Quantification of Ploidy in Proteobacteria Revealed the Existence of Monoploid, (Mero-)Oligoploid and Polyploid Species
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{"title"=>"Quantification of ploidy in proteobacteria revealed the existence of monoploid, (mero-)oligoploid and polyploid species", "type"=>"journal", "authors"=>[{"first_name"=>"Vito", "last_name"=>"Pecoraro", "scopus_author_id"=>"38061969200"}, {"first_name"=>"Karolin", "last_name"=>"Zerulla", "scopus_author_id"=>"36931936100"}, {"first_name"=>"Christian", "last_name"=>"Lange", "scopus_author_id"=>"57197436988"}, {"first_name"=>"Jörg", "last_name"=>"Soppa", "scopus_author_id"=>"7003369219"}], "year"=>2011, "source"=>"PLoS ONE", "identifiers"=>{"issn"=>"19326203", "scopus"=>"2-s2.0-79551653079", "pui"=>"361218382", "doi"=>"10.1371/journal.pone.0016392", "sgr"=>"79551653079", "pmid"=>"21305010"}, "id"=>"244ba8c2-b5f8-3177-ac35-98fb88ca129f", "abstract"=>"Bacteria are generally assumed to be monoploid (haploid). This assumption is mainly based on generalization of the results obtained with the most intensely studied model bacterium, Escherichia coli (a gamma-proteobacterium), which is monoploid during very slow growth. However, several species of proteobacteria are oligo- or polyploid, respectively. To get a better overview of the distribution of ploidy levels, genome copy numbers were quantified in four species of three different groups of proteobacteria. A recently developed Real Time PCR approach, which had been used to determine the ploidy levels of halophilic archaea, was optimized for the quantification of genome copy numbers of bacteria. Slow-growing (doubling time 103 minutes) and fast-growing (doubling time 25 minutes) E. coli cultures were used as a positive control. The copy numbers of the origin and terminus region of the chromosome were determined and the results were in excellent agreement with published data. The approach was also used to determine the ploidy levels of Caulobacter crescentus (an alpha-proteobacterium) and Wolinella succinogenes (an epsilon-proteobacterium), both of which are monoploid. In contrast, Pseudomonas putida (a gamma-proteobacterium) contains 20 genome copies and is thus polyploid. A survey of the proteobacteria with experimentally-determined genome copy numbers revealed that only three to four of 11 species are monoploid and thus monoploidy is not typical for proteobacteria. The ploidy level is not conserved within the groups of proteobacteria, and there are no obvious correlations between the ploidy levels with other parameters like genome size, optimal growth temperature or mode of life.", "link"=>"http://www.mendeley.com/research/quantification-ploidy-proteobacteria-revealed-existence-monoploid-merooligoploid-polyploid-species", "reader_count"=>69, "reader_count_by_academic_status"=>{"Unspecified"=>3, "Professor > Associate Professor"=>2, "Researcher"=>17, "Student > Doctoral Student"=>2, "Student > Ph. D. Student"=>21, "Student > Postgraduate"=>4, "Other"=>5, "Student > Master"=>5, "Student > Bachelor"=>7, "Professor"=>2, "Lecturer"=>1}, "reader_count_by_user_role"=>{"Unspecified"=>3, "Professor > Associate Professor"=>2, "Researcher"=>17, "Student > Doctoral Student"=>2, "Student > Ph. D. Student"=>21, "Student > Postgraduate"=>4, "Other"=>5, "Student > Master"=>5, "Student > Bachelor"=>7, "Professor"=>2, "Lecturer"=>1}, "reader_count_by_subject_area"=>{"Unspecified"=>6, "Engineering"=>1, "Environmental Science"=>1, "Biochemistry, Genetics and Molecular Biology"=>15, "Agricultural and Biological Sciences"=>43, "Immunology and Microbiology"=>3}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>1}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>3}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>43}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>15}, "Unspecified"=>{"Unspecified"=>6}, "Environmental Science"=>{"Environmental Science"=>1}}, "reader_count_by_country"=>{"United States"=>1, "Japan"=>2, "Denmark"=>1, "Mexico"=>1, "Germany"=>2, "Spain"=>2}, "group_count"=>5}

