Pan-genome and core genome of 21 <i>M</i>. <i>haemolytica</i> isolates.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2016-02-29 07:41:57"}
  • {"files"=>["https://ndownloader.figshare.com/files/4785637"], "description"=>"<p>The tree was generated from full genome alignment produced using Mauve in Geneious version 6.1.8 using Tamura-Nei distance correction with no specified outgroup. The scale length is equal to 0.001 nucleotide substitutions per site.</p>", "links"=>[], "tags"=>["spacer", "S 6 strains", "Bovine Sources Bovine", "Integrative conjugative elements", "S 1", "pathogenesis", "antimicrobial resistance development", "glycosyl transferases group 1 gene", "Comparative Genomic Analysis", "stress response protein", "infection", "serotypes 1", "genome", "Mannheimia haemolytica"], "article_id"=>3079213, "categories"=>["Medicine", "Microbiology", "Genetics", "Pharmacology", "Biotechnology", "Environmental Sciences not elsewhere classified", "Ecology", "Immunology", "Biological Sciences not elsewhere classified", "Cancer", "Infectious Diseases", "Virology"], "users"=>["Cassidy L. Klima", "Shaun R. Cook", "Rahat Zaheer", "Chad Laing", "Vick P. Gannon", "Yong Xu", "Jay Rasmussen", "Andrew Potter", "Steve Hendrick", "Trevor W. Alexander", "Tim A. McAllister"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0149520.g001", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/UPGMA_phylogenetic_tree_based_on_whole_genome_sequence_alignment_of_11_i_Mannheimia_haemolytica_i_strains_/3079213", "title"=>"UPGMA phylogenetic tree based on whole genome sequence alignment of 11 <i>Mannheimia haemolytica</i> strains.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2016-02-29 07:41:57"}
  • {"files"=>["https://ndownloader.figshare.com/files/4785826"], "description"=>"<p>Panel A: Cas loci present in serotype 1, 6 and 2 genomes. Panel B: consensus sequence for leader and trailer regions of CRISPR arrays. Underlined regions are complementary to psi-tag. Panel C: Sequences of the 6 unique direct repeats detected in CRISPR arrays. Panel D: CRISPR array spacer and direct repeat organization. Diamonds represent direct repeat sequences while numbered tiles represent spacer sequences. Panel E: 3D structure of direct repeats found in CRISPR arrays. Psi-tag indicated by grey shaded regions. Panel F: sequence alignment of protospacers with suspected protospacer adjacent motif (PAM) highlighted in grey (TTC).</p>", "links"=>[], "tags"=>["spacer", "S 6 strains", "Bovine Sources Bovine", "Integrative conjugative elements", "S 1", "pathogenesis", "antimicrobial resistance development", "glycosyl transferases group 1 gene", "Comparative Genomic Analysis", "stress response protein", "infection", "serotypes 1", "genome", "Mannheimia haemolytica"], "article_id"=>3079408, "categories"=>["Medicine", "Microbiology", "Genetics", "Pharmacology", "Biotechnology", "Environmental Sciences not elsewhere classified", "Ecology", "Immunology", "Biological Sciences not elsewhere classified", "Cancer", "Infectious Diseases", "Virology"], "users"=>["Cassidy L. Klima", "Shaun R. Cook", "Rahat Zaheer", "Chad Laing", "Vick P. Gannon", "Yong Xu", "Jay Rasmussen", "Andrew Potter", "Steve Hendrick", "Trevor W. Alexander", "Tim A. McAllister"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0149520.g007", "stats"=>{"downloads"=>0, "page_views"=>12, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Schematic_of_CRISPR_Cas_systems_identified_in_whole_genome_sequence_analysis_of_11_i_Mannheimia_haemolytica_genomes_i_/3079408", "title"=>"Schematic of CRISPR-Cas systems identified in whole genome sequence analysis of 11 <i>Mannheimia haemolytica genomes</i>.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2016-02-29 07:41:57"}
  • {"files"=>["https://ndownloader.figshare.com/files/4785868"], "description"=>"<p>Metadata for prophage identified within the genomes of 11 strains of <i>Mannheimia haemolytica</i>.