The Plant Ontology Facilitates Comparisons of Plant Development Stages Across Species
AuthorWalls, Ramona L
Gandolfo, Maria Alejandra
Mungall, Christopher J
Stevenson, Dennis W
AffiliationUniv Arizona, Inst Bio5
MetadataShow full item record
PublisherFRONTIERS MEDIA SA
CitationWalls, R. L., Cooper, L., Elser, J., Gandolfo, M. A., Mungall, C. J., Smith, B., ... & Jaiswal, P. (2019). The Plant Ontology Facilitates Comparisons of Plant Development Stages Across Species. Frontiers in Plant Science, 10.
JournalFRONTIERS IN PLANT SCIENCE
RightsCopyright © 2019 Walls, Cooper, Elser, Gandolfo, Mungall, Smith, Stevenson and Jaiswal. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
Collection InformationThis item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at firstname.lastname@example.org.
AbstractThe Plant Ontology (PO) is a community resource consisting of standardized terms, definitions, and logical relations describing plant structures and development stages, augmented by a large database of annotations from genomic and phenomic studies. This paper describes the structure of the ontology and the design principles we used in constructing PO terms for plant development stages. It also provides details of the methodology and rationale behind our revision and expansion of the PO to cover development stages for all plants, particularly the land plants (bryophytes through angiosperms). As a case study to illustrate the general approach, we examine variation in gene expression across embryo development stages in Arabidopsis and maize, demonstrating how the PO can be used to compare patterns of expression across stages and in developmentally different species. Although many genes appear to be active throughout embryo development, we identified a small set of uniquely expressed genes for each stage of embryo development and also between the two species. Evaluating the different sets of genes expressed during embryo development in Arabidopsis or maize may inform future studies of the divergent developmental pathways observed in monocotyledonous versus dicotyledonous species. The PO and its annotation database (http://www.planteome.org) make plant data for any species more discoverable and accessible through common formats, thus providing support for applications in plant pathology, image analysis, and comparative development and evolution.
NoteOpen access journal
VersionFinal published version
SponsorsNational Science Foundation [IOS-0822201]; cROP: Common Reference Ontologies and Applications for Plant Biology [IOS-1340112]
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