From Plant Ontology Wiki
Summary and Announcements
The latest release of the Plant Ontology, version #20, is available on our Plant Ontology Browser.
This full release features the addition of 48 new terms, for both the Plant Anatomical Entity (44) and Plant Structure Development Stage (4) branches.
- This Release also includes new and updated annotation data for:
- Additional annotation data was contributed by our collaborators for cotton (Gossypium hirsutum); (AgBase) and Arabidopsis thaliana. (TAIR).
- Includes all revisions of the Plant Ontology from Revision #1761 to 2199- available on the SVN Site
-For more information, please see also: Details_of_Changes_to_Release_20
The release features revision to the following sections:
Major Revisions to the plant anatomical entity branch:
- New terms were added to describe the parts of the perianth (PO:0009058), specifically to describe the different forms of a fused perianth (PO:0025880), such as that found in Musa flowers.
- Thirteen new terms were added to describe the different types of protoxylem (PO:0000272) tissue in the roots and shoots of vascular plants.
- A term was created for plant sap (PO:0025538) and six sub-classes were added to specify from which part of the plant the sap was collected.
- We revised the existing tapetum cell (PO:0025543) (was 'tapetal cell') and added three child terms to specify the different types. In collaboration with the Gene Ontology, the corresponding GO biological process terms (anther wall tapetum cell differentiation; GO:0048657 and anther wall tapetum cell fate specification; GO:0010234) were also revised to match.
- Inflorescence branch (PO:0009081) and its child terms were extensively revised. The existing term paraclade (PO:0004720) was merged into primary inflorescence branch (PO:0006321) and three new child terms were created the describe different types of paraclades: accessory paraclade (PO:0025546); cauline paraclade (PO:0025547); rosette paraclade (PO:0025548).
- All the children of inflorescence branch (PO:0009081) designating the different branching orders (primary, secondary etc) were renamed from xxx inflorescence axis to xxx inflorescence branch.
- All the children of infructescence branch (PO:0025243) designating the different branching orders (primary, secondary etc) were renamed from xxx infructescence axis to xxx infructescence branch.
- trichome PO:0000282 terms:
- Two new direct children of plant structure (PO:0009011) were added to describe the apical regions of different types of trichome (PO:0000282): trichome apex (new PO:0025550) and trichome tip (new PO:0025549). These have this unusual parentage since they can be part of a multicellular trichome (PO:0000282) (making them a 'portion of plant tissue (PO:0009007)', or part of a unicellular trichome (new PO:0025537), in which case they are a GO cellular component: unicellular trichome apex (GO:0090552) or unicellular trichome tip (GO:0090553).
We also added the subclasses: multicellular trichome apex (new PO:0025551) and multicellular trichome tip (PO:0025535) and a new term was added to describe a unicellular trichome (new PO:0025537).
- For additional minor revisions, please see: Details_of_Changes_to_Release_20
Revisions to the plant structure development stage branch
- Major revisions were made to flower development stage (PO:0007615) and its sub-classes. The five existing sub-classes which were revised into a new set of three classes and sub-classes which better describe flower development across flowering plants.
- A new term flower meristem transition stage (PO:0025588) was added to describe the transition of the meristem from a vegetative to reproductive state.
- The second stage is the floral organ formation stage (PO:0025585) which encompasses three sub-classes (formerly direct children of flower development stage (PO:0007615)) and ends with the onset of the flowering stage (PO:0025586).
- Sub-classes- Renamed terms:
- floral organ meristem development stage (PO:0007601); was: 1 flower meristem visible stage
- floral organ primordium development stage (PO:0007602); was: 2 flower meristem notched stage
- floral organ differentiation stage (PO:0007600); was: 3 floral organ development stage
- Sub-classes- Renamed terms:
- The new third stage is the flowering stage (PO:0007616) which was formerly called 4 anthesis stage. The flowering stage begins when pollen is released by anther dehiscence (GO:0009901) and/or the stigma (PO:0009073) is receptive and ends with the process of pollination (GO:0009856), and/or floral organ senescence (GO:0080187).
- The new flowering stage (PO:0007616) also encompasses 5 post anthesis stage (PO:0007617) which was merged into it. Although the term 'post-anthesis' is widely used in the plant science literature, we felt it was not clearly defined as to what processes were occurring. Annotations on 5 post anthesis stage (PO:0007617) were moved to the new flowering stage (PO:0007616) term.
New relation added to order the stages
A new relation "preceded_by" was added to the Plant Ontology in order to order the plant structure development stages.
This was used in the revision of the flower development stages, as shown below:
You can find more details about the new 'preceded_by' relation on the Relations_in_the_Plant_Ontology wiki page.
Other new PSDS terms
- collective phyllome structure development stage (PO:0025578): A collective plant organ structure development stage (PO:0025338) that has as primary participant collective phyllome structure (PO:0025023).
- phyllome development stage (PO:0025579): A plant organ development stage (PO:0025339) that has a primary participant a phyllome (PO:0025023).
List of species with annotation data in release #20
Oryza sativa (Rice)
Zea mays (maize, corn)
Lycopersicon esculentum (tomato)
Solanum insanum/Solanum melongena (eggplant)
Fragaria vesca (strawberry)
Vitis vinifera (grape)
Gossypium hirsutum (cotton)
Other Solanum species:
- Anisodus acutangulus
- Atropa baetica
- Capsicum annuum (pepper)
- Coffea arabica (coffee)
- Datura strumonium (jimson weed)
- Hyoscyamus niger (black henbane)
- Nicotiana tabacum (tobacco)
- Petunia hybrida (hybrid petunia)
- Physalis spp
- Solanum chmielewskii
- Solanum pennellii
- Solanum tuberosum (potato)