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Reconstructing the Backbone of the Saccharomycotina Yeast Phylogeny Using Genome-Scale Data

Xing-Xing Shen, View ORCID ProfileXiaofan Zhou, View ORCID ProfileJacek Kominek, Cletus P. Kurtzman, View ORCID ProfileChris Todd Hittinger and View ORCID ProfileAntonis Rokas
G3: Genes, Genomes, Genetics December 1, 2016 vol. 6 no. 12 3927-3939; https://doi.org/10.1534/g3.116.034744
Xing-Xing Shen
Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee 37235
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Xiaofan Zhou
Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee 37235
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  • ORCID record for Xiaofan Zhou
Jacek Kominek
Laboratory of Genetics, Genome Center of Wisconsin, DOE Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, Wisconsin 53706
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  • ORCID record for Jacek Kominek
Cletus P. Kurtzman
Mycotoxin Prevention and Applied Microbiology Research Unit, National Center for Agricultural Utilization Research, Agricultural Research Service, U.S. Department of Agriculture, Peoria, Illinois 61604
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  • For correspondence: antonis.rokas@vanderbilt.edu
Chris Todd Hittinger
Laboratory of Genetics, Genome Center of Wisconsin, DOE Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, Wisconsin 53706
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  • ORCID record for Chris Todd Hittinger
  • For correspondence: antonis.rokas@vanderbilt.edu
Antonis Rokas
Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee 37235
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  • ORCID record for Antonis Rokas
  • For correspondence: antonis.rokas@vanderbilt.edu
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Data supplements

  • Supplemental Material for Shen, et al, 2016

    Files in this Data Supplement:

    • Figure S1 - Box plots of GC content for the 1,233 nuclear protein-coding BUSCO genes in each of the 96 taxa used in this study. (.pdf, 3,849 KB)
    • Figure S2 - Distribution of the best-fitting amino acid substitution models across the amino acid alignments of the 1,233 BUSCO genes used in this study. (.pdf, 253 KB)
    • Figure S3 - Venn diagrams illustrating the overlaps between subsets (left, Top 25%; right, Top 50%) of 1,233 genes displaying the highest average bootstrap support (ABS) and the highest average relative tree certainty (RTC) in their ML gene trees. (.pdf, 560 KB)
    • Figure S4 - Illustration of occupancy for each taxon and gene in our data matrices. Each row corresponds to a taxon and each column corresponds to a BUSCO gene. (.pdf, 2,880 KB)
    • Figure S5 - Distribution of gene alignment lengths across the 1,233 BUSCO genes used in this study. (.pdf, 296 KB)
    • Figure S6 - The phylogenetic relationships of Saccharomycotina yeasts inferred from the concatenation-based analysis of the C12 data matrix. (.pdf, 314 KB)
    • Figure S7 - The phylogenetic relationships of Saccharomycotina yeasts inferred from the coalescence-based analysis of the C12 data matrix. (.pdf, 310 KB)
    • Figure S8 - Phylogenetic supernetwork of Saccharomycotina yeasts inferred from the 1,233 partial gene trees estimated from the AA data matrix (a) and the C12 data matrix (b). (.pdf, 674 KB)
    • Figure S9 - Conflicts in the phylogenetic relationships of Saccharomycotina yeasts inferred from the concatenation-based (a) and coalescence-based (b) analysis of the 308 genes in the AA data matrix whose bootstrap consensus gene trees had the highest average bootstrap support (top 25%). (.pdf, 350 KB)
    • Table S1 - List of all taxa used in this study. (.xlsx, 23 KB)
    • Table S2 - Summary of assessment of 96 genome assemblies. (.xlsx, 15 KB)
    • Table S3 - Summary of 1,233-gene, 96-taxon data matrix. (.xlsx, 40 KB)
    • Table S4 - GO term enrichment analysis of 1,437 BUSCO genes. (.xlsx, 20 KB)
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Volume 6 Issue 12, December 2016

G3: Genes|Genomes|Genetics: 6 (12)

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Reconstructing the Backbone of the Saccharomycotina Yeast Phylogeny Using Genome-Scale Data

Xing-Xing Shen, View ORCID ProfileXiaofan Zhou, View ORCID ProfileJacek Kominek, Cletus P. Kurtzman, View ORCID ProfileChris Todd Hittinger and View ORCID ProfileAntonis Rokas
G3: Genes, Genomes, Genetics December 1, 2016 vol. 6 no. 12 3927-3939; https://doi.org/10.1534/g3.116.034744
Xing-Xing Shen
Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee 37235
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Xiaofan Zhou
Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee 37235
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Xiaofan Zhou
Jacek Kominek
Laboratory of Genetics, Genome Center of Wisconsin, DOE Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, Wisconsin 53706
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Jacek Kominek
Cletus P. Kurtzman
Mycotoxin Prevention and Applied Microbiology Research Unit, National Center for Agricultural Utilization Research, Agricultural Research Service, U.S. Department of Agriculture, Peoria, Illinois 61604
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • For correspondence: antonis.rokas@vanderbilt.edu
Chris Todd Hittinger
Laboratory of Genetics, Genome Center of Wisconsin, DOE Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, Wisconsin 53706
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Chris Todd Hittinger
  • For correspondence: antonis.rokas@vanderbilt.edu
Antonis Rokas
Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee 37235
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Antonis Rokas
  • For correspondence: antonis.rokas@vanderbilt.edu
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Citation

Reconstructing the Backbone of the Saccharomycotina Yeast Phylogeny Using Genome-Scale Data

Xing-Xing Shen, View ORCID ProfileXiaofan Zhou, View ORCID ProfileJacek Kominek, Cletus P. Kurtzman, View ORCID ProfileChris Todd Hittinger and View ORCID ProfileAntonis Rokas
G3: Genes, Genomes, Genetics December 1, 2016 vol. 6 no. 12 3927-3939; https://doi.org/10.1534/g3.116.034744
Xing-Xing Shen
Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee 37235
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Xiaofan Zhou
Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee 37235
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Xiaofan Zhou
Jacek Kominek
Laboratory of Genetics, Genome Center of Wisconsin, DOE Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, Wisconsin 53706
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Jacek Kominek
Cletus P. Kurtzman
Mycotoxin Prevention and Applied Microbiology Research Unit, National Center for Agricultural Utilization Research, Agricultural Research Service, U.S. Department of Agriculture, Peoria, Illinois 61604
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • For correspondence: antonis.rokas@vanderbilt.edu
Chris Todd Hittinger
Laboratory of Genetics, Genome Center of Wisconsin, DOE Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, Wisconsin 53706
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Chris Todd Hittinger
  • For correspondence: antonis.rokas@vanderbilt.edu
Antonis Rokas
Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee 37235
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Antonis Rokas
  • For correspondence: antonis.rokas@vanderbilt.edu

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