Introduction to the Plant Ontology™ Laurel Cooper* 1, Justin Elser 1, Maria A. Gandolfo 3, Chris Mungall 4, Pankaj Jaiswal 1, Barry Smith 5, Dennis Wm. Stevenson 2, Ramona Walls 2 (in alphabetical order) 1.Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 2.The New York Botanical Garden, Bronx, NY 3.Department of Plant Biology, Cornell University, Ithaca, NY 4.Lawrence Berkeley National Lab, Berkeley, CA 5.Department of Philosophy, University at Buffalo, NY

What is Plant Ontology? An arrangement of controlled vocabularies that describe: – Plant Anatomy and Morphological features – Growth and Developmental Stages Based on internationally published/accepted terminology and their definitions A tool for annotation of plant phenotypes and gene expression patterns across all plant species

POC homepage:

Basic Goals of Plant Ontology: Encompass all plants: include terms and annotations from non- flowering plants: Gymnosperms, lycopods, ferns and mosses Create mappings to other ontologies such as PATO, CARO CL and GO Logical (genus-differentia) definitions, follow OBO principles is_a completeness Be a tool for comparative genomics across plant taxa

Phyllogenetic Tree of Plants Bowman et al, Cell, 2007

Plant Genomic Resources Rapidly Expanding:

Top level terms from dev browser POC homepage:

Plant Cells terms currently in Plant Structure:

Example- Plant Epidermal Cell

Proposed new organization of Plant Cell terms part_of Mirrors organization of Plant Structure: Sporophytic cell- e.g. embryonic cell Gametophytic cell- e.g. megagametophytic cell Whole plant cell - can occur in a gametophyte or sporophyte, e.g. axial cell

Plant Stem Cells in the PO:

High Resolution Analysis of Gene Expression in Shoot and Root Stem Cells (Stahl and Simon, Int. J. Dev. Biol. 2005) Root meristem Activation of genes during cell differentiation The plant hormone, auxin shifts from the apical half to concentrate at the basal pole of the embryo

Cell types of the root meristem ((Stahl and Simon, Int. J. Dev. Biol. 2005)

Gene Expression Map of the Arabidopsis Shoot Apical Meristem Yadav et al, PNAS regions of Shoot Apical Meristems: -Central zone narrow (CZ) (red) and broad (green) -Rib meristem (RM) (blue) -Peripheral zone (PZ) (cyan) - L1 layer (black). Hierarchical clustering of 47 characterized differentially expressed genes within the SAM

GO Enrichment Yadov et al, PNAS 2009 (E) Relative percentage of selected Gene Ontology (GO) groups identified in different DEG sectors. Note the number above each column represents a sum of total number of genes detected for a particular GO term in various sectors.

View Annotations in PO (Gene products) Click to view the annotation details

Shoot and Leaf Initiation from Single Cells in the Moss Physcomitrella patens Harrison et al, Current Biology, 2009 Three presumptive leaves (gray arrows) flank a single apical initial cell (red arrow)

Shoot Apices of Selaginella Kraussiania Jones and Drinnan,Int’l J. Plant Biol, 2009 Merophytes- apical cell derivativess

PO Highlights 2010: -Reorganization of PO terms to encompass non- flowering plants - ongoing - Annotations of gene products and phenotypes in a wider variety of plant species- ASPB, BSA workshops this summer- Phenote - Integrate data from current studies on new model plants, for example: -genome annotations -microarray data sets -high quality Next-Generation expression datasets

Suggestions for Interaction with Cell Type Ontology: -Terms unique to the PO could retain the PO ID -Annotations of those terms could be handled by the PO curators -Terms shared by the PO and other ontologies represented in the CL could list the PO ID as an alternate ID, for example: zygote, gamete, epidermal cell -Unique upper level terms with common lower level children- mirroring of sites? -Similar structures and organization?

Acknowledgements: Your name could be here, too!