On the Complexity of the Saccharomyces bayanus Taxon: Hybridization and Potential Hybrid Speciation
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{"title"=>"On the complexity of the Saccharomyces bayanus taxon: Hybridization and potential hybrid speciation", "type"=>"journal", "authors"=>[{"first_name"=>"Laura", "last_name"=>"Peŕez-Través", "scopus_author_id"=>"36504756900"}, {"first_name"=>"Christian A.", "last_name"=>"Lopes", "scopus_author_id"=>"7103222947"}, {"first_name"=>"Amparo", "last_name"=>"Querol", "scopus_author_id"=>"7004161461"}, {"first_name"=>"Eladio", "last_name"=>"Barrio", "scopus_author_id"=>"7006706407"}], "year"=>2014, "source"=>"PLoS ONE", "identifiers"=>{"pmid"=>"24705561", "sgr"=>"84899119838", "doi"=>"10.1371/journal.pone.0093729", "scopus"=>"2-s2.0-84899119838", "pui"=>"372921893", "isbn"=>"1932-6203 (Electronic)\\n1932-6203 (Linking)", "issn"=>"19326203"}, "id"=>"39b38bac-a28d-3304-8192-30f3bdc79958", "abstract"=>"Although the genus Saccharomyces has been thoroughly studied, some species in the genus has not yet been accurately resolved; an example is S. bayanus, a taxon that includes genetically diverse lineages of pure and hybrid strains. This diversity makes the assignation and classification of strains belonging to this species unclear and controversial. They have been subdivided by some authors into two varieties (bayanus and uvarum), which have been raised to the species level by others. In this work, we evaluate the complexity of 46 different strains included in the S. bayanus taxon by means of PCR-RFLP analysis and by sequencing of 34 gene regions and one mitochondrial gene. Using the sequence data, and based on the S. bayanus var. bayanus reference strain NBRC 1948, a hypothetical pure S. bayanus was reconstructed for these genes that showed alleles with similarity values lower than 97% with the S. bayanus var. uvarum strain CBS 7001, and of 99-100% with the non S. cerevisiae portion in S. pastorianus Weihenstephan 34/70 and with the new species S. eubayanus. Among the S. bayanus strains under study, different levels of homozygosity, hybridization and introgression were found; however, no pure S. bayanus var. bayanus strain was identified. These S. bayanus hybrids can be classified into two types: homozygous (type I) and heterozygous hybrids (type II), indicating that they have been originated by different hybridization processes. Therefore, a putative evolutionary scenario involving two different hybridization events between a S. bayanus var. uvarum and unknown European S. eubayanus-like strains can be postulated to explain the genomic diversity observed in our S. bayanus var. bayanus strains.", "link"=>"http://www.mendeley.com/research/complexity-saccharomyces-bayanus-taxon-hybridization-potential-hybrid-speciation", "reader_count"=>51, "reader_count_by_academic_status"=>{"Unspecified"=>1, "Professor > Associate Professor"=>3, "Researcher"=>9, "Student > Doctoral Student"=>4, "Student > Ph. D. Student"=>12, "Student > Master"=>10, "Other"=>2, "Student > Bachelor"=>6, "Professor"=>4}, "reader_count_by_user_role"=>{"Unspecified"=>1, "Professor > Associate Professor"=>3, "Researcher"=>9, "Student > Doctoral Student"=>4, "Student > Ph. D. Student"=>12, "Student > Master"=>10, "Other"=>2, "Student > Bachelor"=>6, "Professor"=>4}, "reader_count_by_subject_area"=>{"Unspecified"=>2, "Environmental Science"=>1, "Biochemistry, Genetics and Molecular Biology"=>11, "Agricultural and Biological Sciences"=>29, "Arts and Humanities"=>1, "Chemical Engineering"=>2, "Chemistry"=>3, "Computer Science"=>2}, "reader_count_by_subdiscipline"=>{"Chemistry"=>{"Chemistry"=>3}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>29}, "Computer Science"=>{"Computer Science"=>2}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>11}, "Unspecified"=>{"Unspecified"=>2}, "Environmental Science"=>{"Environmental Science"=>1}, "Chemical Engineering"=>{"Chemical Engineering"=>2}, "Arts and Humanities"=>{"Arts and Humanities"=>1}}, "reader_count_by_country"=>{"Canada"=>1, "United States"=>3, "Brazil"=>1, "Mexico"=>1, "France"=>1, "Spain"=>2}, "group_count"=>3}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/1450977"], "description"=>"<p>Numbers at nodes correspond to the bootstrap values based on 1000 pseudo-replicates. The scale is in nucleotide substitutions per site. All the strains are indicated in bold, except the <i>S. pastorianus</i> ones.