Comparative Genomic Characterization of Francisella tularensis Strains Belonging to Low and High Virulence Subspecies
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{"title"=>"Comparative genomic characterization of Francisella tularensis strains belonging to low and high virulence subspecies", "type"=>"journal", "authors"=>[{"first_name"=>"Mia D.", "last_name"=>"Champion", "scopus_author_id"=>"26648070700"}, {"first_name"=>"Qiandong", "last_name"=>"Zeng", "scopus_author_id"=>"8947609300"}, {"first_name"=>"Eli B.", "last_name"=>"Nix", "scopus_author_id"=>"57191146694"}, {"first_name"=>"Francis E.", "last_name"=>"Nano", "scopus_author_id"=>"7003505955"}, {"first_name"=>"Paul", "last_name"=>"Keim", "scopus_author_id"=>"7007034048"}, {"first_name"=>"Chinnappa D.", "last_name"=>"Kodira", "scopus_author_id"=>"6506334958"}, {"first_name"=>"Mark", "last_name"=>"Borowsky", "scopus_author_id"=>"8780823700"}, {"first_name"=>"Sarah", "last_name"=>"Young", "scopus_author_id"=>"56804211200"}, {"first_name"=>"Michael", "last_name"=>"Koehrsen", "scopus_author_id"=>"24168865100"}, {"first_name"=>"Reinhard", "last_name"=>"Engels", "scopus_author_id"=>"8947606600"}, {"first_name"=>"Matthew", "last_name"=>"Pearson", "scopus_author_id"=>"16029635900"}, {"first_name"=>"Clint", "last_name"=>"Howarth", "scopus_author_id"=>"26648493700"}, {"first_name"=>"Lisa", "last_name"=>"Larson", "scopus_author_id"=>"36904185900"}, {"first_name"=>"Jared", "last_name"=>"White", "scopus_author_id"=>"23978873700"}, {"first_name"=>"Lucia", "last_name"=>"Alvarado", "scopus_author_id"=>"26648029200"}, {"first_name"=>"Mats", "last_name"=>"Forsman", "scopus_author_id"=>"7005163392"}, {"first_name"=>"Scott W.", "last_name"=>"Bearden", "scopus_author_id"=>"6701562402"}, {"first_name"=>"Anders", "last_name"=>"Sjöstedt", "scopus_author_id"=>"7006329721"}, {"first_name"=>"Richard", "last_name"=>"Titball", "scopus_author_id"=>"7005676571"}, {"first_name"=>"Stephen L.", "last_name"=>"Michell", "scopus_author_id"=>"6603289911"}, {"first_name"=>"Bruce", "last_name"=>"Birren", "scopus_author_id"=>"7003582624"}, {"first_name"=>"James", "last_name"=>"Galagan", "scopus_author_id"=>"6603329136"}], "year"=>2009, "source"=>"PLoS Pathogens", "identifiers"=>{"sgr"=>"67249166181", "isbn"=>"1553-7374 (Electronic)\\r1553-7366 (Linking)", "pmid"=>"19478886", "doi"=>"10.1371/journal.ppat.1000459", "scopus"=>"2-s2.0-67249166181", "issn"=>"15537366", "pui"=>"354743715"}, "id"=>"33e73e10-897a-3c7d-a2e9-652fdd986154", "abstract"=>"Tularemia is a geographically widespread, severely debilitating, and occasionally lethal disease in humans. It is caused by infection by a gram-negative bacterium, Francisella tularensis. In order to better understand its potency as an etiological agent as well as its potential as a biological weapon, we have completed draft assemblies and report the first complete genomic characterization of five strains belonging to the following different Francisella subspecies (subsp.): the F. tularensis subsp. tularensis FSC033, F. tularensis subsp. holarctica FSC257 and FSC022, and F. tularensis subsp. novicida GA99-3548 and GA99-3549 strains. Here, we report the sequencing of these strains and comparative genomic analysis with recently available public Francisella sequences, including the rare F. tularensis subsp. mediasiatica FSC147 strain isolate from the Central Asian Region. We report evidence for the occurrence of large-scale rearrangement events in strains of the holarctica subspecies, supporting previous proposals that further phylogenetic subdivisions of the Type B clade are likely. We also find a significant enrichment of disrupted or absent ORFs proximal to predicted breakpoints in the FSC022 strain, including a genetic component of the Type I restriction-modification defense system. Many of the pseudogenes identified are also disrupted in the closely related rarely human