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  • {"files"=>["https://ndownloader.figshare.com/files/801950"], "description"=>"<p>Genome copy numbers in <i>C. crescentus</i>.</p>", "links"=>[], "tags"=>["numbers"], "article_id"=>472324, "categories"=>["Genetics", "Microbiology"], "users"=>["Vito Pecoraro", "Karolin Zerulla", "Christian Lange", "Jörg Soppa"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0016392.t002", "stats"=>{"downloads"=>3, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Genome_copy_numbers_in_C_crescentus_/472324", "title"=>"Genome copy numbers in <i>C. crescentus</i>.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2011-01-31 00:38:44"}
  • {"files"=>["https://ndownloader.figshare.com/files/801823"], "description"=>"<p>Standard and analysis fragments used for copy number quantifications.</p>", "links"=>[], "tags"=>["fragments"], "article_id"=>472195, "categories"=>["Genetics", "Microbiology"], "users"=>["Vito Pecoraro", "Karolin Zerulla", "Christian Lange", "Jörg Soppa"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0016392.t006", "stats"=>{"downloads"=>8, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Standard_and_analysis_fragments_used_for_copy_number_quantifications_/472195", "title"=>"Standard and analysis fragments used for copy number quantifications.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2011-01-31 00:36:35"}
  • {"files"=>["https://ndownloader.figshare.com/files/400687", "https://ndownloader.figshare.com/files/400715", "https://ndownloader.figshare.com/files/400748", "https://ndownloader.figshare.com/files/400780", "https://ndownloader.figshare.com/files/400806"], "description"=>"<div><p>Bacteria are generally assumed to be monoploid (haploid). This assumption is mainly based on generalization of the results obtained with the most intensely studied model bacterium, <em>Escherichia coli</em> (a gamma-proteobacterium), which is monoploid during very slow growth. However, several species of proteobacteria are oligo- or polyploid, respectively. To get a better overview of the distribution of ploidy levels, genome copy numbers were quantified in four species of three different groups of proteobacteria. A recently developed Real Time PCR approach, which had been used to determine the ploidy levels of halophilic archaea, was optimized for the quantification of genome copy numbers of bacteria. Slow-growing (doubling time 103 minutes) and fast-growing (doubling time 25 minutes) <em>E. coli</em> cultures were used as a positive control. The copy numbers of the origin and terminus region of the chromosome were determined and the results were in excellent agreement with published data. The approach was also used to determine the ploidy levels of <em>Caulobacter crescentus</em> (an alpha-proteobacterium) and <em>Wolinella succinogenes</em> (an epsilon-proteobacterium), both of which are monoploid. In contrast, <em>Pseudomonas putida</em> (a gamma-proteobacterium) contains 20 genome copies and is thus polyploid. A survey of the proteobacteria with experimentally-determined genome copy numbers revealed that only three to four of 11 species are monoploid and thus monoploidy is not typical for proteobacteria. The ploidy level is not conserved within the groups of proteobacteria, and there are no obvious correlations between the ploidy levels with other parameters like genome size, optimal growth temperature or mode of life.</p> </div>", "links"=>[], "tags"=>["quantification", "ploidy", "proteobacteria", "revealed", "polyploid"], "article_id"=>139147, "categories"=>["Genetics", "Microbiology"], "users"=>["Vito Pecoraro", "Karolin Zerulla", "Christian Lange", "Jörg Soppa"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0016392.s001", "https://dx.doi.org/10.1371/journal.pone.0016392.s002", "https://dx.doi.org/10.1371/journal.pone.0016392.s003", "https://dx.doi.org/10.1371/journal.pone.0016392.s004", "https://dx.doi.org/10.1371/journal.pone.0016392.s005"], "stats"=>{"downloads"=>17, "page_views"=>17, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Quantification_of_Ploidy_in_Proteobacteria_Revealed_the_Existence_of_Monoploid_Mero_Oligoploid_and_Polyploid_Species/139147", "title"=>"Quantification of Ploidy in Proteobacteria Revealed the Existence of Monoploid, (Mero-)Oligoploid and Polyploid Species", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2011-01-31 02:32:27"}
  • {"files"=>["https://ndownloader.figshare.com/files/801920"], "description"=>"<p>Genome copy numbers in <i>W. succinogenes</i>.</p>", "links"=>[], "tags"=>["numbers"], "article_id"=>472293, "categories"=>["Genetics", "Microbiology"], "users"=>["Vito Pecoraro", "Karolin Zerulla", "Christian Lange", "Jörg Soppa"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0016392.t003", "stats"=>{"downloads"=>2, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Genome_copy_numbers_in_W_succinogenes_/472293", "title"=>"Genome copy numbers in <i>W. succinogenes</i>.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2011-01-31 00:38:13"}
  • {"files"=>["https://ndownloader.figshare.com/files/801891"], "description"=>"<p>Origin and termini copy numbers in <i>P. putida</i>.</p>", "links"=>[], "tags"=>["termini", "numbers"], "article_id"=>472260, "categories"=>["Genetics", "Microbiology"], "users"=>["Vito Pecoraro", "Karolin Zerulla", "Christian Lange", "Jörg Soppa"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0016392.t004", "stats"=>{"downloads"=>7, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Origin_and_termini_copy_numbers_in_P_putida_/472260", "title"=>"Origin and termini copy numbers in <i>P. putida</i>.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2011-01-31 00:37:40"}
  • {"files"=>["https://ndownloader.figshare.com/files/801852"], "description"=>"a<p>the genome copy number is highly variable, depending on developmental stage and morph of host <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0016392#pone.0016392-Spence1\" target=\"_blank\">[33]</a>.</p>b<p>No. origins/No. termini.</p>c<p>9 genomes for ammonia-limited chemostat cultures, 17 genomes for fast-growing batch cultures <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0016392#pone.0016392-Postgate1\" target=\"_blank\">[19]</a>.</p>", "links"=>[], "tags"=>["proteobacterial", "experimentally", "ploidy"], "article_id"=>472223, "categories"=>["Genetics", "Microbiology"], "users"=>["Vito Pecoraro", "Karolin Zerulla", "Christian Lange", "Jörg Soppa"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0016392.t005", "stats"=>{"downloads"=>6, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Overview_of_proteobacterial_species_with_experimentally_determined_ploidy_level_and_selected_parameters_/472223", "title"=>"Overview of proteobacterial species with experimentally determined ploidy level and selected parameters.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2011-01-31 00:37:03"}

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Relative Metric

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