</p>", "links"=>[], "tags"=>["Computational biology", "Comparative genomics", "Genome complexity", "Genome evolution", "Evolutionary biology", "Evolutionary processes", "hybridization", "Evolutionary genetics", "genetics", "genomics", "microbiology", "Mycology", "Fungal classification", "Fungal evolution", "organisms", "fungi", "yeast", "systems biology", "sequences"], "article_id"=>987890, "categories"=>["Biological Sciences"], "users"=>["Laura Pérez-Través", "Christian A. Lopes", "Amparo Querol", "Eladio Barrio"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0093729.g001", "stats"=>{"downloads"=>0, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Phylogenetic_tree_obtained_with_the_partial_sequences_of_the_nuclear_MNL1_gene_/987890", "title"=>"Phylogenetic tree obtained with the partial sequences of the nuclear <i>MNL1</i> gene.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-04-04 03:43:02"}
  • {"files"=>["https://ndownloader.figshare.com/files/1450978"], "description"=>"<p>Each square corresponds to a copy of each gene region according to its chromosome location, indicated in the map on the left. ‘<i>eubayanus</i>’ alleles are indicated as black squares and ‘<i>uvarum</i>’ alleles as gray squares. The genes order differs between <i>S. bayanus</i> var. <i>bayanus</i> and <i>S. bayanus</i> var. <i>uvarum</i>, as depicted, due to the presence of two translocations. The first involves chromosomes VI and X in <i>S. bayanus</i> var. <i>bayanus</i> and chromosomes VItX and XtVI in <i>S. bayanus</i> var. <i>uvarum</i>, while the second involves chromosomes IItIV, IVtII and XIV in <i>S. bayanus</i> var. <i>bayanus</i> and chromosomes IItIItIV, IVtIItII and XIVtIItIV in <i>S. bayanus</i> var. <i>uvarum</i>.</p>", "links"=>[], "tags"=>["Computational biology", "Comparative genomics", "Genome complexity", "Genome evolution", "Evolutionary biology", "Evolutionary processes", "hybridization", "Evolutionary genetics", "genetics", "genomics", "microbiology", "Mycology", "Fungal classification", "Fungal evolution", "organisms", "fungi", "yeast", "systems biology", "34", "genes", "strains"], "article_id"=>987891, "categories"=>["Biological Sciences"], "users"=>["Laura Pérez-Través", "Christian A. Lopes", "Amparo Querol", "Eladio Barrio"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0093729.g002", "stats"=>{"downloads"=>1, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_RFLPs_of_34_nuclear_genes_from_the_S_bayanus_strains_analyzed_in_this_work_/987891", "title"=>"RFLPs of 34 nuclear genes from the <i>S. bayanus</i> strains analyzed in this work.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-04-04 03:43:02"}
  • {"files"=>["https://ndownloader.figshare.com/files/1450979"], "description"=>"<p><b>A- NJ tree</b>. Numbers at nodes correspond to the bootstrap values based on 1000 pseudo-replicates. The scale is in nucleotide substitutions per site. Strains with a controversial adscription are indicated in bold. <b>B- Variable positions on the different COX2 haplotypes</b>. A dot indicates the presence of the same nucleotide at this position. Haplotype U-I is used as a reference.</p>", "links"=>[], "tags"=>["Computational biology", "Comparative genomics", "Genome complexity", "Genome evolution", "Evolutionary biology", "Evolutionary processes", "hybridization", "Evolutionary genetics", "genetics", "genomics", "microbiology", "Mycology", "Fungal classification", "Fungal evolution", "organisms", "fungi", "yeast", "systems biology", "sequences", "mitochondrial"], "article_id"=>987892, "categories"=>["Biological Sciences"], "users"=>["Laura Pérez-Través", "Christian A. Lopes", "Amparo Querol", "Eladio Barrio"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0093729.g003", "stats"=>{"downloads"=>0, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Phylogenetic_analysis_of_the_partial_sequences_of_the_mitochondrial_COX2_gene_/987892", "title"=>"Phylogenetic analysis of the partial sequences of the mitochondrial <i>COX2</i> gene.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-04-04 03:43:02"}