pathogenic F. tularensis subsp. mediasiatica FSC147 strain, including modulator of drug activity B (mdaB) (FTT0961), which encodes a known NADPH quinone reductase involved in oxidative stress resistance. We have also identified genes exhibiting sequence similarity to effectors of the Type III (T3SS) and components of the Type IV secretion systems (T4SS). One of the genes, msrA2 (FTT1797c), is disrupted in F. tularensis subsp. mediasiatica and has recently been shown to mediate bacterial pathogen survival in host organisms. Our findings suggest that in addition to the duplication of the Francisella Pathogenicity Island, and acquisition of individual loci, adaptation by gene loss in the more recently emerged tularensis, holarctica, and mediasiatica subspecies occurred and was distinct from evolutionary events that differentiated these subspecies, and the novicida subspecies, from a common ancestor. Our findings are applicable to future studies focused on variations in Francisella subspecies pathogenesis, and of broader interest to studies of genomic pathoadaptation in bacteria.", "link"=>"http://www.mendeley.com/research/comparative-genomic-characterization-francisella-tularensis-strains-belonging-low-high-virulence-sub", "reader_count"=>73, "reader_count_by_academic_status"=>{"Unspecified"=>1, "Professor > Associate Professor"=>11, "Researcher"=>28, "Student > Doctoral Student"=>2, "Student > Ph. D. Student"=>11, "Student > Postgraduate"=>3, "Student > Master"=>7, "Other"=>2, "Student > Bachelor"=>4, "Lecturer"=>1, "Professor"=>3}, "reader_count_by_user_role"=>{"Unspecified"=>1, "Professor > Associate Professor"=>11, "Researcher"=>28, "Student > Doctoral Student"=>2, "Student > Ph. D. Student"=>11, "Student > Postgraduate"=>3, "Student > Master"=>7, "Other"=>2, "Student > Bachelor"=>4, "Lecturer"=>1, "Professor"=>3}, "reader_count_by_subject_area"=>{"Unspecified"=>2, "Biochemistry, Genetics and Molecular Biology"=>3, "Agricultural and Biological Sciences"=>56, "Medicine and Dentistry"=>3, "Business, Management and Accounting"=>1, "Social Sciences"=>4, "Immunology and Microbiology"=>4}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>3}, "Social Sciences"=>{"Social Sciences"=>4}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>4}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>56}, "Business, Management and Accounting"=>{"Business, Management and Accounting"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>3}, "Unspecified"=>{"Unspecified"=>2}}, "reader_count_by_country"=>{"Sweden"=>2, "United States"=>6, "United Kingdom"=>1, "Chile"=>1, "Spain"=>1}, "group_count"=>8}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/896369"], "description"=>"<p>Genome comparative maps were constructed using CGview software to map pairwise blastn alignments between several <i>Francisella</i> genomes (minimum percent identity = 95 and expected threshold = 1e-5). Specifically, five newly sequenced Francisella genomes (<i>F. tularensis</i> subsp. <i>holarctica</i> FSC257 and FSC022; <i>F. tularensis</i> subsp. <i>tularensis</i> FSC033; and <i>F. tularensis</i> subsp. <i>novicida</i> GA99-3548, and GA99-3549 strains) were aligned to the <i>F. tularensis</i> subsp. <i>holarctica</i> OSU18 reference sequence (outside blue track of genome map). A high degree of similarity between the genomes (>95%) is evident from the continuous blocks of synteny (colored regions).