Genomic Analyses of the Microsporidian Nosema ceranae, an Emergent Pathogen of Honey Bees
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{"title"=>"Genomic analyses of the microsporidian Nosema ceranae, an emergent pathogen of honey bees", "type"=>"journal", "authors"=>[{"first_name"=>"R. Scott", "last_name"=>"Cornman", "scopus_author_id"=>"6603361474"}, {"first_name"=>"Yan Ping", "last_name"=>"Chen", "scopus_author_id"=>"15047807200"}, {"first_name"=>"Michael C.", "last_name"=>"Schatz", "scopus_author_id"=>"7102406086"}, {"first_name"=>"Craig", "last_name"=>"Street", "scopus_author_id"=>"19036357300"}, {"first_name"=>"Yan", "last_name"=>"Zhao", "scopus_author_id"=>"7407398112"}, {"first_name"=>"Brian", "last_name"=>"Desany", "scopus_author_id"=>"14633694900"}, {"first_name"=>"Michael", "last_name"=>"Egholm", "scopus_author_id"=>"7003454634"}, {"first_name"=>"Stephen", "last_name"=>"Hutchison", "scopus_author_id"=>"7006378847"}, {"first_name"=>"Jeffery S.", "last_name"=>"Pettis", "scopus_author_id"=>"7004714365"}, {"first_name"=>"W. Ian", "last_name"=>"Lipkin", "scopus_author_id"=>"7005714572"}, {"first_name"=>"Jay D.", "last_name"=>"Evans", "scopus_author_id"=>"7407667162"}], "year"=>2009, "source"=>"PLoS Pathogens", "identifiers"=>{"pui"=>"354959159", "sgr"=>"67650930861", "issn"=>"15537366", "pmid"=>"19503607", "scopus"=>"2-s2.0-67650930861", "doi"=>"10.1371/journal.ppat.1000466", "isbn"=>"10.1371/journal.ppat.1000466"}, "id"=>"e0079297-9e34-30b6-887e-8eb8878384df", "abstract"=>"Recent steep declines in honey bee health have severely impacted the beekeeping industry, presenting new risks for agricultural commodities that depend on insect pollination. Honey bee declines could reflect increased pressures from parasites and pathogens. The incidence of the microsporidian pathogen Nosema ceranae has increased significantly in the past decade. Here we present a draft assembly (7.86 MB) of the N. ceranae genome derived from pyrosequence data, including initial gene models and genomic comparisons with other members of this highly derived fungal lineage. N. ceranae has a strongly AT-biased genome (74% A+T) and a diversity of repetitive elements, complicating the assembly. Of 2,614 predicted protein-coding sequences, we conservatively estimate that 1,366 have homologs in the microsporidian Encephalitozoon cuniculi, the most closely related published genome sequence. We identify genes conserved among microsporidia that lack clear homology outside this group, which are of special interest as potential virulence factors in this group of obligate parasites. A substantial fraction of the diminutive N. ceranae proteome consists of novel and transposable-element proteins. For a majority of well-supported gene models, a conserved sense-strand motif can be found within 15 bases upstream of the start codon; a previously uncharacterized version of this motif is also present in E. cuniculi. These comparisons provide insight into the architecture, regulation, and evolution of microsporidian genomes, and will drive investigations into honey bee-Nosema interactions.", "link"=>"http://www.mendeley.com/research/genomic-analyses-microsporidian-nosema-ceranae-emergent-pathogen-honey-bees", "reader_count"=>171, "reader_count_by_academic_status"=>{"Unspecified"=>4, "Professor > Associate Professor"=>14, "Librarian"=>1, "Researcher"=>42, "Student > Doctoral Student"=>11, "Student > Ph. D. Student"=>52, "Student > Postgraduate"=>5, "Student > Master"=>14, "Other"=>6, "Student > Bachelor"=>12, "Lecturer"=>2, "Lecturer > Senior Lecturer"=>1, "Professor"=>7}, "reader_count_by_user_role"=>{"Unspecified"=>4, "Professor > Associate Professor"=>14, "Librarian"=>1, "Researcher"=>42, "Student > Doctoral Student"=>11, "Student > Ph. D. Student"=>52, "Student > Postgraduate"=>5, "Student > Master"=>14, "Other"=>6, "Student > Bachelor"=>12, "Lecturer"=>2, "Lecturer > Senior Lecturer"=>1, "Professor"=>7}, "reader_count_by_subject_area"=>{"Unspecified"=>5, "Environmental Science"=>5, "Biochemistry, Genetics