Genes but Not Genomes Reveal Bacterial Domestication of Lactococcus Lactis
Publication Date
December 17, 2010
Journal
PLOS ONE
Authors
Delphine Passerini, Charlotte Beltramo, Michele Coddeville, Yves Quentin, et al
Volume
5
Issue
12
Pages
e15306
DOI
https://dx.plos.org/10.1371/journal.pone.0015306
Publisher URL
http://journals.plos.org/plosone/article?id=10.1371%2Fjournal.pone.0015306
PubMed
http://www.ncbi.nlm.nih.gov/pubmed/21179431
PubMed Central
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3003715
Europe PMC
http://europepmc.org/abstract/MED/21179431
Web of Science
000285572900017
Scopus
78650750997
Mendeley
http://www.mendeley.com/research/genes-not-genomes-reveal-bacterial-domestication-lactococcus-lactis
Events
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Mendeley | Further Information

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CrossRef

Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/811812"], "description"=>"<p>White circles correspond to dairy strains, and black circles to non-dairy strains. The size of the circles is proportional to the number of strains belonging to each ST (indicated in brackets). Clonal complexes (CC) are indicated in gray. Solid lines link SLV (Single Locus Variant, i.e. STs sharing five of the six loci). Dotted lines link DLV (Double Locus Variant, i.e. STs sharing four of the six loci). The ST15 is predicted to be the ancestor genotype of the major CC.</p>", "links"=>[], "tags"=>["32"], "article_id"=>482182, "categories"=>["Microbiology", "Evolutionary Biology"], "users"=>["Delphine Passerini", "Charlotte Beltramo", "Michele Coddeville", "Yves Quentin", "Paul Ritzenthaler", "Marie-Line Daveran-Mingot", "Pascal Le Bourgeois"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0015306.g001", "stats"=>{"downloads"=>1, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_eBURST_analysis_of_32_L_lactis_subsp_lactis_strains_/482182", "title"=>"eBURST analysis of 32 <i>L. lactis</i> subsp. <i>lactis</i> strains.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2010-12-17 00:36:22"}
  • {"files"=>["https://ndownloader.figshare.com/files/812150"], "description"=>"a<p>: Number of different STs in the population studied.</p>b<p>: Standard deviation (SD) values from datasets containing more than 1500 STs were not calculated due to the limitations of the DnaSP software.</p>c<p>: New π<sub>MAX</sub> value and π<sub>MAX</sub>/π ratio after removal of 7 STs are indicated in parentheses.</p>d<p>: New π<sub>MAX</sub> value and π<sub>MAX</sub>/π ratio after removal of 17 STs are indicated in parentheses.</p>e<p>: New π<sub>MAX</sub> value and π<sub>MAX</sub>/π ratio after removal of 22 STs are indicated in parentheses.</p>f<p>: New π<sub>MAX</sub> value and π<sub>MAX</sub>/π ratio after removal of ST80 are indicated in parentheses.</p>", "links"=>[], "tags"=>["microbiology", "Evolutionary biology"], "article_id"=>482516, "categories"=>["Microbiology", "Evolutionary Biology"], "users"=>["Delphine Passerini", "Charlotte Beltramo", "Michele Coddeville", "Yves Quentin", "Paul Ritzenthaler", "Marie-Line Daveran-Mingot", "Pascal Le Bourgeois"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0015306.t001", "stats"=>{"downloads"=>3, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Study_of_some_statistics_used_to_measure_gene_diversity_according_to_the_size_and_the_population_structure_of_strain_samples_/482516", "title"=>"Study of some statistics used to measure gene diversity according to the size and the population structure of strain samples.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2010-12-17 00:41:56"}