</p>", "links"=>[], "tags"=>["alignments", "genome", "sequences"], "article_id"=>566784, "categories"=>["Evolutionary Biology", "Medicine", "Genetics", "Microbiology", "Infectious Diseases"], "users"=>["Mia D. Champion", "Qiandong Zeng", "Eli B. Nix", "Francis E. Nano", "Paul Keim", "Chinnappa D. Kodira", "Mark Borowsky", "Sarah Young", "Michael Koehrsen", "Reinhard Engels", "Matthew Pearson", "Clint Howarth", "Lisa Larson", "Jared White", "Lucia Alvarado", "Mats Forsman", "Scott W. Bearden", "Anders Sjöstedt", "Richard Titball", "Stephen L. Michell", "Bruce Birren", "James Galagan"], "doi"=>"https://dx.doi.org/10.1371/journal.ppat.1000459.g001", "stats"=>{"downloads"=>0, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Pairwise_alignments_between_five_new_Francisella_genome_sequences_and_a_reference_genome_exhibit_95_sequence_conservation_/566784", "title"=>"Pairwise alignments between five new <i>Francisella</i> genome sequences and a reference genome exhibit >95% sequence conservation.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-05-29 01:53:04"}
  • {"files"=>["https://ndownloader.figshare.com/files/897490"], "description"=>"<p>Phylogenetic Differentiation Associated with Gain and Loss of Genes Regulating Competence (E values>1e-10).</p>", "links"=>[], "tags"=>["differentiation", "genes", "regulating", "competence"], "article_id"=>567917, "categories"=>["Evolutionary Biology", "Medicine", "Genetics", "Microbiology", "Infectious Diseases"], "users"=>["Mia D. Champion", "Qiandong Zeng", "Eli B. Nix", "Francis E. Nano", "Paul Keim", "Chinnappa D. Kodira", "Mark Borowsky", "Sarah Young", "Michael Koehrsen", "Reinhard Engels", "Matthew Pearson", "Clint Howarth", "Lisa Larson", "Jared White", "Lucia Alvarado", "Mats Forsman", "Scott W. Bearden", "Anders Sjöstedt", "Richard Titball", "Stephen L. Michell", "Bruce Birren", "James Galagan"], "doi"=>"https://dx.doi.org/10.1371/journal.ppat.1000459.t006", "stats"=>{"downloads"=>0, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Phylogenetic_Differentiation_Associated_with_Gain_and_Loss_of_Genes_Regulating_Competence_E_values_gt_1e_10_/567917", "title"=>"Phylogenetic Differentiation Associated with Gain and Loss of Genes Regulating Competence (E values>1e-10).", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2009-05-29 02:11:57"}
  • {"files"=>["https://ndownloader.figshare.com/files/896779"], "description"=>"<p>A comparison of genome rearrangement patterns between the more ancestral <i>F. tularensis</i> subsp. <i>holarctica</i> FSC022 japonica strain and representative strains of the main <i>holarctica</i> group (<i>F. tularensis</i> subsp. <i>holarctica</i> LVS and <i>F. tularensis</i> subsp. <i>holarctica</i> OSU18) was done using MAUVE (A). MAUVE uses an anchored alignment algorithm that permits reordering of the alignment anchors for identification of rearrangements. Colored Local Collinear Blocks (LCBs) are regions of sequence alignment that are free of rearrangements. Each LCB is defined by the anchor regions or predicted sites of rearrangement. A default LCB cutoff of 175, and a filtering for larger blocks containing 10 Kb or larger was done in Mauve. Sequence inversions are denoted by differential positioning of the LCBs relative to a reference axis. A zoomed-in section of the whole-genome alignment is shown so that the annotated ORFs are visible (black outlined boxes). The small red ORFs are rRNA genes. ORFs proximal to predicted rearrangement breakpoints (red circles) have been color coded and labeled (FWD, INV). A summary of the predicted protein products for these genes is provided in (B). These include genes that have been identified as being either disrupted or absent in the <i>F. tularensis</i> subsp. <i>holarctica</i> subspecies.</p>", "links"=>[], "tags"=>["alignment", "genomes", "lineage", "identifies", "conserved", "regions", "pseudogenes", "proximal"], "article_id"=>567194, "categories"=>["Evolutionary Biology", "Medicine", "Genetics", "Microbiology", "Infectious Diseases"], "users"=>["Mia D. Champion", "Qiandong Zeng", "Eli B. Nix", "Francis E. Nano", "Paul Keim", "Chinnappa D. Kodira", "Mark Borowsky", "Sarah Young", "Michael Koehrsen", "Reinhard Engels", "Matthew Pearson", "Clint Howarth", "Lisa Larson", "Jared White", "Lucia Alvarado", "Mats Forsman", "Scott W. Bearden", "Anders Sjöstedt", "Richard Titball", "Stephen L. Michell", "Bruce Birren", "James Galagan"], "doi"=>"https://dx.doi.org/10.1371/journal.ppat.1000459.g004", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Multiple_alignment_of_Francisella_genomes_of_the_Type_B_lineage_identifies_conserved_sequence_regions_with_rearrangements_pseudogenes_are_found_proximal_to_predicted_breakpoints_/567194", "title"=>"Multiple alignment of <i>Francisella</i> genomes of the Type B lineage identifies conserved sequence regions with rearrangements; pseudogenes are found proximal to predicted breakpoints.