</p>", "links"=>[], "tags"=>["spacer", "S 6 strains", "Bovine Sources Bovine", "Integrative conjugative elements", "S 1", "pathogenesis", "antimicrobial resistance development", "glycosyl transferases group 1 gene", "Comparative Genomic Analysis", "stress response protein", "infection", "serotypes 1", "genome", "Mannheimia haemolytica"], "article_id"=>3079444, "categories"=>["Medicine", "Microbiology", "Genetics", "Pharmacology", "Biotechnology", "Environmental Sciences not elsewhere classified", "Ecology", "Immunology", "Biological Sciences not elsewhere classified", "Cancer", "Infectious Diseases", "Virology"], "users"=>["Cassidy L. Klima", "Shaun R. Cook", "Rahat Zaheer", "Chad Laing", "Vick P. Gannon", "Yong Xu", "Jay Rasmussen", "Andrew Potter", "Steve Hendrick", "Trevor W. Alexander", "Tim A. McAllister"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0149520.t002", "stats"=>{"downloads"=>0, "page_views"=>14, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Metadata_for_prophage_identified_within_the_genomes_of_11_strains_of_i_Mannheimia_haemolytica_i_/3079444", "title"=>"Metadata for prophage identified within the genomes of 11 strains of <i>Mannheimia haemolytica</i>.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2016-02-29 07:41:57"}
  • {"files"=>["https://ndownloader.figshare.com/files/4785841"], "description"=>"<p>Genes are represented as arrows. Grey background indicated regions >94.5% sequence identity. Panel A: proposed ICE genes arrangement. Panel B: resistance gene regions with alignments against cassettes found in other bacterial species.</p>", "links"=>[], "tags"=>["spacer", "S 6 strains", "Bovine Sources Bovine", "Integrative conjugative elements", "S 1", "pathogenesis", "antimicrobial resistance development", "glycosyl transferases group 1 gene", "Comparative Genomic Analysis", "stress response protein", "infection", "serotypes 1", "genome", "Mannheimia haemolytica"], "article_id"=>3079417, "categories"=>["Medicine", "Microbiology", "Genetics", "Pharmacology", "Biotechnology", "Environmental Sciences not elsewhere classified", "Ecology", "Immunology", "Biological Sciences not elsewhere classified", "Cancer", "Infectious Diseases", "Virology"], "users"=>["Cassidy L. Klima", "Shaun R. Cook", "Rahat Zaheer", "Chad Laing", "Vick P. Gannon", "Yong Xu", "Jay Rasmussen", "Andrew Potter", "Steve Hendrick", "Trevor W. Alexander", "Tim A. McAllister"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0149520.g008", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Schematic_of_putative_integrative_conjugative_elements_identified_in_whole_genome_sequences_of_i_Mannheimia_haemolytica_i_/3079417", "title"=>"Schematic of putative integrative conjugative elements identified in whole genome sequences of <i>Mannheimia haemolytica</i>.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2016-02-29 07:41:57"}
  • {"files"=>["https://ndownloader.figshare.com/files/4785712"], "description"=>"<p>For both the pan-genome and the core genome, the number of genes is plotted as a function of the number <i>n</i> of strains sequential added. The curve for the pan-genome represents the least-squares fit for the function y = Ax<sup>B</sup> + C with the best fit obtained with a correlation r<sup>2</sup> = 0.999 for A = 613.27 ± 1.08, B = 0.81, C = 2050.92 ± 10.41. The curve for the core genome represents the least-squares fit for the function y = Ae<sup>Bx</sup> + C with the best fit obtained with a correlation r<sup>2</sup> = 0.948 for A = 1444.89 ± 118.98, B = -0.32, C = 1409.54 ± 1.2.</p>", "links"=>[], "tags"=>["spacer", "S 6 strains", "Bovine Sources Bovine", "Integrative conjugative elements", "S 1", "pathogenesis", "antimicrobial resistance development", "glycosyl transferases group 1 gene", "Comparative Genomic Analysis", "stress response protein", "infection", "serotypes 1", "genome", "Mannheimia haemolytica"], "article_id"=>3079294, "categories"=>["Medicine", "Microbiology", "Genetics", "Pharmacology", "Biotechnology", "Environmental Sciences not elsewhere classified", "Ecology", "Immunology", "Biological Sciences not elsewhere classified", "Cancer", "Infectious Diseases", "Virology"], "users"=>["Cassidy L. Klima", "Shaun R. Cook", "Rahat Zaheer", "Chad Laing", "Vick P. Gannon", "Yong Xu", "Jay Rasmussen", "Andrew Potter", "Steve Hendrick", "Trevor W. Alexander", "Tim A. McAllister"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0149520.g003", "stats"=>{"downloads"=>0, "page_views"=>13, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Pan_genome_and_core_genome_of_21_i_M_i_i_haemolytica_i_isolates_/3079294", "title"=>"Pan-genome and core genome of 21 <i>M</i>. <i>haemolytica</i> isolates.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2016-02-29 07:41:57"}

PMC Usage Stats | Further Information

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Relative Metric

{"start_date"=>"2016-01-01T00:00:00Z", "end_date"=>"2016-12-31T00:00:00Z", "subject_areas"=>[]}
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