  • {"files"=>["https://ndownloader.figshare.com/files/404898", "https://ndownloader.figshare.com/files/404927", "https://ndownloader.figshare.com/files/404945", "https://ndownloader.figshare.com/files/404962", "https://ndownloader.figshare.com/files/404975", "https://ndownloader.figshare.com/files/405002"], "description"=>"<div><h3>Background</h3><p>The population structure and diversity of <em>Lactococcus lactis</em> subsp. <em>lactis</em>, a major industrial bacterium involved in milk fermentation, was determined at both gene and genome level. Seventy-six lactococcal isolates of various origins were studied by different genotyping methods and thirty-six strains displaying unique macrorestriction fingerprints were analyzed by a new multilocus sequence typing (MLST) scheme. This gene-based analysis was compared to genomic characteristics determined by pulsed-field gel electrophoresis (PFGE).</p> <h3>Methodology/Principal Findings</h3><p>The MLST analysis revealed that <em>L. lactis</em> subsp. <em>lactis</em> is essentially clonal with infrequent intra- and intergenic recombination; also, despite its taxonomical classification as a subspecies, it displays a genetic diversity as substantial as that within several other bacterial species. Genome-based analysis revealed a genome size variability of 20%, a value typical of bacteria inhabiting different ecological niches, and that suggests a large pan-genome for this subspecies. However, the genomic characteristics (macrorestriction pattern, genome or chromosome size, plasmid content) did not correlate to the MLST-based phylogeny, with strains from the same sequence type (ST) differing by up to 230 kb in genome size.</p> <h3>Conclusion/Significance</h3><p>The gene-based phylogeny was not fully consistent with the traditional classification into dairy and non-dairy strains but supported a new classification based on ecological separation between “environmental” strains, the main contributors to the genetic diversity within the subspecies, and “domesticated” strains, subject to recent genetic bottlenecks. Comparison between gene- and genome-based analyses revealed little relationship between core and dispensable genome phylogenies, indicating that clonal diversification and phenotypic variability of the “domesticated” strains essentially arose through substantial genomic flux within the dispensable genome.</p> </div>", "links"=>[], "tags"=>["genes", "genomes", "bacterial", "domestication"], "article_id"=>140017, "categories"=>["Microbiology", "Evolutionary Biology"], "users"=>["Delphine Passerini", "Charlotte Beltramo", "Michele Coddeville", "Yves Quentin", "Paul Ritzenthaler", "Marie-Line Daveran-Mingot", "Pascal Le Bourgeois"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0015306.s001", "https://dx.doi.org/10.1371/journal.pone.0015306.s002", "https://dx.doi.org/10.1371/journal.pone.0015306.s003", "https://dx.doi.org/10.1371/journal.pone.0015306.s004", "https://dx.doi.org/10.1371/journal.pone.0015306.s005", "https://dx.doi.org/10.1371/journal.pone.0015306.s006"], "stats"=>{"downloads"=>20, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Genes_but_Not_Genomes_Reveal_Bacterial_Domestication_of_Lactococcus_Lactis_/140017", "title"=>"Genes but Not Genomes Reveal Bacterial Domestication of <em>Lactococcus Lactis</em>", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2010-12-17 00:00:17"}
  • {"files"=>["https://ndownloader.figshare.com/files/811984"], "description"=>"<p>The genome features (chromosome/plasmid content size, presence of genes of industrial importance) of the 36 <i>L. lactis</i> subsp. <i>lactis</i> strains are compared to MLST-based strain relatedness. From left-to-right: neighbor-joining tree of the 36 strains, strain name; strain origin (color code: green  =  plant, brown  =  animal skin, white  =  milk, red  =  starter strains, black  =  cheese, unmarked  =  uncertain origin); genetic groups determined from the NJ tree; clonal complexes determined by eBURST; ST numbering; presence of <i>citP</i> gene (red dot), <i>lacE</i> gene (blue diamond), and <i>prtP</i> gene (green triangle); chromosome (black rectangles) and plasmid content (white rectangles) sizes. Derivative strains are indicated by an asterisk. The two dashed red lines indicate mean chromosome and genome size, respectively.</p>", "links"=>[], "tags"=>["gene-based", "genome"], "article_id"=>482351, "categories"=>["Microbiology", "Evolutionary Biology"], "users"=>["Delphine Passerini", "Charlotte Beltramo", "Michele Coddeville", "Yves Quentin", "Paul Ritzenthaler", "Marie-Line Daveran-Mingot", "Pascal Le Bourgeois"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0015306.g003", "stats"=>{"downloads"=>1, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Comparison_of_gene_based_phylogeny_strain_origins_and_genome_properties_/482351", "title"=>"Comparison of gene-based phylogeny, strain origins, and genome properties.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2010-12-17 00:39:11"}