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-05-29 01:59:54"}
  • {"files"=>["https://ndownloader.figshare.com/files/897562"], "description"=>"<p>GenBank Accession Numbers for Francisella Strains Used in This Study.</p>", "links"=>[], "tags"=>["accession", "numbers", "francisella", "strains"], "article_id"=>567989, "categories"=>["Evolutionary Biology", "Medicine", "Genetics", "Microbiology", "Infectious Diseases"], "users"=>["Mia D. Champion", "Qiandong Zeng", "Eli B. Nix", "Francis E. Nano", "Paul Keim", "Chinnappa D. Kodira", "Mark Borowsky", "Sarah Young", "Michael Koehrsen", "Reinhard Engels", "Matthew Pearson", "Clint Howarth", "Lisa Larson", "Jared White", "Lucia Alvarado", "Mats Forsman", "Scott W. Bearden", "Anders Sjöstedt", "Richard Titball", "Stephen L. Michell", "Bruce Birren", "James Galagan"], "doi"=>"https://dx.doi.org/10.1371/journal.ppat.1000459.t007", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_GenBank_Accession_Numbers_for_Francisella_Strains_Used_in_This_Study_/567989", "title"=>"GenBank Accession Numbers for Francisella Strains Used in This Study.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2009-05-29 02:13:09"}
  • {"files"=>["https://ndownloader.figshare.com/files/897279"], "description"=>"<p>Phylogenetic Differentiation Associated with Gene Gain and Loss.</p>", "links"=>[], "tags"=>["differentiation"], "article_id"=>567715, "categories"=>["Evolutionary Biology", "Medicine", "Genetics", "Microbiology", "Infectious Diseases"], "users"=>["Mia D. Champion", "Qiandong Zeng", "Eli B. Nix", "Francis E. Nano", "Paul Keim", "Chinnappa D. Kodira", "Mark Borowsky", "Sarah Young", "Michael Koehrsen", "Reinhard Engels", "Matthew Pearson", "Clint Howarth", "Lisa Larson", "Jared White", "Lucia Alvarado", "Mats Forsman", "Scott W. Bearden", "Anders Sjöstedt", "Richard Titball", "Stephen L. Michell", "Bruce Birren", "James Galagan"], "doi"=>"https://dx.doi.org/10.1371/journal.ppat.1000459.t003", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Phylogenetic_Differentiation_Associated_with_Gene_Gain_and_Loss_/567715", "title"=>"Phylogenetic Differentiation Associated with Gene Gain and Loss.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2009-05-29 02:08:35"}
  • {"files"=>["https://ndownloader.figshare.com/files/443675", "https://ndownloader.figshare.com/files/443748", "https://ndownloader.figshare.com/files/443908"], "description"=>"<div><p>Tularemia is a geographically widespread, severely debilitating, and occasionally lethal disease in humans. It is caused by infection by a gram-negative bacterium, <em>Francisella tularensis</em>. In order to better understand its potency as an etiological agent as well as its potential as a biological weapon, we have completed draft assemblies and report the first complete genomic characterization of five strains belonging to the following different <em>Francisella</em> subspecies (subsp.): the <em>F. tularensis</em> subsp. <em>tularensis</em> FSC033, <em>F. tularensis</em> subsp. <em>holarctica</em> FSC257 and FSC022, and <em>F. tularensis</em> subsp. <em>novicida</em> GA99-3548 and GA99-3549 strains. Here, we report the sequencing of these strains and comparative genomic analysis with recently available public <em>Francisella</em> sequences, including the rare <em>F. tularensis</em> subsp. <em>mediasiatica</em> FSC147 strain