Plant Structure Development Stages

Objectives
Organizing principles and rationales
Top nodes in the Plant Structure Developmental Stages branch
References

Objectives

The Plant Structure Developmental Stage branch of the Plant Ontology describes developmental stages of plant structures such as organs, tissues, or whole plants. It includes terms for developmental stages of organs and organ systems of a 'generic' flowering plant (e.g., flower development stage), as well as more generic development stages that can be applied across land plants (e.g., leaf development stage). Series of developmental stages are defined based on temporal landmarks delineated by morphological and anatomical changes, as described in published literature for several species, namely (but not limited to) Arabidopsis, maize and rice. Instead of providing detailed species-specific staging in a form of a 'parallel bins' for each structure, we opted to integrate existing species-specific temporal ontologies (available from TAIR and Gramene), creating standardized, 'generic' staging system for each plant structure. This ontology is the first multi-species representation of developmental stages in angiosperms - it is applicable to Arabidopsis, maize and rice, but also flexible enough to allow incorporation of developmental stages of other vascular and non-vascular plants.

There is a very specific purpose for creating such ontology - primarily to facilitate cross database queries and to foster its consistent use for annotations of developmental stage specific gene expressions, for meaningful description of phenotypes, and for standardized description of biological samples in plant databases and in the plant research community. Its comprehensiveness is therefore restricted by its main purpose - cross-species comparison and cross-database queries.

This ontology is part of our web-accessible database and it can be searched using the ontology browser at the POC web site. It is structured as a simple hierarchicy, with the top nodes corresponding to the top nodes of the PO's plant structure branch.

Organizing principles and rationales

While creating this ontology, the POC agreed to avoid conceptual overlaps with the Gene Ontology (GO), which already has plant development terms as a part of the Biological process branch. Unlike the GO biological process terms, which descripe developmental process, PO plant sturcture development stage terms describe the stages in the life cycle of a plant or of part of a plant that are delimited by particular landmarks, either developmental processes from GO or morphological and anatomical changes observed the plant structure.

To display the correct progression of development stages, alphabetical or numerical prefixes were added to the term names in many plant structure nodes (for example, see children terms of 'leaf development stages' or 'root development stages'). However, and the PO moves forward, these alphanumerical prefixes are being removed. The correct ordering of stages can instead be specified using relations such as 'precedes' or 'is_preceded_by'.

Species-specific terms as synonyms

Similar to the plant anatomical entity aspect of the Plant Ontology, synonymy was used to link the species-specific stages from existing temporal ontologies at Gramene and TAIR to the 'generic' developmental stages in the PO. A user can find species-specific terms from the respective databases on a term detail page (in the synonym field) in the ontology browser. On the same term detail page, in the External References filed, the URL links to the mapped keyword(s) in Gramene and TAIR are provided.

When describing generic developmental stages of a flowering plant, it was not possible to have 'all inclusive' stages that would be pertinent to all monocots and eudicots. An example is 'embryo development stages', with several children terms, each describing a specific stage of embryo development in either well-studied model dicots (Arabidopsis and Capsella), or in monocots, namely grasses. Since embryo development in Arabidopsis and in grasses follows very different developmental patterns, there are only few terms (stages) common for both, such as 'proembryo stage' or 'transition stage'. Species-specific stages of Arabidopsis embryo development from TAIR ontology were added as synonyms to the corresonding stages in PO, while stages describing embryo development in rice in the existing Gramene ontology will be soon added as synonyms to the pertinent stages in the PO. Therefore, synonymy, as applied in PO, facilitates cross-species comparison, although, in this particular case, such comparison is only possible at higher level, i.e., 'embryo development stages'. At the same time, synonymy allows for a retrieval of species-specific information. For example, by choosing species-specific filter options in the ontology browser, it is possible to search for terms/stages pertinent for Arabidopsis embryo development and also to retrieve genes expressed during embryo development only in Arabidopsis or in rice.

Relationship types

The primary term-to-term relationship used in this branch of the ontology is the 'is_a' (subClassOf, in OWL) relation. For example, 2 leaf expansion stage is_a (subClassOf) the parent term, leaf developmental stage, which in turn is a subclass of the plant organ development stage.

