Strain-Level Diversity of Secondary Metabolism in Streptomyces albus
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{"title"=>"Strain-level diversity of secondary metabolism in Streptomyces albus", "type"=>"journal", "authors"=>[{"first_name"=>"Ryan F.", "last_name"=>"Seipke", "scopus_author_id"=>"23989747600"}], "year"=>2015, "source"=>"PLoS ONE", "identifiers"=>{"scopus"=>"2-s2.0-84922424354", "doi"=>"10.1371/journal.pone.0116457", "sgr"=>"84922424354", "pmid"=>"25635820", "issn"=>"19326203", "pui"=>"601957191"}, "id"=>"7aafd600-b4a1-3afb-9b74-eb7a2b09237b", "abstract"=>"Streptomyces spp. are robust producers of medicinally-, industrially- and agriculturally-important small molecules. Increased resistance to antibacterial agents and the lack of new antibiotics in the pipeline have led to a renaissance in natural product discovery. This endeavor has benefited from inexpensive high quality DNA sequencing technology, which has generated more than 140 genome sequences for taxonomic type strains and environmental Streptomyces spp. isolates. Many of the sequenced streptomycetes belong to the same species. For instance, Streptomyces albus has been isolated from diverse environmental niches and seven strains have been sequenced, consequently this species has been sequenced more than any other streptomycete, allowing valuable analyses of strain-level diversity in secondary metabolism. Bioinformatics analyses identified a total of 48 unique biosynthetic gene clusters harboured by Streptomyces albus strains. Eighteen of these gene clusters specify the core secondary metabolome of the species. Fourteen of the gene clusters are contained by one or more strain and are considered auxiliary, while 16 of the gene clusters encode the production of putative strain-specific secondary metabolites. Analysis of Streptomyces albus strains suggests that each strain of a Streptomyces species likely harbours at least one strain-specific biosynthetic gene cluster. Importantly, this implies that deep sequencing of a species will not exhaust gene cluster diversity and will continue to yield novelty.", "link"=>"http://www.mendeley.com/research/strainlevel-diversity-secondary-metabolism-streptomyces-albus", "reader_count"=>60, "reader_count_by_academic_status"=>{"Unspecified"=>2, "Professor > Associate Professor"=>2, "Student > Doctoral Student"=>4, "Researcher"=>8, "Student > Ph. D. Student"=>19, "Student > Postgraduate"=>2, "Student > Master"=>10, "Student > Bachelor"=>11, "Professor"=>2}, "reader_count_by_user_role"=>{"Unspecified"=>2, "Professor > Associate Professor"=>2, "Student > Doctoral Student"=>4, "Researcher"=>8, "Student > Ph. D. Student"=>19, "Student > Postgraduate"=>2, "Student > Master"=>10, "Student > Bachelor"=>11, "Professor"=>2}, "reader_count_by_subject_area"=>{"Unspecified"=>4, "Engineering"=>2, "Biochemistry, Genetics and Molecular Biology"=>15, "Agricultural and Biological Sciences"=>34, "Pharmacology, Toxicology and Pharmaceutical Science"=>2, "Chemistry"=>2, "Computer Science"=>1}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>2}, "Chemistry"=>{"Chemistry"=>2}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>34}, "Computer Science"=>{"Computer Science"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>15}, "Unspecified"=>{"Unspecified"=>4}, "Pharmacology, Toxicology and Pharmaceutical Science"=>{"Pharmacology, Toxicology and Pharmaceutical Science"=>2}}, "reader_count_by_country"=>{"United States"=>2, "Denmark"=>1, "Brazil"=>1, "United Kingdom"=>1, "Germany"=>1, "Spain"=>2}, "group_count"=>1}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/1877024"], "description"=>"<p>A phylogeny was inferred for <i>Mycobacterium tuberculosis</i> and 120 sequenced streptomycetes based on concatenated partial sequences of <i>aptD-gyrB-recA-rpoB</i>. FastTree local support values (expressed as a whole number) are indicated at each node. <i>Streptomyces albus</i> strains are highlighted in red. The scale bar indicates 5% estimated sequence divergence.</p>", "links"=>[], "tags"=>["gene clusters encode", "biosynthetic gene clusters harboured", "gene clusters", "species", "quality DNA sequencing technology", "Streptomyces albus Streptomyces spp", "taxonomic type strains", "gene cluster diversity", "Streptomyces albus strains", "140 genome sequences"], "article_id"=>1298462, "categories"=>["Biological Sciences"], "users"=>["Ryan F. Seipke"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0116457.g001", "stats"=>{"downloads"=>1, "page_views"=>22, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_An_approximately_maximum_likelihood_phylogenetic_tree_of_sequenced_Streptomyces_species_/1298462", "title"=>"An approximately maximum likelihood phylogenetic tree of sequenced <i>Streptomyces</i> species.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-01-30 03:09:53"}