and Molecular Biology"=>19, "Agricultural and Biological Sciences"=>127, "Medicine and Dentistry"=>5, "Veterinary Science and Veterinary Medicine"=>4, "Chemistry"=>4, "Computer Science"=>1, "Immunology and Microbiology"=>1}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>5}, "Chemistry"=>{"Chemistry"=>4}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>127}, "Computer Science"=>{"Computer Science"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>19}, "Unspecified"=>{"Unspecified"=>5}, "Environmental Science"=>{"Environmental Science"=>5}, "Veterinary Science and Veterinary Medicine"=>{"Veterinary Science and Veterinary Medicine"=>4}}, "reader_count_by_country"=>{"Canada"=>2, "United States"=>9, "Denmark"=>1, "Brazil"=>1, "United Kingdom"=>5, "Mexico"=>2, "France"=>2, "Thailand"=>1, "Germany"=>1, "Spain"=>1}, "group_count"=>4}

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  • {"files"=>["https://ndownloader.figshare.com/files/896025"], "description"=>"<p>The horizontal axis is the proportion of G+C in the first two codon positions (GC1,2), whereas the vertical axis represents the G+C content of the third position (GC3). Substitutions at the third position are usually synonymous and thus are expected to reflect mutational equilibrium in the absence of other evolutionary forces such as codon bias. The two genomes overlap very little in G+C content of genes, and differ more at the third position than at the first two positions.</p>", "links"=>[], "tags"=>["ecology/environmental microbiology", "evolutionary biology/evolutionary and comparative genetics", "evolutionary biology/genomics", "evolutionary biology/microbial evolution and genomics", "genetics and genomics", "genetics and genomics/genome projects", "genetics and genomics/microbial evolution and genomics", "Infectious diseases"], "article_id"=>566464, "categories"=>["Evolutionary Biology", "Genetics", "Infectious Diseases", "Ecology"], "users"=>["R. Scott Cornman", "Yan Ping Chen", "Michael C. Schatz", "Craig Street", "Yan Zhao", "Brian Desany", "Michael Egholm", "Stephen Hutchison", "Jeffery S. Pettis", "W. Ian Lipkin", "Jay D. Evans"], "doi"=>"https://dx.doi.org/10.1371/journal.ppat.1000466.g004", "stats"=>{"downloads"=>0, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_G_C_content_of_N_ceranae_and_E_cuniculi_genes_/566464", "title"=>"G+C content of <i>N. ceranae</i> and <i>E. cuniculi</i> genes.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-06-05 01:47:44"}
  • {"files"=>["https://ndownloader.figshare.com/files/896285"], "description"=>"*<p>See text for assignment method.</p>", "links"=>[], "tags"=>["genes", "homologous", "orthologous", "microsporidian"], "article_id"=>566733, "categories"=>["Evolutionary Biology", "Genetics", "Infectious Diseases", "Ecology"], "users"=>["R. Scott Cornman", "Yan Ping Chen", "Michael C. Schatz", "Craig Street", "Yan Zhao", "Brian Desany", "Michael Egholm", "Stephen Hutchison", "Jeffery S. Pettis", "W. Ian Lipkin", "Jay D. Evans"], "doi"=>"https://dx.doi.org/10.1371/journal.ppat.1000466.t002", "stats"=>{"downloads"=>1, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Estimates_of_the_number_of_N_ceranae_genes_that_are_homologous_or_orthologous_to_genes_in_the_microsporidian_E_cuniculi_and_yeast_/566733", "title"=>"Estimates of the number of <i>N. ceranae</i> genes that are homologous or orthologous to genes in the microsporidian <i>E. cuniculi</i> and yeast.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2009-06-05 01:52:13"}
