Goal 2. Plant Structure Development Stages

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Back to Wood_anatomy_ontology_meeting,_2012_at_NYBG,_agenda

Contents

1. Review existing development stage terms and definitions

Devlopment stage branch of PO mirrors the plant structure branch of the PO:

File:top_level_PO1.jpg

Example of how development stages are organized:

seed trichome development stages: File:seed_trichome_dev_stage.jpg

seed trichome development stage (PO:0025371): A trichome development stage that has as primary participant a seed trichome.

comment: Seed trichome development stage consists of the following sub stages: seed trichome initiation stage (PO:0025370), seed trichome elongation stage (PO:0025371), seed trichome secondary wall biosynthesis stage(PO:0025372) and seed trichome maturation stage (PO:0025373).


seed trichome elongation stage (PO:0025371): A seed trichome development stage which occurs during the interval between the onset of seed trichome elongation and the onset of seed trichome secondary wall biosynthesis.

comment: Refers to the GO Biological Process terms: seed trichome elongation (GO:0090378) and secondary cell wall biogenesis involved in seed trichome differentiation (GO:0090379).

Development stages as a timeline

is_a and part_of/has_part relations for development stages

Example: seed dormant stage has_part embryo dormant stage

2. Develop list of development stage terms that are missing

secondary xylem development stages - see below for terms and definitions. See paper by Junika 87

secondary phloem development stage - see below for definition

bark development stage - no definition was developed at the meeting

cambial dormant stage

add whole plant growth stages for climbing plants:

unsupported stage - A whole plant growth stage before the plant reaches a support. Plant does not twine or use other special means of support during this stage.

supported stage - A whole plant growth stage during which a plant uses twining or other specialized means of support.


pendulous (this is a growth form, not a stage, although some epiphytes may go through an upright and a pendulous stage)


> early wood stage

> late wood stage


tentative suggestions, can come back to them if need arises:

primary xylem development stages


shoot axis or stem development stages

3. Work on definitions of new terms

secondary phloem development stage

def.: A vascular tissue development stage that has as primary participant a portion of secondary phloem.

comment: During a secondary phloem development stage, the cells of secondary phloem (PO:0005043), including sieve elements (PO:0025406), phloem fiber cells (PO:0004519), and parenchyma cells (PO:0000074), undergo cellular developmental processes (GO:0048869) such as cell division (GO:0051301), cell growth (GO:0016049), cell differentiation (GO:0030154), or cell death (GO:0008219).

We will work on subtypes of this stage in the future.


wood development stages

Proposed definitions.

secondary xylem development stage

def.: A vascular tissue development stage that has as primary participant a portion of secondary xylem during the interval between the beginning of a cell division stage of secondary xylem (PO:id) and the death of the last living cell in the secondary xylem.

comment: During a secondary xylem development stage (also called a wood development stage), the cells of secondary xylem (PO:0005848), including tracheary elements (PO:0000290), xylem fiber cells (PO:0000274), and wood parenchyma cells (PO:0004525) undergo cellular developmental processes (GO:0048869) such as cell division (GO:0051301), cell growth (GO:0016049), cell differentiation (GO:0030154), or cell death (GO:0008219). The transition from sapwood to heartwood marks the end of secondary xylem development.

synonyms: wood development stage, sapwood development stage

Note: The stages below are not stages of a secondary xylem cell, but a stage of secondary xylem tissue that is defined by what its cells are doing. We don't need stages for cell types, because one could just use the GO:process that the cell is undergoing.


>cell division stage of secondary xylem

Def.: A secondary xylem development stage (PO:id) that occurs during the interval between the first and last cell division in a portion of secondary xylem tissue (PO:0005848), during which cells are produced by divisions of cambial initials (PO:0000295) or xylem mother cells (PO:id).

Comment: This stage includes production of xylem mother cells by cambial initials and production of tracheary elements (PO:0000290) or other cells by xylem mother cells. Precedes a cell differentiation stage of secondary xylem (PO:id), although cell differentiation may begin before a cell division stage of secondary xylem ends.


>cell differentiation stage of secondary xylem

Def.: A secondary xylem development stage (PO:id) that occurs during the interval between the end of a cell division stage of secondary xylem (PO:id) and the death of the last living cell in the secondary xylem.