  • {"files"=>["https://ndownloader.figshare.com/files/1877034", "https://ndownloader.figshare.com/files/1877035"], "description"=>"<div><p><i>Streptomyces</i> spp. are robust producers of medicinally-, industrially- and agriculturally-important small molecules. Increased resistance to antibacterial agents and the lack of new antibiotics in the pipeline have led to a renaissance in natural product discovery. This endeavor has benefited from inexpensive high quality DNA sequencing technology, which has generated more than 140 genome sequences for taxonomic type strains and environmental <i>Streptomyces</i> spp. isolates. Many of the sequenced streptomycetes belong to the same species. For instance, <i>Streptomyces albus</i> has been isolated from diverse environmental niches and seven strains have been sequenced, consequently this species has been sequenced more than any other streptomycete, allowing valuable analyses of strain-level diversity in secondary metabolism. Bioinformatics analyses identified a total of 48 unique biosynthetic gene clusters harboured by <i>Streptomyces albus</i> strains. Eighteen of these gene clusters specify the core secondary metabolome of the species. Fourteen of the gene clusters are contained by one or more strain and are considered auxiliary, while 16 of the gene clusters encode the production of putative strain-specific secondary metabolites. Analysis of <i>Streptomyces albus</i> strains suggests that each strain of a <i>Streptomyces</i> species likely harbours at least one strain-specific biosynthetic gene cluster. Importantly, this implies that deep sequencing of a species will not exhaust gene cluster diversity and will continue to yield novelty.</p></div>", "links"=>[], "tags"=>["gene clusters encode", "biosynthetic gene clusters harboured", "gene clusters", "species", "quality DNA sequencing technology", "Streptomyces albus Streptomyces spp", "taxonomic type strains", "gene cluster diversity", "Streptomyces albus strains", "140 genome sequences"], "article_id"=>1298472, "categories"=>["Biological Sciences"], "users"=>["Ryan F. Seipke"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0116457.s001", "https://dx.doi.org/10.1371/journal.pone.0116457.s002"], "stats"=>{"downloads"=>5, "page_views"=>13, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Strain_Level_Diversity_of_Secondary_Metabolism_in_Streptomyces_albus_/1298472", "title"=>"Strain-Level Diversity of Secondary Metabolism in <i>Streptomyces albus</i>", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2015-01-30 03:09:53"}
  • {"files"=>["https://ndownloader.figshare.com/files/1877032"], "description"=>"<p>*Denotes a gene cluster encoded on a plasmid</p><p>**Denotes a gene cluster composed of partial antiSMASH gene clusters that likely represent a single cluster according to NaPDoS analysis</p><p>***AntiSMASH did not report a cumulative MultiGeneBlast score, because the gene cluster is spread over multiple contigs</p><p>Strain-specific gene clusters encoded by <i>Streptomyces albus</i>.</p>", "links"=>[], "tags"=>["gene clusters encode", "biosynthetic gene clusters harboured", "gene clusters", "species", "quality DNA sequencing technology", "Streptomyces albus Streptomyces spp", "taxonomic type strains", "gene cluster diversity", "Streptomyces albus strains", "140 genome sequences"], "article_id"=>1298470, "categories"=>["Biological Sciences"], "users"=>["Ryan F. Seipke"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0116457.t005", "stats"=>{"downloads"=>15, "page_views"=>20, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Strain_specific_gene_clusters_encoded_by_Streptomyces_albus_/1298470", "title"=>"Strain-specific gene clusters encoded by <i>Streptomyces albus</i>.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2015-01-30 03:09:53"}
  • {"files"=>["https://ndownloader.figshare.com/files/1877029"], "description"=>"<p>The percentage in braces reflects the total number of gene clusters conserved in the pairwise comparison with respect to the strains listed vertically.</p><p>Pairwise comparison of gene clusters encoding putative secondary metabolites from <i>Streptomyces albus</i> strains.</p>", "links"=>[], "tags"=>["gene clusters encode", "biosynthetic gene clusters harboured", "gene clusters", "species", "quality DNA sequencing technology", "Streptomyces albus Streptomyces spp", "taxonomic type strains", "gene cluster diversity", "Streptomyces albus strains", "140 genome sequences"], "article_id"=>1298467, "categories"=>["Biological Sciences"], "users"=>["Ryan F. Seipke"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0116457.t002", "stats"=>{"downloads"=>7, "page_views"=>13, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Pairwise_comparison_of_gene_clusters_encoding_putative_secondary_metabolites_from_Streptomyces_albus_strains_/1298467", "title"=>"Pairwise comparison of gene clusters encoding putative secondary metabolites from <i>Streptomyces albus</i> strains.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2015-01-30 03:09:53"}