  • {"files"=>["https://ndownloader.figshare.com/files/895634"], "description"=>"<p>Alignment begins with the start codon, which is interrupted by an intron in the ribosomal protein L19. The gene model for the <i>E. cuniculi</i> L6 protein was modified based on comparison with the <i>N. ceranae</i> nucleotide sequence and translation. Introns were manually aligned to illustrate regions of sequence conservation. Ncer = <i>N. ceranae</i>, Ecun = <i>E. cuniculi</i>.</p>", "links"=>[], "tags"=>["ribosomal", "genes", "orthologs"], "article_id"=>566078, "categories"=>["Evolutionary Biology", "Genetics", "Infectious Diseases", "Ecology"], "users"=>["R. Scott Cornman", "Yan Ping Chen", "Michael C. Schatz", "Craig Street", "Yan Zhao", "Brian Desany", "Michael Egholm", "Stephen Hutchison", "Jeffery S. Pettis", "W. Ian Lipkin", "Jay D. Evans"], "doi"=>"https://dx.doi.org/10.1371/journal.ppat.1000466.g001", "stats"=>{"downloads"=>2, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Alignment_of_the_5_region_of_six_ribosomal_protein_genes_in_N_ceranae_that_contain_predicted_introns_together_with_the_five_orthologs_of_these_genes_in_E_cuniculi_/566078", "title"=>"Alignment of the 5′ region of six ribosomal protein genes in <i>N. ceranae</i> that contain predicted introns, together with the five orthologs of these genes in <i>E. cuniculi</i>.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-06-05 01:41:18"}
  • {"files"=>["https://ndownloader.figshare.com/files/895778"], "description"=>"<p>A. Sequence logo of motif identified by MEME and representative unaligned sequence upstream of the start codon (the last three positions) of <i>N. ceranae</i> genes. B. Sequence logo of motif identified by MEME and representative unaligned sequence upstream of the start codon of <i>E. cuniculi</i> genes. See text for details.</p>", "links"=>[], "tags"=>["sense-strand", "motif", "upstream", "codons"], "article_id"=>566220, "categories"=>["Evolutionary Biology", "Genetics", "Infectious Diseases", "Ecology"], "users"=>["R. Scott Cornman", "Yan Ping Chen", "Michael C. Schatz", "Craig Street", "Yan Zhao", "Brian Desany", "Michael Egholm", "Stephen Hutchison", "Jeffery S. Pettis", "W. Ian Lipkin", "Jay D. Evans"], "doi"=>"https://dx.doi.org/10.1371/journal.ppat.1000466.g002", "stats"=>{"downloads"=>1, "page_views"=>14, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Conserved_sense_strand_motif_upstream_of_start_codons_of_N_ceranae_and_E_cuniculi_genes_/566220", "title"=>"Conserved sense-strand motif upstream of start codons of <i>N. ceranae</i> and <i>E. cuniculi</i> genes.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-06-05 01:43:40"}
  • {"files"=>["https://ndownloader.figshare.com/files/896362"], "description"=>"*<p>Sequence lengths in base pairs.</p>", "links"=>[], "tags"=>["genome"], "article_id"=>566819, "categories"=>["Evolutionary Biology", "Genetics", "Infectious Diseases", "Ecology"], "users"=>["R. Scott Cornman", "Yan Ping Chen", "Michael C. Schatz", "Craig Street", "Yan Zhao", "Brian Desany", "Michael Egholm", "Stephen Hutchison", "Jeffery S. Pettis", "W. Ian Lipkin", "Jay D. Evans"], "doi"=>"https://dx.doi.org/10.1371/journal.ppat.1000466.t001", "stats"=>{"downloads"=>0, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Statistics_of_draft_N_ceranae_genome_assembly_analyzed_in_this_paper_/566819", "title"=>"Statistics of draft <i>N. ceranae</i> genome assembly analyzed in this paper.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2009-06-05 01:53:39"}
  • {"files"=>["https://ndownloader.figshare.com/files/896150"], "description"=>"<p>Lines are used instead of points in order to highlight the variation among species. The microsporidians <i>N. ceranae</i> and <i>E. cuniculi</i> differ concordantly from the four fungal genomes, which together represent a diversity of phylogenetic positions and life-history strategies, including facultative pathogens. The concordance of the microsporidian annotations imply that common ancestry and/or shared life-history traits have shaped the allocation of their genomes to various functional categories. Terms in black boxes are notably more common in the microsporidia, whereas terms in red boxes are notably less common. Note that for all species the frequencies sum to one and therefore are not independent.