Release 20

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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).


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
  • 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:

File:Preceded_by.png

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

Arabidopsis thaliana

Oryza sativa (Rice)

Zea mays (maize, corn)

Lycopersicon esculentum (tomato)

Solanum insanum/Solanum melongena (eggplant)

Fragaria vesca (strawberry)

Physcomitrella patens

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)
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