  • {"files"=>["https://ndownloader.figshare.com/files/1450980"], "description"=>"<p>Possible origins of the <i>S. bayanus</i> (<i>S. uvarum x S. eubayanus</i>) hybrid strains.</p>", "links"=>[], "tags"=>["Computational biology", "Comparative genomics", "Genome complexity", "Genome evolution", "Evolutionary biology", "Evolutionary processes", "hybridization", "Evolutionary genetics", "genetics", "genomics", "microbiology", "Mycology", "Fungal classification", "Fungal evolution", "organisms", "fungi", "yeast", "systems biology", "origins", "uvarum", "hybrid"], "article_id"=>987893, "categories"=>["Biological Sciences"], "users"=>["Laura Pérez-Través", "Christian A. Lopes", "Amparo Querol", "Eladio Barrio"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0093729.g004", "stats"=>{"downloads"=>3, "page_views"=>34, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Possible_origins_of_the_S_bayanus_S_uvarum_x_S_eubayanus_hybrid_strains_/987893", "title"=>"Possible origins of the <i>S. bayanus</i> (<i>S. uvarum x S. eubayanus</i>) hybrid strains.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-04-04 03:43:02"}
  • {"files"=>["https://ndownloader.figshare.com/files/1450981"], "description"=>"NT<p>, neotype,</p>T<p>, type.</p><p>Culture collection abbreviated as follows: CECT, Colección Española de Cultivos Tipo, Valencia, Spain; CBS, Centraalbureau voor Schimmelcultures, Utrecht, The Netherlands; DSMZ, German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany; NBRC; NCAIM, National Collection of Agricultural and Industrial Microorganisms, Faculty of Food Sciences, Corvinus University of Budapest, Hungary; NCYC, National Collection of Yeast Cultures, Norwich, UK; ZIM, ZIM Culture Collection of Industrial Microorganisms, University of Ljubljana, Slovenia.</p>", "links"=>[], "tags"=>["Computational biology", "Comparative genomics", "Genome complexity", "Genome evolution", "Evolutionary biology", "Evolutionary processes", "hybridization", "Evolutionary genetics", "genetics", "genomics", "microbiology", "Mycology", "Fungal classification", "Fungal evolution", "organisms", "fungi", "yeast", "systems biology", "strains"], "article_id"=>987894, "categories"=>["Biological Sciences"], "users"=>["Laura Pérez-Través", "Christian A. Lopes", "Amparo Querol", "Eladio Barrio"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0093729.t001", "stats"=>{"downloads"=>5, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_List_of_Saccharomyces_strains_analyzed_in_the_present_study_/987894", "title"=>"List of <i>Saccharomyces</i> strains analyzed in the present study.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-04-04 03:43:02"}
  • {"files"=>["https://ndownloader.figshare.com/files/1450982"], "description"=>"<p>For those genes exhibited between the CBS 7001 and NBRC 1948 similarities ≥99.6% (in bold), additional sequences were obtained for <i>S. bayanus</i> strains CECT 11186 or CBS 424, exhibiting divergent alleles, and their similarities to CBS 7001 and W 34/70 are also provided. Those gene sequence comparisons for which <i>S. pastorianus</i> Weihenstephan 34/70 contains only ‘<i>cerevisiae</i>’ alleles are indicated by ‘none’ (i.e., no <i>eubayanus</i> alleles are present to compare).