Winemaking and Bioprocesses Strongly Shaped the Genetic Diversity of the Ubiquitous Yeast Torulaspora delbrueckii
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{"title"=>"Winemaking and bioprocesses strongly shaped the genetic diversity of the ubiquitous yeast Torulaspora delbrueckii", "type"=>"journal", "authors"=>[{"first_name"=>"Warren", "last_name"=>"Albertin", "scopus_author_id"=>"8610869000"}, {"first_name"=>"Laura", "last_name"=>"Chasseriaud", "scopus_author_id"=>"56135213100"}, {"first_name"=>"Guillaume", "last_name"=>"Comte", "scopus_author_id"=>"56136069300"}, {"first_name"=>"Aurélie", "last_name"=>"Panfili", "scopus_author_id"=>"57192125376"}, {"first_name"=>"Adline", "last_name"=>"Delcamp", "scopus_author_id"=>"42061337300"}, {"first_name"=>"Franck", "last_name"=>"Salin", "scopus_author_id"=>"7007135164"}, {"first_name"=>"Philippe", "last_name"=>"Marullo", "scopus_author_id"=>"18634827800"}, {"first_name"=>"Marina", "last_name"=>"Bely", "scopus_author_id"=>"18633686200"}], "year"=>2014, "source"=>"PLoS ONE", "identifiers"=>{"issn"=>"19326203", "pui"=>"372971374", "doi"=>"10.1371/journal.pone.0094246", "sgr"=>"84899558896", "scopus"=>"2-s2.0-84899558896", "isbn"=>"1932-6203 (Electronic)\\r1932-6203 (Linking)", "pmid"=>"24718638"}, "id"=>"797ccf58-19d6-32a9-b7f5-33c9e939755d", "abstract"=>"The yeast Torulaspora delbrueckii is associated with several human activities including oenology, bakery, distillery, dairy industry, etc. In addition to its biotechnological applications, T. delbrueckii is frequently isolated in natural environments (plant, soil, insect). T. delbrueckii is thus a remarkable ubiquitous yeast species with both wild and anthropic habitats, and appears to be a perfect yeast model to search for evidence of human domestication. For that purpose, we developed eight microsatellite markers that were used for the genotyping of 110 strains from various substrates and geographical origins. Microsatellite analysis showed four genetic clusters: two groups contained most nature strains from Old World and Americas respectively, and two clusters were associated with winemaking and other bioprocesses. Analysis of molecular variance (AMOVA) confirmed that human activities significantly shaped the genetic variability of T. delbrueckii species. Natural isolates are differentiated on the basis of geographical localisation, as expected for wild population. The domestication of T. delbrueckii probably dates back to the Roman Empire for winemaking (∼ 1900 years ago), and to the Neolithic era for bioprocesses (∼ 4000 years ago). Microsatellite analysis also provided valuable data regarding the life-cycle of the species, suggesting a mostly diploid homothallic life. In addition to population genetics and ecological studies, the microsatellite tool will be particularly useful for further biotechnological development of T. delbrueckii strains for winemaking and other bioprocesses.", "link"=>"http://www.mendeley.com/research/winemaking-bioprocesses-strongly-shaped-genetic-diversity-ubiquitous-yeast-torulaspora-delbrueckii", "reader_count"=>49, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>3, "Researcher"=>9, "Student > Doctoral Student"=>5, "Student > Ph. D. Student"=>9, "Student > Postgraduate"=>4, "Student > Master"=>4, "Student > Bachelor"=>8, "Professor"=>6, "Other"=>1}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>3, "Researcher"=>9, "Student > Doctoral Student"=>5, "Student > Ph. D. Student"=>9, "Student > Postgraduate"=>4, "Student > Master"=>4, "Student > Bachelor"=>8, "Professor"=>6, "Other"=>1}, "reader_count_by_subject_area"=>{"Unspecified"=>1, "Engineering"=>1, "Environmental Science"=>2, "Biochemistry, Genetics and Molecular Biology"=>7, "Agricultural and Biological Sciences"=>31, "Medicine and Dentistry"=>1, "Chemistry"=>2, "Social Sciences"=>1, "Computer Science"=>1, "Immunology and Microbiology"=>1, "Economics, Econometrics and Finance"=>1}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>1}, "Medicine and Dentistry"=>{"Medicine and Dentistry"=>1}, "Chemistry"=>{"Chemistry"=>2}, "Social Sciences"=>{"Social Sciences"=>1}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>1}, "Economics, Econometrics and Finance"=>{"Economics, Econometrics and Finance"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>31}, "Computer Science"=>{"Computer Science"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>7}, "Unspecified"=>{"Unspecified"=>1}, "Environmental Science"=>{"Environmental Science"=>2}}, "reader_count_by_country"=>{"Brazil"=>1, "Mexico"=>1, "France"=>4, "Spain"=>1}, "group_count"=>3}

Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/1457497"], "description"=>"<p>A: For <i>Alu</i>I restriction, four patterns were produced: 170 pb+160 pb+80 pb+70 pb+55 pb+40 pb+30 pb for <i>T. delbrueckii</i> and <i>T. quercuum</i>; 170 pb+160 pb+120 pb+70 pb+55 pb+30 pb for <i>T. maleeae</i> and <i>T. indica</i>; 170 pb+160 pb+95 pb+80 pb+70 pb+30 pb for <i>T. franciscae</i>, <i>T. microellipsoides</i>, <i>T. pretoriensis</i>; and 330 pb+170 pb+75 pb+30 pb for <i>T. globosa</i>. B: For <i>Pst</i>I restriction, two patterns were produced: 600pb (no restriction) for <i>T. maleeae</i>, <i>T. quercuum</i>, <i>T. indica</i>, <i>T. microellipsoides</i> and <i>T. globosa</i>; or 480 pb+120 pb for <i>T. delbrueckii</i>, <i>T. franciscae</i> and <i>T. pretoriensis</i>. Blue and pink bands represent internal upper and lower markers respectively.</p>", "links"=>[], "tags"=>["biotechnology", "Applied microbiology", "Industrial microbiology", "ecology", "Evolutionary ecology", "microbial ecology", "Population ecology", "Evolutionary biology", "Evolutionary processes", "natural selection", "Organismal evolution", "Microbial evolution", "population genetics", "Genetic polymorphism", "Evolutionary genetics", "genetics", "microbiology", "organisms", "fungi", "yeast", "Population biology", "patterns", "amplicon", "generated"], "article_id"=>993388, "categories"=>["Biological Sciences", "Ecology"], "users"=>["Warren Albertin", "Laura Chasseriaud", "Guillaume Comte", "Aurélie Panfili", "Adline Delcamp", "Franck Salin", "Philippe Marullo", "Marina Bely"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0094246.g002", "stats"=>{"downloads"=>4, "page_views"=>12, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Restriction_patterns_of_D1_D2_amplicon_generated_by_Alu_I_A_or_Pst_I_B_for_Torulaspora_species_/993388", "title"=>"Restriction patterns of D1/D2 amplicon generated by <i>Alu</i>I (A) or <i>Pst</i>I (B) for <i>Torulaspora</i> species.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-04-09 03:35:36"}
  • {"files"=>["https://ndownloader.figshare.com/files/1457506"], "description"=>"<p>Allele size in pb. Forward primers were tailed on 5′-end with M13 sequence (CACGACGTTGTAAAACGAC). Tm is the melting temperature used for microsatellite amplification (see Materials and Methods). CLIB230<sup>T</sup> is synonymous of CBS 1146<sup>T</sup>.</p>", "links"=>[], "tags"=>["biotechnology", "Applied microbiology", "Industrial microbiology", "ecology", "Evolutionary ecology", "microbial ecology", "Population ecology", "Evolutionary biology", "Evolutionary processes", "natural selection", "Organismal evolution", "Microbial evolution", "population genetics", "Genetic polymorphism", "Evolutionary genetics", "genetics", "microbiology", "organisms", "fungi", "yeast", "Population biology", "loci"], "article_id"=>993397, "categories"=>["Biological Sciences", "Ecology"], "users"=>["Warren Albertin", "Laura Chasseriaud", "Guillaume Comte", "Aurélie Panfili", "Adline Delcamp", "Franck Salin", "Philippe Marullo", "Marina Bely"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0094246.t001", "stats"=>{"downloads"=>3, "page_views"=>23, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Microsatellite_loci_for_Torulaspora_delbrueckii_genotyping_/993397", "title"=>"Microsatellite loci for <i>Torulaspora delbrueckii</i> genotyping.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-04-09 03:35:36"}