isolate from the Central Asian Region. We report evidence for the occurrence of large-scale rearrangement events in strains of the <em>holarctica</em> subspecies, supporting previous proposals that further phylogenetic subdivisions of the Type B clade are likely. We also find a significant enrichment of disrupted or absent ORFs proximal to predicted breakpoints in the FSC022 strain, including a genetic component of the Type I restriction-modification defense system. Many of the pseudogenes identified are also disrupted in the closely related rarely human pathogenic <em>F. tularensis</em> subsp. <em>mediasiatica</em> FSC147 strain, including modulator of drug activity B (<em>mdaB</em>) (FTT0961), which encodes a known NADPH quinone reductase involved in oxidative stress resistance. We have also identified genes exhibiting sequence similarity to effectors of the Type III (T3SS) and components of the Type IV secretion systems (T4SS). One of the genes, <em>msrA2</em> (FTT1797c), is disrupted in <em>F. tularensis</em> subsp. <em>mediasiatica</em> and has recently been shown to mediate bacterial pathogen survival in host organisms. Our findings suggest that in addition to the duplication of the <em>Francisella</em> Pathogenicity Island, and acquisition of individual loci, adaptation by gene loss in the more recently emerged <em>tularensis</em>, <em>holarctica</em>, and <em>mediasiatica</em> subspecies occurred and was distinct from evolutionary events that differentiated these subspecies, and the <em>novicida</em> subspecies, from a common ancestor. Our findings are applicable to future studies focused on variations in <em>Francisella</em> subspecies pathogenesis, and of broader interest to studies of genomic pathoadaptation in bacteria.</p></div>", "links"=>[], "tags"=>["comparative", "genomic", "characterization", "strains", "belonging", "virulence", "subspecies"], "article_id"=>147444, "categories"=>["Evolutionary Biology", "Medicine", "Genetics", "Microbiology", "Cancer"], "users"=>["Mia D. Champion", "Qiandong Zeng", "Eli B. Nix", "Francis E. Nano", "Paul Keim", "Chinnappa D. Kodira", "Mark Borowsky", "Sarah Young", "Michael Koehrsen", "Reinhard Engels", "Matthew Pearson", "Clint Howarth", "Lisa Larson", "Jared White", "Lucia Alvarado", "Mats Forsman", "Scott W. Bearden", "Anders Sjöstedt", "Richard Titball", "Stephen L. Michell", "Bruce Birren", "James Galagan"], "doi"=>["https://dx.doi.org/10.1371/journal.ppat.1000459.s001", "https://dx.doi.org/10.1371/journal.ppat.1000459.s002", "https://dx.doi.org/10.1371/journal.ppat.1000459.s003"], "stats"=>{"downloads"=>27, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Comparative_Genomic_Characterization_of_Francisella_tularensis_Strains_Belonging_to_Low_and_High_Virulence_Subspecies/147444", "title"=>"Comparative Genomic Characterization of <em>Francisella tularensis</em> Strains Belonging to Low and High Virulence Subspecies", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2009-05-29 02:04:04"}
  • {"files"=>["https://ndownloader.figshare.com/files/897220"], "description"=>"<p>IS Element Summary Table.</p>", "links"=>[], "tags"=>["computational biology/comparative sequence analysis", "computational biology/genomics", "evolutionary biology/bioinformatics", "evolutionary biology/evolutionary and comparative genetics", "evolutionary biology/genomics", "evolutionary biology/microbial evolution and genomics", "genetics and genomics/bioinformatics", "genetics and genomics/comparative genomics", "genetics and genomics/genetics of disease", "genetics and genomics/genome projects", "genetics and genomics/genomics", "genetics and genomics/microbial evolution and genomics", "genetics and genomics/population genetics", "infectious diseases/bacterial infections", "microbiology/microbial evolution and genomics"], "article_id"=>567632, "categories"=>["Evolutionary