</p>", "links"=>[], "tags"=>["abundant", "ontology", "slim", "classification", "descending", "compared", "abundance", "applied", "genomes"], "article_id"=>566594, "categories"=>["Evolutionary Biology", "Genetics", "Infectious Diseases", "Ecology"], "users"=>["R. Scott Cornman", "Yan Ping Chen", "Michael C. Schatz", "Craig Street", "Yan Zhao", "Brian Desany", "Michael Egholm", "Stephen Hutchison", "Jeffery S. Pettis", "W. Ian Lipkin", "Jay D. Evans"], "doi"=>"https://dx.doi.org/10.1371/journal.ppat.1000466.g005", "stats"=>{"downloads"=>0, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_twenty_most_abundant_ontology_terms_of_the_GO_Slim_classification_for_yeast_S_cerevisiae_in_descending_order_and_compared_with_the_abundance_of_these_terms_applied_to_five_other_genomes_as_described_in_the_Materials_and_Methods_/566594", "title"=>"The twenty most abundant ontology terms of the GO Slim classification for yeast, <i>S. cerevisiae</i>, in descending order and compared with the abundance of these terms applied to five other genomes as described in the Materials and Methods.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-06-05 01:49:54"}
  • {"files"=>["https://ndownloader.figshare.com/files/896313"], "description"=>"<p><i>N. ceranae</i> predicted proteins that are candidate constituents of a mitosome.</p>", "links"=>[], "tags"=>["proteins", "constituents"], "article_id"=>566767, "categories"=>["Evolutionary Biology", "Genetics", "Infectious Diseases", "Ecology"], "users"=>["R. Scott Cornman", "Yan Ping Chen", "Michael C. Schatz", "Craig Street", "Yan Zhao", "Brian Desany", "Michael Egholm", "Stephen Hutchison", "Jeffery S. Pettis", "W. Ian Lipkin", "Jay D. Evans"], "doi"=>"https://dx.doi.org/10.1371/journal.ppat.1000466.t003", "stats"=>{"downloads"=>1, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_N_ceranae_predicted_proteins_that_are_candidate_constituents_of_a_mitosome_/566767", "title"=>"<i>N. ceranae</i> predicted proteins that are candidate constituents of a mitosome.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2009-06-05 01:52:47"}
  • {"files"=>["https://ndownloader.figshare.com/files/895914"], "description"=>"<p>The horizontal axis is the distance from the start codon in bases (5′ to 3′ with the ATG not shown at the 3′ end), and the vertical axis is the proportion of genes in the sample (n = 292, see text) in which the first base of a cytosine triplet occurs that number of bases upstream of the start. Both genomes show a much higher frequency of CCC occurring close to the start codon than do random sequences of the same length and base composition (“N-random” and “E-random” refer to the base composition of <i>N. ceranae</i> and <i>E. cuniculi</i> sequences, respectively). For x-axis values of 1 or 2, the frequency is zero by definition.</p>", "links"=>[], "tags"=>["nucleotide", "motifs", "shown", "upstream"], "article_id"=>566352, "categories"=>["Evolutionary Biology", "Genetics", "Infectious Diseases", "Ecology"], "users"=>["R. Scott Cornman", "Yan Ping Chen", "Michael C. Schatz", "Craig Street", "Yan Zhao", "Brian Desany", "Michael Egholm", "Stephen Hutchison", "Jeffery S. Pettis", "W. Ian Lipkin", "Jay D. Evans"], "doi"=>"https://dx.doi.org/10.1371/journal.ppat.1000466.g003", "stats"=>{"downloads"=>1, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Over_representation_of_the_nucleotide_sequence_CCC_common_to_both_motifs_shown_in_Figure_2_in_the_region_upstream_of_start_codons_/566352", "title"=>"Over-representation of the nucleotide sequence ‘CCC’, common to both motifs shown in Figure 2, in the region upstream of start codons.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-06-05 01:45:52"}