Terms in the plant structure development stage branch of the PO are linked to terms in the plant anatomical entity branch of the PO via the 'has_participant' and 'participates_in' relations. For example, trichome development stage has_participant trichome or vascular leaf participates_in sporophyte development stage.

Top nodes in the Plant Structure Developmental Stages Ontology

Terms plant structure development stage branch of the PO are are organized as a hierarchy that mirrors the hierarchy of plant structure branch of the PO:

plant structure development stage, PO:0009012
    (i) collective plant structure development stage, PO:0025338
    (i) plant organ development stage, PO:0025339
    (i) plant tissue development stage, PO:0025423
    (i) seed development stage, PO:0001170
    (i) trichome development stage, PO:0025368
    (i) whole plant development stage, PO:0007033

Two top nodes, 'fruit development stages' and 'inflorescence development stages' don't have any generic stages, due to the complex nature of their development and vast differences in formation of these organs among flowering plants. In both cases, it was impossible to create generic stages of fruit and inflorescence development that would be pertinent for eudicots and monocots. At later times, if required, a limited number of higher level species-specific terms may be added to facilitate gene annotations and phenotype description.

Flower developmental stages

The goal was to include common stages for a generic flower, and for all floral organs, starting with primordial stage ('primordium visible') for each respective floral organ. The following floral organs are included:

3 floral organ stages, PO:0007600
    (i) androecium development stages, PO:0007605
    (i) calyx developmental stages, PO:0007603
    (i) corolla development stages, PO:0007604
    (i) gynoecium development stages, PO:0007606
    (i) lemma development stages, PO:0001047
    (i) lodicule development stages, PO:0001049
    (i) palea development stages, PO:0001048

Ovule and megagametophyte development stages encompass monosporic, bisporic and tetrasporic types of embryo sac development (Reiser and Fisher, 1993). To accommodate this, seven generic stages are created, from 'A megaspore mother cell enlarges' to the last 'G eight nucleate megagametophyte stage'.

Anther and pollen development stages are based on the descriptions for Arabidopsis (Sanders et al, 1999, Regan anf Moffatt, 1990), and for maize (Bedinger and Russell, 1994). Terms in the anther node describes morphological changes specifically in the anther tissues, while pollen node includes stages of two- and three-celled pollen development.

Leaf developmental stages

The main four stages of leaf development were based on description by Poethig (1997) , and on description of leaf development stages in rice (Itoh et al, 2005). The following instances of 'leaf development stages' are pertinent for simple leaf and compound leaf, encompassing eudicots and monocots:

leaf developmental stages, PO:0001050
    (i) 1 leaf initiation stage, PO:0001051
    (i) 2 leaf expansion stage, PO:0001052
    (i) 3 leaf fully expanded, PO:0001053
    (i) 4 leaf senescence stage, PO:0001054

Root development stages

Instead of creating separate developmental stages for primary, lateral and crown root, we defined several 'generic' stages of root development, common for all three root types. Based on descriptions for cereal root development (Hochholdinger et al, 2004), and for Arabidopsis lateral root development (Casimiro et al, 2003), there are five generic stages of root development:

root developmental stages, PO:0007520
    (i) 1 root primordium formation, PO:0007505
    (i) 2 root meristem formation, PO:0007527
    (i) 3 establishment of tissue systems, PO:0007525
    (i) 4 root elongation, PO:0001031
    (i) 5 root hair formation, PO:0007519

Seed development stages

Similar to the flower development stages node, general progression of seed development is described, as well as developmental stages of seed parts (endosperm and embryo), which are included as children nodes. The exception is the seed coat (not represented in this ontology) - due to the complex and variable nature of its development. It was difficult to define the common stages for species with single integument vs. those with inner and outer integument, and also stages that would be common for monocot (for instance, grasses) and eudicots.

Stages of embryo development are based on classic studies of model plant species (Arabidopsis and Capsella), reviewed by West and Harada (1993), and in cereal crops, maize (Abbe and Stein, 1954, Sheridan and Clark, 1987) and rice (Itoh et al, 2005) in particular. Endosperm development stages are based on descriptions of free-nuclear endosperm development in Arabidopsis and cereals (Olsen, 2004), also taking into consideration endosperm patterning in both persistent and transient endosperms (Costa et al, 2004).

Whole plant development stages

Whole plant development stages are described in more detail on a separate page.

References