Biology", "Medicine", "Genetics", "Microbiology", "Infectious Diseases"], "users"=>["Mia D. Champion", "Qiandong Zeng", "Eli B. Nix", "Francis E. Nano", "Paul Keim", "Chinnappa D. Kodira", "Mark Borowsky", "Sarah Young", "Michael Koehrsen", "Reinhard Engels", "Matthew Pearson", "Clint Howarth", "Lisa Larson", "Jared White", "Lucia Alvarado", "Mats Forsman", "Scott W. Bearden", "Anders Sjöstedt", "Richard Titball", "Stephen L. Michell", "Bruce Birren", "James Galagan"], "doi"=>"https://dx.doi.org/10.1371/journal.ppat.1000459.t002", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_IS_Element_Summary_Table_/567632", "title"=>"IS Element Summary Table.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2009-05-29 02:07:12"}
  • {"files"=>["https://ndownloader.figshare.com/files/897426"], "description"=>"<p>Phylogenetic Differentiation Associated with Gain and Loss of Genes with Sequence Similarity to T4SS Components.</p>", "links"=>[], "tags"=>["differentiation", "genes", "t4ss"], "article_id"=>567854, "categories"=>["Evolutionary Biology", "Medicine", "Genetics", "Microbiology", "Infectious Diseases"], "users"=>["Mia D. Champion", "Qiandong Zeng", "Eli B. Nix", "Francis E. Nano", "Paul Keim", "Chinnappa D. Kodira", "Mark Borowsky", "Sarah Young", "Michael Koehrsen", "Reinhard Engels", "Matthew Pearson", "Clint Howarth", "Lisa Larson", "Jared White", "Lucia Alvarado", "Mats Forsman", "Scott W. Bearden", "Anders Sjöstedt", "Richard Titball", "Stephen L. Michell", "Bruce Birren", "James Galagan"], "doi"=>"https://dx.doi.org/10.1371/journal.ppat.1000459.t005", "stats"=>{"downloads"=>0, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Phylogenetic_Differentiation_Associated_with_Gain_and_Loss_of_Genes_with_Sequence_Similarity_to_T4SS_Components_/567854", "title"=>"Phylogenetic Differentiation Associated with Gain and Loss of Genes with Sequence Similarity to T4SS Components.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2009-05-29 02:10:54"}
  • {"files"=>["https://ndownloader.figshare.com/files/896961"], "description"=>"<p>Pairwise sequence alignments using <i>F. tularensis</i> subsp. <i>holarctica</i> (Type B) strains as a reference were further analyzed for evidence of gene decay proximal to predicted breakpoint sites. Total ORF counts were used to determine the percentage of pseudogenes (y-axis) relative to the distance from the predicted breakpoint (x-axis). Pseudogene enrichment was determined using Fisher's Exact Test to derive p-values. Our findings show the highest percentages of pseudogenes are found within 1 kb of the predicted breakpoints indicating that genome rearrangement events have likely promoted gene decay in strains of the Type B lineage.</p>", "links"=>[], "tags"=>["pairwise", "alignments", "provides", "pseudogene", "enrichment", "kb", "breakpoints"], "article_id"=>567388, "categories"=>["Evolutionary Biology", "Medicine", "Genetics", "Microbiology", "Infectious Diseases"], "users"=>["Mia D. Champion", "Qiandong Zeng", "Eli B. Nix", "Francis E. Nano", "Paul Keim", "Chinnappa D. Kodira", "Mark Borowsky", "Sarah Young", "Michael Koehrsen", "Reinhard Engels", "Matthew Pearson", "Clint Howarth", "Lisa Larson", "Jared White", "Lucia Alvarado", "Mats Forsman", "Scott W. Bearden", "Anders Sjöstedt", "Richard Titball", "Stephen L. Michell", "Bruce Birren", "James Galagan"], "doi"=>"https://dx.doi.org/10.1371/journal.ppat.1000459.g005", "stats"=>{"downloads"=>0, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Comparisons_of_pairwise_sequence_alignments_provides_evidence_of_pseudogene_enrichment_within_1_kb_of_predicted_breakpoints_in_Type_B_strains_/567388", "title"=>"Comparisons of pairwise sequence alignments provides evidence of pseudogene enrichment within 1 kb of predicted breakpoints in Type B strains.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-05-29 02:03:08"}
