Exploring Saccharomycotina Yeast Ecology Through an Ecological Ontology Framework.
controlled vocabulary
dynamic
formal
isolation environment
macroecology
statistical enrichment
Journal
Yeast (Chichester, England)
ISSN: 1097-0061
Titre abrégé: Yeast
Pays: England
ID NLM: 8607637
Informations de publication
Date de publication:
18 Sep 2024
18 Sep 2024
Historique:
revised:
26
08
2024
received:
02
07
2024
accepted:
03
09
2024
medline:
19
9
2024
pubmed:
19
9
2024
entrez:
19
9
2024
Statut:
aheadofprint
Résumé
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.
Types de publication
Journal Article
Review
Langues
eng
Sous-ensembles de citation
IM
Subventions
Organisme : This work was supported by the NSF for Distinguished Young Scholars of Zhejiang Province (LR23C140001), Key Research Project of Zhejiang Lab (2021PE0AC04), National Institute of Allergy and Infectious Diseases (R01 AI153356), National Institute of Food and Agriculture Hatch Project (7005101), Burroughs Wellcome Fund, Directorate for Biological Sciences (DEB-2110403, DEB-2110404), Office of the Vice Chancellor for Research and Graduate Education with funding from the Wisconsin Alumni Research Foundation H.I. Romnes Faculty Fellowship, and DOE Great Lakes Bioenergy Research Center (DOE BER Office of Science DE-SC0018409).
Informations de copyright
© 2024 The Author(s). Yeast published by John Wiley & Sons Ltd.
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