  • {"files"=>["https://ndownloader.figshare.com/files/1457505"], "description"=>"<p><i>F<sub>IT</sub></i> represents the total deficit of heterozygotes, <i>F<sub>IS</sub></i> the deficit of heterozygotes within the population, <i>F<sub>ST</sub></i> the fixation index. *** indicates a significant effect at 0.1%. Ho stands for observed heterozygosity, and did not fit the Hardy-Weinberg hypothesis (pval<<0.001) for all eight loci.</p>", "links"=>[], "tags"=>["biotechnology", "Applied microbiology", "Industrial microbiology", "ecology", "Evolutionary ecology", "microbial ecology", "Population ecology", "Evolutionary biology", "Evolutionary processes", "natural selection", "Organismal evolution", "Microbial evolution", "population genetics", "Genetic polymorphism", "Evolutionary genetics", "genetics", "microbiology", "organisms", "fungi", "yeast", "Population biology", "observed", "heterozygosity"], "article_id"=>993396, "categories"=>["Biological Sciences", "Ecology"], "users"=>["Warren Albertin", "Laura Chasseriaud", "Guillaume Comte", "Aurélie Panfili", "Adline Delcamp", "Franck Salin", "Philippe Marullo", "Marina Bely"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0094246.t002", "stats"=>{"downloads"=>3, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_F_statistics_and_observed_heterozygosity_in_Torulaspora_delbrueckii_population_/993396", "title"=>"F-statistics and observed heterozygosity in <i>Torulaspora delbrueckii</i> population.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-04-09 03:35:36"}
  • {"files"=>["https://ndownloader.figshare.com/files/1457496"], "description"=>"<p>3 strains (CLIB 230, CLIB 503, MUCL 27828) are not represented since their precise isolation location is unknown. More details on European isolates (grey box) can be found on <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0094246#pone.0094246.s001\" target=\"_blank\">Figure S1</a>.</p>", "links"=>[], "tags"=>["biotechnology", "Applied microbiology", "Industrial microbiology", "ecology", "Evolutionary ecology", "microbial ecology", "Population ecology", "Evolutionary biology", "Evolutionary processes", "natural selection", "Organismal evolution", "Microbial evolution", "population genetics", "Genetic polymorphism", "Evolutionary genetics", "genetics", "microbiology", "organisms", "fungi", "yeast", "Population biology", "localisation", "strains"], "article_id"=>993387, "categories"=>["Biological Sciences", "Ecology"], "users"=>["Warren Albertin", "Laura Chasseriaud", "Guillaume Comte", "Aurélie Panfili", "Adline Delcamp", "Franck Salin", "Philippe Marullo", "Marina Bely"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0094246.g001", "stats"=>{"downloads"=>0, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Geographical_localisation_of_the_T_delbrueckii_strains_used_in_this_study_/993387", "title"=>"Geographical localisation of the <i>T. delbrueckii</i> strains used in this study.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-04-09 03:35:36"}
  • {"files"=>["https://ndownloader.figshare.com/files/1457507", "https://ndownloader.figshare.com/files/1457508", "https://ndownloader.figshare.com/files/1457509"], "description"=>"<div><p>The yeast <i>Torulaspora delbrueckii</i> is associated with several human activities including oenology, bakery, distillery, dairy industry, etc. In addition to its biotechnological applications, <i>T. delbrueckii</i> is frequently isolated in natural environments (plant, soil, insect). <i>T. delbrueckii</i> is thus a remarkable ubiquitous yeast species with both wild and anthropic habitats, and appears to be a perfect yeast model to search for evidence of human domestication. For that purpose, we developed eight microsatellite markers that were used for the genotyping of 110 strains from various substrates and geographical origins. Microsatellite analysis showed four genetic clusters: two groups contained most nature strains from Old World and Americas respectively, and two clusters were associated with winemaking and other bioprocesses. Analysis of molecular variance (AMOVA) confirmed that human activities significantly shaped the genetic variability of <i>T. delbrueckii</i> species. Natural isolates are differentiated on the basis of geographical localisation, as expected for wild population. The domestication of <i>T. delbrueckii</i> probably dates back to the Roman Empire for winemaking (∼1900 years ago), and to the Neolithic era for bioprocesses (∼4000 years ago). Microsatellite analysis also provided valuable data regarding the life-cycle of the species, suggesting a mostly diploid homothallic life. In addition to population genetics and ecological studies, the microsatellite tool will be particularly useful for further biotechnological development of <i>T. delbrueckii</i> strains for winemaking and other bioprocesses.</p></div>", "links"=>[], "tags"=>["biotechnology", "Applied microbiology", "Industrial microbiology", "ecology", "Evolutionary ecology", "microbial ecology", "Population ecology", "Evolutionary biology", "Evolutionary processes", "natural selection", "Organismal evolution", "Microbial evolution", "population genetics", "Genetic polymorphism", "Evolutionary genetics", "genetics", "microbiology", "organisms", "fungi", "yeast", "Population biology", "winemaking", "bioprocesses", "shaped", "ubiquitous"], "article_id"=>993398, "categories"=>["Biological Sciences", "Ecology"], "users"=>["Warren Albertin", "Laura Chasseriaud", "Guillaume Comte", "Aurélie Panfili", "Adline Delcamp", "Franck Salin", "Philippe Marullo", "Marina Bely"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0094246.s001", "https://dx.doi.org/10.1371/journal.pone.0094246.s002", "https://dx.doi.org/10.1371/journal.pone.0094246.s003"], "stats"=>{"downloads"=>5, "page_views"=>13, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Winemaking_and_Bioprocesses_Strongly_Shaped_the_Genetic_Diversity_of_the_Ubiquitous_Yeast_Torulaspora_delbrueckii_/993398", "title"=>"Winemaking and Bioprocesses Strongly Shaped the Genetic Diversity of the Ubiquitous Yeast <i>Torulaspora delbrueckii</i>", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2014-04-09 03:35:36"}
  • {"files"=>["https://ndownloader.figshare.com/files/1457504"], "description"=>"<p>A: Dendrogram tree built using Bruvo's distance and Neighbor-Joining's clustering. The robustness of the node was assessed using multiscale bootstrap resampling and approximated unbiased test (n = 1000 boots). Bootstrap results are shown only for the main nodes. B: Barplot representing structure results (K = 5). The posterior probability (y-axis) of assignment of each strain (vertical bar) to ancestral groups is shown by colors (dark green, green, blue, red and darkblue colors represent each 5 ancestral populations). Heterozygous strains, meaning strains with at least one heterozygote locus, are indicated by black stars.</p>", "links"=>[], "tags"=>["biotechnology", "Applied microbiology", "Industrial microbiology", "ecology", "Evolutionary ecology", "microbial ecology", "Population ecology", "Evolutionary biology", "Evolutionary processes", "natural selection", "Organismal evolution", "Microbial evolution", "population genetics", "Genetic polymorphism", "Evolutionary genetics", "genetics", "microbiology", "organisms", "fungi", "yeast", "Population biology", "relationships", "110", "strains", "microsatellite"], "article_id"=>993395, "categories"=>["Biological Sciences", "Ecology"], "users"=>["Warren Albertin", "Laura Chasseriaud", "Guillaume Comte", "Aurélie Panfili", "Adline Delcamp", "Franck Salin", "Philippe Marullo", "Marina Bely"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0094246.g003", "stats"=>{"downloads"=>0, "page_views"=>12, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Genetic_relationships_between_110_T_delbrueckii_strains_using_eight_microsatellite_markers_/993395", "title"=>"Genetic relationships between 110 <i>T. delbrueckii</i> strains using eight microsatellite markers.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-04-09 03:35:36"}

PMC Usage Stats | Further Information

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Relative Metric

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