  • {"files"=>["https://ndownloader.figshare.com/files/444269", "https://ndownloader.figshare.com/files/444298", "https://ndownloader.figshare.com/files/444317", "https://ndownloader.figshare.com/files/444339", "https://ndownloader.figshare.com/files/444353", "https://ndownloader.figshare.com/files/444370", "https://ndownloader.figshare.com/files/444448", "https://ndownloader.figshare.com/files/444535", "https://ndownloader.figshare.com/files/444617", "https://ndownloader.figshare.com/files/444649", "https://ndownloader.figshare.com/files/444695", "https://ndownloader.figshare.com/files/444733", "https://ndownloader.figshare.com/files/444765", "https://ndownloader.figshare.com/files/444787", "https://ndownloader.figshare.com/files/444805", "https://ndownloader.figshare.com/files/444844", "https://ndownloader.figshare.com/files/444896", "https://ndownloader.figshare.com/files/444956", "https://ndownloader.figshare.com/files/445018"], "description"=>"<div><p>Recent steep declines in honey bee health have severely impacted the beekeeping industry, presenting new risks for agricultural commodities that depend on insect pollination. Honey bee declines could reflect increased pressures from parasites and pathogens. The incidence of the microsporidian pathogen <em>Nosema ceranae</em> has increased significantly in the past decade. Here we present a draft assembly (7.86 MB) of the <em>N. ceranae</em> genome derived from pyrosequence data, including initial gene models and genomic comparisons with other members of this highly derived fungal lineage. <em>N. ceranae</em> has a strongly AT-biased genome (74% A+T) and a diversity of repetitive elements, complicating the assembly. Of 2,614 predicted protein-coding sequences, we conservatively estimate that 1,366 have homologs in the microsporidian <em>Encephalitozoon cuniculi</em>, the most closely related published genome sequence. We identify genes conserved among microsporidia that lack clear homology outside this group, which are of special interest as potential virulence factors in this group of obligate parasites. A substantial fraction of the diminutive <em>N. ceranae</em> proteome consists of novel and transposable-element proteins. For a majority of well-supported gene models, a conserved sense-strand motif can be found within 15 bases upstream of the start codon; a previously uncharacterized version of this motif is also present in <em>E. cuniculi</em>. These comparisons provide insight into the architecture, regulation, and evolution of microsporidian genomes, and will drive investigations into honey bee–<em>Nosema</em> interactions.</p></div>", "links"=>[], "tags"=>["genomic", "analyses", "microsporidian", "emergent", "pathogen", "bees"], "article_id"=>147571, "categories"=>["Cancer", "Evolutionary Biology", "Genetics", "Ecology"], "users"=>["R. Scott Cornman", "Yan Ping Chen", "Michael C. Schatz", "Craig Street", "Yan Zhao", "Brian Desany", "Michael Egholm", "Stephen Hutchison", "Jeffery S. Pettis", "W. Ian Lipkin", "Jay D. Evans"], "doi"=>["https://dx.doi.org/10.1371/journal.ppat.1000466.s001", "https://dx.doi.org/10.1371/journal.ppat.1000466.s002", "https://dx.doi.org/10.1371/journal.ppat.1000466.s003", "https://dx.doi.org/10.1371/journal.ppat.1000466.s004", "https://dx.doi.org/10.1371/journal.ppat.1000466.s005", "https://dx.doi.org/10.1371/journal.ppat.1000466.s006", "https://dx.doi.org/10.1371/journal.ppat.1000466.s007", "https://dx.doi.org/10.1371/journal.ppat.1000466.s008", "https://dx.doi.org/10.1371/journal.ppat.1000466.s009", "https://dx.doi.org/10.1371/journal.ppat.1000466.s010", "https://dx.doi.org/10.1371/journal.ppat.1000466.s011", "https://dx.doi.org/10.1371/journal.ppat.1000466.s012", "https://dx.doi.org/10.1371/journal.ppat.1000466.s013", "https://dx.doi.org/10.1371/journal.ppat.1000466.s014", "https://dx.doi.org/10.1371/journal.ppat.1000466.s015", "https://dx.doi.org/10.1371/journal.ppat.1000466.s016", "https://dx.doi.org/10.1371/journal.ppat.1000466.s017", "https://dx.doi.org/10.1371/journal.ppat.1000466.s018", "https://dx.doi.org/10.1371/journal.ppat.1000466.s019"], "stats"=>{"downloads"=>0, "page_views"=>50, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Genomic_Analyses_of_the_Microsporidian_Nosema_ceranae_an_Emergent_Pathogen_of_Honey_Bees/147571", "title"=>"Genomic Analyses of the Microsporidian <em>Nosema ceranae</em>, an Emergent Pathogen of Honey Bees", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2009-06-05 02:06:11"}

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Relative Metric

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