  • {"files"=>["https://ndownloader.figshare.com/files/896632"], "description"=>"<p>The evolutionary history of 20 Francisella strains was inferred from analysis of genome-wide SNP sequences. Genome-wide SNPs at least 20 bp apart were selected for further analysis using MEGA4 software. The tree is drawn to scale, with branch lengths calculated using the average pathway method and are in the units of the number of changes over the whole sequence. <i>Francisella</i> strains sequenced at the Broad Institute are in red. The differentiation of <i>F. tularensis</i> subsp. <i>novicida</i> predated differentiation of the more pathogenic <i>F. tularensis</i> subsp. <i>tularensis</i> and <i>F. tularensis</i> subsp. <i>holarctica</i> subspecies from a common ancestor. Our data indicates differential rates of evolution along the Type A.II and Type A.I lineages, as evident from the branch lengths. The Type B FSC022 strain diverged prior to the radiation of the main <i>holarctica</i> group and also has a greatly reduced branch length, consistent with a much slower rate of evolution. The <i>F. tularensis</i> subsp. <i>mediasiatica</i> FSC147 strain is phylogenetically more closely related to the Type A.II lineage even though its pathogenicity is characteristic of Type B strains.</p>", "links"=>[], "tags"=>["20", "strains", "genome-wide", "snp", "sequences", "inferred", "parsimony"], "article_id"=>567050, "categories"=>["Evolutionary Biology", "Medicine", "Genetics", "Microbiology", "Infectious Diseases"], "users"=>["Mia D. Champion", "Qiandong Zeng", "Eli B. Nix", "Francis E. Nano", "Paul Keim", "Chinnappa D. Kodira", "Mark Borowsky", "Sarah Young", "Michael Koehrsen", "Reinhard Engels", "Matthew Pearson", "Clint Howarth", "Lisa Larson", "Jared White", "Lucia Alvarado", "Mats Forsman", "Scott W. Bearden", "Anders Sjöstedt", "Richard Titball", "Stephen L. Michell", "Bruce Birren", "James Galagan"], "doi"=>"https://dx.doi.org/10.1371/journal.ppat.1000459.g003", "stats"=>{"downloads"=>0, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Phylogeny_of_20_Francisella_strains_by_analysis_of_Genome_wide_SNP_sequences_and_inferred_using_Maximum_Parsimony_method_/567050", "title"=>"Phylogeny of 20 <i>Francisella</i> strains by analysis of Genome-wide SNP sequences and inferred using Maximum Parsimony method.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-05-29 01:57:30"}
  • {"files"=>["https://ndownloader.figshare.com/files/896524"], "description"=>"<p>Whole genome alignments and dotplot comparisons between Type B strains of <i>Francisella</i>: (A) <i>F. tularensis</i> subsp. <i>holarctica</i> OSU18 and <i>F. tularensis</i> subsp. <i>holarctica</i> FSC022 (reference genome) and (B) <i>F. tularensis</i> subsp. <i>holarctica</i> LVS, <i>F. tularensis</i> subsp. <i>holarctica</i> OSU18 (reference genome), <i>F. tularensis</i> subsp. <i>holarctica</i> FSC257, <i>F. tularensis</i> subsp. <i>holarctica</i> FTA. Alignments were filtered for overlap percentages greater than or equal to 90%. Dotplot (B) shows a nearly linear, overlapping alignment between all of the Type B strains of the main <i>holarctica</i> lineage (not all of the strains of the Type B radiation lineage are shown for clarity), with the notable exception of comparisons between the <i>F. tularensis</i> subsp. <i>holarctica</i> OSU18 and <i>F. tularensis</i> subsp. <i>holarctica</i> FSC257 strains. In contrast, numerous rearrangements are evident from comparisons between the <i>F. tularensis</i> subsp. <i>holarctica</i> FSC022 <i>japonica</i> strain and all of the other Type B strains of the main <i>holarctica</i> lineage (A) (only comparison to the <i>F. tularensis</i> subsp. <i>holarctica</i> OSU18 strain is shown here).