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Exploring Saccharomycotina Yeast Ecology Through an Ecological Ontology Framework
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  • Marie-Claire Harrison,
  • Dana A. Opulente,
  • John Wolters,
  • Xing-Xing Shen,
  • Xiaofan Zhou,
  • Marizeth Goenewald,
  • Chris Hittinger,
  • Antonis Rokas,
  • Abigail LaBella
Marie-Claire Harrison
Vanderbilt University
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Dana A. Opulente
Villanova University
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John Wolters
University of Wisconsin-Madison
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Xing-Xing Shen
Vanderbilt University
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Xiaofan Zhou
Vanderbilt University
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Marizeth Goenewald
Westerdijk Fungal Biodiversity Institute
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Chris Hittinger
University of Wisconsin-Madison
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Antonis Rokas
Vanderbilt University
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Abigail LaBella
The University of North Carolina at Charlotte

Corresponding Author:[email protected]

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Abstract

Yeasts in the subphylum Saccharomycotina are found across the globe in disparate ecosystems. A major aim of yeast research is to understand the diversity and evolution of ecological traits, such as carbon metabolic breadth, insect association, and cactophily. This includes studying aspects of ecological traits like genetic architecture or association with other phenotypic traits. Genomic resources in the Saccharomycotina have grown rapidly. Ecological data, however, are still limited for many species, especially those only known from species descriptions where usually only a limited number of strains are studied. Moreover, ecological information is recorded in natural language format limiting high throughput computational analysis. To address these limitations, we developed an ontological framework for the analysis of yeast ecology. A total of 1,088 yeast strains were added to the Ontology of Yeast Environments (OYE) and analyzed in a machine-learning framework to connect genotype to ecology. This framework is flexible and can be extended to additional isolates, species, or environmental sequencing data. Widespread adoption of OYE would greatly aid the study of macroecology in the Saccharomycotina subphylum.
Submitted to Yeast
Submission Checks Completed
Assigned to Editor
Reviewer(s) Assigned
03 Jul 2024Review(s) Completed, Editorial Evaluation Pending
18 Jul 2024Reviewer(s) Assigned
13 Aug 2024Editorial Decision: Revise Minor
26 Aug 20241st Revision Received
27 Aug 2024Submission Checks Completed
27 Aug 2024Assigned to Editor
27 Aug 2024Review(s) Completed, Editorial Evaluation Pending
03 Sep 2024Editorial Decision: Accept