The Plant Ontology Facilitates Comparisons of Plant Development Stages Across Species

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

doi:10.3389/fpls.2019.00631

Title: The Plant Ontology Facilitates Comparisons of Plant Development Stages Across Species

Journal Article · 04 June 2019 · Frontiers in Plant Science

DOI: https://doi.org/10.3389/fpls.2019.00631 · OSTI ID:1628293

Walls, Ramona L. ^[1]; Cooper, Laurel ^[2]; Elser, Justin ^[2]; Gandolfo, Maria Alejandra ^[3]; Mungall, Christopher J. ^[4]; Smith, Barry ^[5]; Stevenson, Dennis W. ^[6]; Jaiswal, Pankaj ^[2]

CyVerse, Bio5 Institute, The University of Arizona, Tucson, AZ (United States)
Oregon State Univ., Corvallis, OR (United States). Dept. of Botany and Plant Pathology
Cornell Univ., Ithaca, NY, (United States). Liberty Hyde Bailey Hortorium, Plant Biology Section, School of Integrative Plant Science
Lawrence Berkeley National Lab (LBNL), Berkeley, CA, (United States). Environmental Genomics and Systems Biology
University at Buffalo, Buffalo, NY, (United States). Dept. of Philosophy
New York Botanical Garden, Bronx, NY, (United States)

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.

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Research Organization:: Lawrence Berkeley National Lab (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC); National Institutes of Health (NIH); Center for Genome Research and Biocomputing (CGRB); Oregon State University (OSU)

Grant/Contract Number:: AC02-05CH11231; DBI-0735191; DBI-1265383

OSTI ID:: 1628293

Journal Information:: Frontiers in Plant Science, Vol. 10; ISSN 1664-462X

Publisher:: Frontiers Research FoundationCopyright Statement

Country of Publication:: United States

Language:: English

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Whole-Plant Growth Stage Ontology for Angiosperms and Its Application in Plant Biology Pujar, Anuradha; Jaiswal, Pankaj; Kellogg, Elizabeth A. Plant Physiology, Vol. 142, Issue 2 https://doi.org/10.1104/pp.106.085720	journal	August 2006
Branching Genes Are Conserved across Species. Genes Controlling a Novel Signal in Pea Are Coregulated by Other Long-Distance Signals Johnson, Xenie; Brcich, Tanya; Dun, Elizabeth A. Plant Physiology, Vol. 142, Issue 3 https://doi.org/10.1104/pp.106.087676	journal	September 2006
Genome-Wide Analysis Reveals Gene Expression and Metabolic Network Dynamics during Embryo Development in Arabidopsis Xiang, Daoquan; Venglat, Prakash; Tibiche, Chabane Plant Physiology, Vol. 156, Issue 1 https://doi.org/10.1104/pp.110.171702	journal	March 2011
Conservation and Divergence of Light-Regulated Genome Expression Patterns during Seedling Development in Rice and Arabidopsis Jiao, Yuling; Ma, Ligeng; Strickland, Elizabeth The Plant Cell, Vol. 17, Issue 12 https://doi.org/10.1105/tpc.105.035840	journal	November 2005
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Rapid Changes in Flowering Time in British Plants Fitter, A. H. Science, Vol. 296, Issue 5573 https://doi.org/10.1126/science.1071617	journal	May 2002
Effects of dependence in high-dimensional multiple testing problems Kim, Kyung In; van de Wiel, Mark A. BMC Bioinformatics, Vol. 9, Issue 1 https://doi.org/10.1186/1471-2105-9-114	journal	February 2008
AISO: Annotation of Image Segments with Ontologies Lingutla, Nikhil; Preece, Justin; Todorovic, Sinisa Journal of Biomedical Semantics, Vol. 5, Issue 1 https://doi.org/10.1186/2041-1480-5-50	journal	January 2014
Uberon, an integrative multi-species anatomy ontology Mungall, Christopher J.; Torniai, Carlo; Gkoutos, Georgios V. Genome Biology, Vol. 13, Issue 1 https://doi.org/10.1186/gb-2012-13-1-r5	journal	January 2012
An ontology approach to comparative phenomics in plants Oellrich, Anika; Walls, Ramona L.; Cannon, Ethalinda Plant Methods, Vol. 11, Issue 1 https://doi.org/10.1186/s13007-015-0053-y	journal	January 2015
SNAP and SPAN: Towards Dynamic Spatial Ontology Grenon, Pierre; Smith, Barry Spatial Cognition & Computation, Vol. 4, Issue 1 https://doi.org/10.1207/s15427633scc0401_5	journal	March 2004
Genome-Wide Patterns of Arabidopsis Gene Expression in Nature Richards, Christina L.; Rosas, Ulises; Banta, Joshua PLoS Genetics, Vol. 8, Issue 4 https://doi.org/10.1371/journal.pgen.1002662	journal	April 2012
Measures for interoperability of phenotypic data: minimum information requirements and formatting Cwiek-Kupczynska, Hanna; Altmann, Thomas; Arend, Daniel RWTH Aachen University https://doi.org/10.18154/rwth-2017-05402	text	January 2016
The Plant Phenology Ontology: A New Informatics Resource for Large-Scale Integration of Plant Phenology Data Stucky, Brian J.; Guralnick, Rob; Deck, John Frontiers in Plant Science, Vol. 9 https://doi.org/10.3389/fpls.2018.00517	journal	May 2018
Photographs and herbarium specimens as tools to document phenological changes in response to global warming Miller-Rushing, A. J.; Primack, R. B.; Primack, D. American Journal of Botany, Vol. 93, Issue 11 https://doi.org/10.3732/ajb.93.11.1667	journal	November 2006

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The sugarcane mitochondrial genome: assembly, phylogenetics and transcriptomics Lloyd Evans, Dyfed; Hlongwane, Thandekile Thandiwe; Joshi, Shailesh V. PeerJ, Vol. 7 https://doi.org/10.7717/peerj.7558	journal	January 2019

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