</p>", "links"=>[], "tags"=>["strains", "occurrence", "rearrangement"], "article_id"=>566949, "categories"=>["Evolutionary Biology", "Medicine", "Genetics", "Microbiology", "Infectious Diseases"], "users"=>["Mia D. Champion", "Qiandong Zeng", "Eli B. Nix", "Francis E. Nano", "Paul Keim", "Chinnappa D. Kodira", "Mark Borowsky", "Sarah Young", "Michael Koehrsen", "Reinhard Engels", "Matthew Pearson", "Clint Howarth", "Lisa Larson", "Jared White", "Lucia Alvarado", "Mats Forsman", "Scott W. Bearden", "Anders Sjöstedt", "Richard Titball", "Stephen L. Michell", "Bruce Birren", "James Galagan"], "doi"=>"https://dx.doi.org/10.1371/journal.ppat.1000459.g002", "stats"=>{"downloads"=>0, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Dotplot_comparison_between_the_Francisella_tularensis_subsp_holarctica_strains_showing_the_occurrence_of_significant_rearrangement_events_/566949", "title"=>"Dotplot comparison between the <i>Francisella tularensis</i> subsp. <i>holarctica</i> strains showing the occurrence of significant rearrangement events.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-05-29 01:55:49"}
  • {"files"=>["https://ndownloader.figshare.com/files/897357"], "description"=>"<p>Phylogenetic Differentiation Associated with Gain and Loss of Genes with Sequence Similarity to T3SS Effectors.</p>", "links"=>[], "tags"=>["differentiation", "genes", "t3ss"], "article_id"=>567780, "categories"=>["Evolutionary Biology", "Medicine", "Genetics", "Microbiology", "Infectious Diseases"], "users"=>["Mia D. Champion", "Qiandong Zeng", "Eli B. Nix", "Francis E. Nano", "Paul Keim", "Chinnappa D. Kodira", "Mark Borowsky", "Sarah Young", "Michael Koehrsen", "Reinhard Engels", "Matthew Pearson", "Clint Howarth", "Lisa Larson", "Jared White", "Lucia Alvarado", "Mats Forsman", "Scott W. Bearden", "Anders Sjöstedt", "Richard Titball", "Stephen L. Michell", "Bruce Birren", "James Galagan"], "doi"=>"https://dx.doi.org/10.1371/journal.ppat.1000459.t004", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Phylogenetic_Differentiation_Associated_with_Gain_and_Loss_of_Genes_with_Sequence_Similarity_to_T3SS_Effectors_/567780", "title"=>"Phylogenetic Differentiation Associated with Gain and Loss of Genes with Sequence Similarity to T3SS Effectors.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2009-05-29 02:09:40"}
  • {"files"=>["https://ndownloader.figshare.com/files/897126"], "description"=>"<p>Gene and Assembly Statistics Summary.</p>", "links"=>[], "tags"=>["computational biology/comparative sequence analysis", "computational biology/genomics", "evolutionary biology/bioinformatics", "evolutionary biology/evolutionary and comparative genetics", "evolutionary biology/genomics", "evolutionary biology/microbial evolution and genomics", "genetics and genomics/bioinformatics", "genetics and genomics/comparative genomics", "genetics and genomics/genetics of disease", "genetics and genomics/genome projects", "genetics and genomics/genomics", "genetics and genomics/microbial evolution and genomics", "genetics and genomics/population genetics", "infectious diseases/bacterial infections", "microbiology/microbial evolution and genomics"], "article_id"=>567538, "categories"=>["Evolutionary Biology", "Medicine", "Genetics", "Microbiology", "Infectious Diseases"], "users"=>["Mia D. Champion", "Qiandong Zeng", "Eli B. Nix", "Francis E. Nano", "Paul Keim", "Chinnappa D. Kodira", "Mark Borowsky", "Sarah Young", "Michael Koehrsen", "Reinhard Engels", "Matthew Pearson", "Clint Howarth", "Lisa Larson", "Jared White", "Lucia Alvarado", "Mats Forsman", "Scott W. Bearden", "Anders Sjöstedt", "Richard Titball", "Stephen L. Michell", "Bruce Birren", "James Galagan"], "doi"=>"https://dx.doi.org/10.1371/journal.ppat.1000459.t001", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Gene_and_Assembly_Statistics_Summary_/567538", "title"=>"Gene and Assembly Statistics Summary.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2009-05-29 02:05:38"}

PMC Usage Stats | Further Information

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Relative Metric

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