</p>", "links"=>[], "tags"=>["Computational biology", "Comparative genomics", "Genome complexity", "Genome evolution", "Evolutionary biology", "Evolutionary processes", "hybridization", "Evolutionary genetics", "genetics", "genomics", "microbiology", "Mycology", "Fungal classification", "Fungal evolution", "organisms", "fungi", "yeast", "systems biology", "34", "protein-coding", "genes", "bayanus", "strains", "alleles", "weihenstephan"], "article_id"=>987895, "categories"=>["Biological Sciences"], "users"=>["Laura Pérez-Través", "Christian A. Lopes", "Amparo Querol", "Eladio Barrio"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0093729.t002", "stats"=>{"downloads"=>4, "page_views"=>66, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Sequence_similarity_for_34_protein_coding_genes_between_the_reference_strain_of_S_bayanus_var_bayanus_NBRC_1948_and_the_reference_strains_of_S_bayanus_var_uvarum_CBS_7001_and_the_eubayanus_alleles_of_the_S_pastorianus_strain_Weihenstephan_34_70_W_34_70_/987895", "title"=>"Sequence similarity for 34 protein-coding genes between the reference strain of <i>S. bayanus var. bayanus</i> (NBRC 1948) and the reference strains of <i>S. bayanus</i> var. <i>uvarum</i> (CBS 7001) and the ‘<i>eubayanus</i>’ alleles of the <i>S. pastorianus</i> strain Weihenstephan 34/70 (W 34/70).", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-04-04 03:43:02"}
  • {"files"=>["https://ndownloader.figshare.com/files/1450983"], "description"=>"<div><p>Although the genus <i>Saccharomyces</i> has been thoroughly studied, some species in the genus has not yet been accurately resolved; an example is <i>S. bayanus</i>, a taxon that includes genetically diverse lineages of pure and hybrid strains. This diversity makes the assignation and classification of strains belonging to this species unclear and controversial. They have been subdivided by some authors into two varieties (<i>bayanus</i> and <i>uvarum</i>), which have been raised to the species level by others. In this work, we evaluate the complexity of 46 different strains included in the <i>S. bayanus</i> taxon by means of PCR-RFLP analysis and by sequencing of 34 gene regions and one mitochondrial gene. Using the sequence data, and based on the <i>S. bayanus var. bayanus</i> reference strain NBRC 1948, a hypothetical pure <i>S. bayanus</i> was reconstructed for these genes that showed alleles with similarity values lower than 97% with the <i>S. bayanus</i> var. <i>uvarum</i> strain CBS 7001, and of 99–100% with the non <i>S</i>. <i>cerevisiae</i> portion in <i>S. pastorianus</i> Weihenstephan 34/70 and with the new species <i>S. eubayanus</i>. Among the <i>S. bayanus</i> strains under study, different levels of homozygosity, hybridization and introgression were found; however, no pure <i>S. bayanus</i> var. <i>bayanus</i> strain was identified. These <i>S. bayanus</i> hybrids can be classified into two types: homozygous (type I) and heterozygous hybrids (type II), indicating that they have been originated by different hybridization processes. Therefore, a putative evolutionary scenario involving two different hybridization events between a <i>S. bayanus</i> var. <i>uvarum</i> and unknown European <i>S. eubayanus</i>-like strains can be postulated to explain the genomic diversity observed in our <i>S. bayanus var. bayanus</i> strains.</p></div>", "links"=>[], "tags"=>["Computational biology", "Comparative genomics", "Genome complexity", "Genome evolution", "Evolutionary biology", "Evolutionary processes", "hybridization", "Evolutionary genetics", "genetics", "genomics", "microbiology", "Mycology", "Fungal classification", "Fungal evolution", "organisms", "fungi", "yeast", "systems biology", "hybrid", "speciation"], "article_id"=>987896, "categories"=>["Biological Sciences"], "users"=>["Laura Pérez-Través", "Christian A. Lopes", "Amparo Querol", "Eladio Barrio"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0093729", "stats"=>{"downloads"=>12, "page_views"=>12, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/On_the_Complexity_of_the_Saccharomyces_bayanus_Taxon_Hybridization_and_Potential_Hybrid_Speciation/987896", "title"=>"On the Complexity of the <i>Saccharomyces bayanus</i> Taxon: Hybridization and Potential Hybrid Speciation", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-04-04 03:43:02"}

PMC Usage Stats | Further Information

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Relative Metric

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