The Plant Ontology Facilitates Comparisons of Plant Development Stages Across Species.

Ramona L Walls,Dennis W Stevenson,Maria Alejandra Gandolfo,Laurel Cooper,Barry Smith,Pankaj Jaiswal,Christopher J Mungall,Justin Elser

doi:10.3389/fpls.2019.00631

Abstract

The 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.

Highlights

Studies that examine patterns of gene expression across species or environments are more powerful when they involve consideration of specific development stages, because they can control for variation in expression through ontogeny (e.g., Richards et al, 2012)
Accessing the Plant Ontology and Associated Annotation Data The most recent version of the Plant Ontology is available through the Planteome browser7, as well as at the OBO Foundry
Raw annotation files can be downloaded from the Planteome SVN repository13 or users can filter and download annotation data using the Planteome AmiGO browser annotation page14

Summary

Introduction

Studies that examine patterns of gene expression across species or environments are more powerful when they involve consideration of specific development stages, because they can control for variation in expression through ontogeny (e.g., Richards et al, 2012). 2013) was designed as a species-neutral vocabulary for plant anatomy, morphology, and development stages that can be used to associate data to a common set of species-neutral terms for plant sciences. PO terms for development stages allow researchers to accurately describe at what stage during the life of a plant, or plant part, a specimen was collected, a physiological parameter was measured, or a gene was expressed. Shared terminology makes it easier to compare results from different species and experiments, or to identify developmental timing that differs from the norm within a species. Development stage data are stored in the Planteome database as annotations that capture associations between a PO term and an entity such as a gene, gene model, protein, mutant phenotype, or Quantitative Trait Locus (QTL)

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Discussion

Conclusion