  • {"files"=>["https://ndownloader.figshare.com/files/1877028"], "description"=>"<p>Accessions and genomic features of <i>Streptomyces</i><i>albus</i> strains.</p>", "links"=>[], "tags"=>["gene clusters encode", "biosynthetic gene clusters harboured", "gene clusters", "species", "quality DNA sequencing technology", "Streptomyces albus Streptomyces spp", "taxonomic type strains", "gene cluster diversity", "Streptomyces albus strains", "140 genome sequences"], "article_id"=>1298466, "categories"=>["Biological Sciences"], "users"=>["Ryan F. Seipke"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0116457.t001", "stats"=>{"downloads"=>1, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Accessions_and_genomic_features_of_Streptomyces_albus_strains_/1298466", "title"=>"Accessions and genomic features of <i>Streptomyces</i><i>albus</i> strains.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2015-01-30 03:09:53"}
  • {"files"=>["https://ndownloader.figshare.com/files/1877031"], "description"=>"<p>* Denotes a gene cluster harboured in duplicate; genomic coordinates for the additional copy are provide in braces.</p><p>**Denotes a gene cluster spread over multiple contigs, which are presented in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0116457#pone.0116457.s002\" target=\"_blank\">S2 Table</a>.</p><p>Auxiliary secondary metabolites produced by <i>Streptomyces albus</i>.</p>", "links"=>[], "tags"=>["gene clusters encode", "biosynthetic gene clusters harboured", "gene clusters", "species", "quality DNA sequencing technology", "Streptomyces albus Streptomyces spp", "taxonomic type strains", "gene cluster diversity", "Streptomyces albus strains", "140 genome sequences"], "article_id"=>1298469, "categories"=>["Biological Sciences"], "users"=>["Ryan F. Seipke"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0116457.t004", "stats"=>{"downloads"=>1, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Auxiliary_secondary_metabolites_produced_by_Streptomyces_albus_/1298469", "title"=>"Auxiliary secondary metabolites produced by <i>Streptomyces albus</i>.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2015-01-30 03:09:53"}
  • {"files"=>["https://ndownloader.figshare.com/files/1877030"], "description"=>"<p>*denotes genomic coordinates were edited manually</p><p>** denotes a gene cluster which was not annotated by antiSMASH 2.0</p><p>***denotes a gene cluster which is spread over multiple contigs (refer to <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0116457#pone.0116457.s002\" target=\"_blank\">S2 Table</a>).</p><p>The core secondary metabolome of <i>Streptomyces albus</i>.</p>", "links"=>[], "tags"=>["gene clusters encode", "biosynthetic gene clusters harboured", "gene clusters", "species", "quality DNA sequencing technology", "Streptomyces albus Streptomyces spp", "taxonomic type strains", "gene cluster diversity", "Streptomyces albus strains", "140 genome sequences"], "article_id"=>1298468, "categories"=>["Biological Sciences"], "users"=>["Ryan F. Seipke"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0116457.t003", "stats"=>{"downloads"=>2, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_core_secondary_metabolome_of_Streptomyces_albus_/1298468", "title"=>"The core secondary metabolome of <i>Streptomyces albus</i>.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2015-01-30 03:09:53"}
  • {"files"=>["https://ndownloader.figshare.com/files/1877027"], "description"=>"<p>NUCmer is part of the MUMmer [<a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0116457#pone.0116457.ref055\" target=\"_blank\">55</a>] and can be downloaded from <a href=\"http://sourceforge.net/projects/mummer/\" target=\"_blank\">http://sourceforge.net/projects/mummer/</a>. NUCmer will align contigs from draft genomes to an intact gene cluster with high shared nucleotide identity. Commands used to perform an analysis of this type are given. Black arrows represent a biosynthetic gene cluster; black and red lines represent contigs in a draft genome sequence.</p>", "links"=>[], "tags"=>["gene clusters encode", "biosynthetic gene clusters harboured", "gene clusters", "species", "quality DNA sequencing technology", "Streptomyces albus Streptomyces spp", "taxonomic type strains", "gene cluster diversity", "Streptomyces albus strains", "140 genome sequences"], "article_id"=>1298465, "categories"=>["Biological Sciences"], "users"=>["Ryan F. Seipke"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0116457.g002", "stats"=>{"downloads"=>1, "page_views"=>26, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Diagrammatic_workflow_of_the_NUCmer_approach_used_to_piece_together_a_biosynthetic_gene_clusters_spread_over_more_than_one_contig_/1298465", "title"=>"Diagrammatic workflow of the NUCmer approach used to piece together a biosynthetic gene clusters spread over more than one contig.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-01-30 03:09:53"}

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{"start_date"=>"2015-01-01T00:00:00Z", "end_date"=>"2015-12-31T00:00:00Z", "subject_areas"=>[]}

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