  • {"files"=>["https://ndownloader.figshare.com/files/812189"], "description"=>"#<p>, 0.05<<i>p</i><0.1 (two tailed test)</p>a<p>, DNA sequences from the <i>cremoris</i> strain MG1363 were used as outgroup.</p><p>-, Not Determined.</p>", "links"=>[], "tags"=>["microbiology", "Evolutionary biology"], "article_id"=>482552, "categories"=>["Microbiology", "Evolutionary Biology"], "users"=>["Delphine Passerini", "Charlotte Beltramo", "Michele Coddeville", "Yves Quentin", "Paul Ritzenthaler", "Marie-Line Daveran-Mingot", "Pascal Le Bourgeois"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0015306.t002", "stats"=>{"downloads"=>3, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Gene_diversity_and_evolution_among_L_lactis_subsp_lactis_strains_/482552", "title"=>"Gene diversity and evolution among <i>L. lactis</i> subsp. <i>lactis</i> strains.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2010-12-17 00:42:32"}
  • {"files"=>["https://ndownloader.figshare.com/files/812089"], "description"=>"<p>For each species, the genome size distribution, summarized as a boxplot, is plotted according to the mean size. The species are ordered by increasing chromosome size diversity. Chromosomes sizes were obtained from sequence data (<a href=\"http://www.ncbi.nlm.nih.gov/genomes/genlist.cgi?taxid=2&type=1&name=Bacteria%20Complete%20Chromosomes\" target=\"_blank\">http://www.ncbi.nlm.nih.gov/genomes/genlist.cgi?taxid=2&type=1&name=Bacteria%20Complete%20Chromosomes</a>). The number of chromosomes sequenced is indicated in brackets. Abbreviations: Lm, <i>L. monocytogenes</i>; St, <i>S. thermophilus</i>; Sa, <i>S. agalactiae</i>; Hp, <i>H. pylori</i>; Hi, <i>H. influenzae</i>; Sau, <i>S. aureus</i>; Se, <i>S. enterica</i>; Spy, <i>S. pyogenes</i>; Vc, <i>V. cholerae</i>; Spn, <i>S. pneumoniae</i>; Cb, <i>C. botulinum</i>; Lll, <i>L. lactis</i> subsp. <i>lactis</i>; Ab, <i>A. baumannii</i>; Ec, <i>E. coli</i>.</p>", "links"=>[], "tags"=>["chromosome", "bacterial"], "article_id"=>482454, "categories"=>["Microbiology", "Evolutionary Biology"], "users"=>["Delphine Passerini", "Charlotte Beltramo", "Michele Coddeville", "Yves Quentin", "Paul Ritzenthaler", "Marie-Line Daveran-Mingot", "Pascal Le Bourgeois"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0015306.g004", "stats"=>{"downloads"=>1, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Comparison_of_chromosome_size_diversity_within_several_bacterial_species_/482454", "title"=>"Comparison of chromosome size diversity within several bacterial species.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2010-12-17 00:40:54"}
  • {"files"=>["https://ndownloader.figshare.com/files/811895"], "description"=>"<p>The unrooted neighbor-joining tree (bootstrap 1000, Kimura 2-parameter model) was constructed from the 2,934-bp concatenated DNA sequences of the six loci. a) Tree constructed from the 32 subspecies <i>lactis</i> strains. b) Same tree after addition of the concatenated sequences from two subspecies <i>cremoris</i> strains. Only bootstrap values >80% are indicated. Open and closed circles correspond to dairy strains and non-dairy strains, respectively. The phylogenetic position of the recently sequenced strain KF147 <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0015306#pone.0015306-Siezen2\" target=\"_blank\">[69]</a> is indicated by an asterisk. This strain differs from strain NCDO2118 (ST25) by only one SNP.</p>", "links"=>[], "tags"=>["relationships", "lactococcal"], "article_id"=>482262, "categories"=>["Microbiology", "Evolutionary Biology"], "users"=>["Delphine Passerini", "Charlotte Beltramo", "Michele Coddeville", "Yves Quentin", "Paul Ritzenthaler", "Marie-Line Daveran-Mingot", "Pascal Le Bourgeois"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0015306.g002", "stats"=>{"downloads"=>0, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Phylogenetic_relationships_between_lactococcal_strains_/482262", "title"=>"Phylogenetic relationships between lactococcal strains.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2010-12-17 00:37:42"}

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