Comment: During a this stage, cells of secondary xylem undergo cell differentiation (GO:0030154), including cell growth (GO:0016049), cell morphogenisis (GO:0000902), or cell death (GO:0008219). Cell death is considered part of differentiation in secondary xylem, because it is an essential part of wood development. This stage succeeds the last cell division in a cell division stage of secondary xylem, even though cell differentiation may begin before all cell division finishes.


> >cell expansion stage of secondary xylem

Def.: A cell differentiation stage of secondary xylem (PO:id) that occurs during the interval between between the end of a cell division stage of secondary xylem (PO:id) and the onset of a secondary cell wall formation stage of secondary xylem (PO:id), and during which the cells undergo cell growth (GO:0016049).

Comment: This stage succeeds a cell division stage of secondary xylem (PO:id) and precedes secondary cell wall biogenesis (GO:0009834).


> >secondary cell wall formation stage of secondary xylem

Def.: A cell differentiation stage of secondary xylem (PO:id) that occurs during the interval between the onset of secondary wall biogenesis (GO:0009834) of the cells in a portion of secondary xylem and the beginning of a cell death stage of secondary xylem (PO:id).

Comment: During this stage, secondary cell walls (GO:0009531) are being formed in a portion of secondary xylem tissue, preventing further expansion of the cells. This stage succeeds a cell expansion stage of secondary xylem (PO:id) and precedes a cell death stage of secondary xylem (PO:id).


> >cell death stage of secondary xylem

Def.: A cell differentiation stage of secondary xylem (PO:id) that occurs during the interval between the first cell death of a tracheary element (PO:0000290) or non-septate fiber and the death of the last wood parenchyma cell or septate fiber in a portion of secondary xylem (PO:0005848).

Comment: During this stage, cells of a portion of secondary xylem are undergoing cell death (GO:0008219), sometimes called apoptosis. Death of the tracheary elements and non-spetate xylem fibers generally precedes the death of wood parenchyma cells and septate xylem fiber cells. Once all cells in portion of secondary xylem are dead, it transitions from sapwood to heartwood, and wood development ends.

synonym: transition to heartwood stage


> > >tracheary element death stage of secondary xylem

Def.: A cell death stage of secondary xylem (PO:id) that occurs during the interval between the first and last cell death of a tracheary element (PO:0000290) or non-septate xylem fiber cell.

Comment: During this stage, the tracheary elements and non-septate xylem fiber cells of a portion of secondary xylem (PO:0005848) undergo cell death (GO:0008219), but most of the wood parenchyma cells (PO:0004525) and septate xylem fiber cells (septate fiber tracheids,PO:0025419, and septate libriform fibers, PO:0025420) remain alive. Precedes a wood parenchyma cell death stage of secondary xylem (PO:id).


> > >wood parenchyma cell death stage of secondary xylem

Def.: A cell death stage of secondary xylem (PO:id) that occurs during the interval between the last cell death of a tracheary element (PO:0000290) or non-septate xylem fiber cell and the last cell death in a portion of secondary xylem (PO:0005848).

Comment: During this stage, the wood parenchyma cells and septate xylem fiber cells (septate fiber tracheids,PO:0025419, and septate libriform fibers, PO:0025420) of a portion of secondary xylem (PO:0005848) undergo cell death (GO:0008219). Succeeds a tracheary element death stage of secondary xylem (PO:id). Once all cells in portion of secondary xylem are dead, it transitions from sapwood to heartwood, and wood development ends.

juvenile and mature wood stage

not sure if these should be development stages or types of wood

core wood (syn. corewood, juvenile wood, crown-formed wood, crown wood) A portion of secondary xylem that has large, usually directional annual changes in anatomy along the radial direction. Begins adjacent to the primary xylem, ends at outer wood, or transition wood if appropriate.

Comments: Usually refers to coniferous woods. Independent of sapwood or heartwood stage.

Forms closer apical meristem (for up to many years) than outer wood.


outer wood (syn. outerwood, mature wood) The secondary xylem that has insignificant or small directional annual changes in anatomy along the radial direction. Begins adjacent to the core wood or transition wood if appropriate, and ends at the vascular cambium.

Comments: Term used mostly for conifers. Independent of sapwood or heartwood stage.


transition wood The zone of secondary xylem that is located between the core wood and the outer wood.


transition age from core wood to outer wood The cambial age at which adjacent growth rings are corewood and outer wood.

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IN DISCUSSION