POC Conf. Call 4-19-11
POC meeting, Webex Conference Call; Date: Tuesday Apr 19th, 2011 10am (PDT)
In attendance:
POC members:
Absent:
Collaborators:
Acceptance of the minutes from the POC_Conf._Call_4-12-11?
Issues arising from last week's meeting:
gametophytic phase and sporophytic phase
sporophytic phase (PO:0028002)
Current definition: A plant life cycle phase that is the product of fertilization. [source: POC:rw]
Comment: During the sporophtyic phase, a plant may produce meiospores by meiosis.
Proposed definition: A plant life cycle phase (or a whole plant growth stage) that begins with fertilization or the division of a non-fertilized embryogenic cell.
Comment: During the sporophtyic phase, a plant may produce meiospores by meiosis. A whole plant in the sporophytic phase usually has twice the chromosome complement of a plant in the gametophytic phase, but not in the case of apogamy or in vitro culture of haploid embryos.
gametophytic phase (PO:0028003)
Current definition: A plant life cycle phase that arises through meiosis. [source: POC:rw]
Comment: During the gametophytic phase, a plant may produce gametes by mitosis.
Proposed definition: A plant life cycle phase (or a whole plant growth stage) that begins with meiosis.
Comment: During the gametophytic phase, a plant may produce gametes by mitosis. In bryophytes and pteridophytes, a gametophytic phase may begin without meiosis by apospory, when damage to a plant in the sporophytic phase leads directly to the growth of a plant that is in the gametophytic phase but bears the chromosome complement that would normally be found in the sporophytic phase. A whole plant in the gametophytic phase usually has half the chromosome complement of a plant in the sporophytic phase, but not in the case of apospory.
Collective plant structures:
vascular and non-vascular shoot systems
The Moss Ontology did not request these terms, but suggest adding them in order to classify shoot systems.
non-vascular shoot system (PO:0030017): A shoot system that does not have as part vascular tissue.
comment: Does not have any xylem of phloem, but may have other conducting cells, such hydroids or leptoids. Can occur in both the gametophytic and sporophytic phases of non-vascular plants.
subsets for bryophytes
Could we use the relation "lacks_part"? Then we could define this class using intersection_of relations, which would be better. CL has used this (lack_plasma_membrane_part). Works better in OWL; translates into something like has_part exactly 0 (some Y).
Child of non-vascular shoot system will be gametophore (see below). A moss sprophyte could also be called a non-vascular shoot system. If we used the lacks_part relation and intersection_of relations, we could make gameotophore a child of shoot system, and the reasoner would infer it was a non-vascular shoot system.
Can't use participates_in gametophytic phase, because the sporophyte of a bryophyte might also be considered a non-vascular shoot system.
vascular shoot system (PO:0030016): A shoot system that has as part vascular tissue.
comment: Has xylem and/or phloem. Occurs only in the sporophytic phase of vascular plants.
participates_in sporophytic phase, has_part vascular system
If we accept these terms, suggest changing definitions of vascular leaf (PO:0009025) and non-vascular leaf (PO:0025075) to "A leaf that is part of a vascular/non-vascular shoot system. This would be better than the current definitions which reference their taxonomy (part of a vascular or non-vascular plant) and would help with reasoning.
root-bourne shoot system (PO:0004544) should be is_a vascular shoot system
gametophore (PO:0030018)
Definition supplied by Moss Ontology: The leafy moss plant. The gametophore is the adult form of the moss gametophyte and bearer of the sex organs (gametangia). Ref: Reski (1998): Development, genetics and molecular biology of mosses. Botanica Acta 111, 1-15.
Suggest is_a shoot system.
Proposed def.: A non-vascular shoot system that consists of the shoot axes and non-vascular leaves of a plant in the gametophytic phase.
participates_in gametophytic phase, develops_from gametophore bud
Comment: A gametophore is the leafy part of the gametophyte of mosses and leafy liverworts, excluding the protonema. Develop from buds that form on the protonema. Antheridia and archegonia arise on the gametophore.
subset for bryophytes
gametophore bud (PO:0030026)
The term "bud" has been requested: Def'n supplied by Moss Ontology: A structure produced by a caulonema and able to develop into a gametophore or a stem that includes an apical cell able to develop into a gametophore. The earliest recognizable stage of gametophore development. Ref: Bill and Nancy Malcolm (2006): Mosses and other Bryophytes, an illustrated glossary, second edition and altered by David Cove
Suggest a new term gametophore bud. This could be a child of bud (PO:0000055: An undeveloped shoot system).
Proposed def'n: A vegetative bud that develops into a gametophore.
Comment: Occurs in mosses and leafy liverworts. Develops from a caulonema cell in mosses.
participates_in gametophytic phase, has_part gametophore apical cell
synonym: brown bud
thallus (PO:0030027)
From Parihar: A simple vegetative plant body not differentiated into root, stem and leaf, and lacking vascular tissues.
From Schofeld: A flattened gametophore in which no leaf-like organs dominate the structure.
Saying a thallus is a gametophore implies that it is a shoot system and therefore a collective plant structure (CPS). As a CPS, it must have more that one organ. This is not true for a thallus (sometime they branch, so you could say they have multiple axes, but it is a stretch. Maybe better to classify it as a whole plant.
proposed def: A whole plant in the gametophytic phase that has a flat growth form and no distinct organs.
Comment: A thallus is a gametophyte of liverworts and pteridophytes and develops from a short-lived protonema. Roughly two dimensional growth results from division of a single apical cell. Thalli may be ribbon or heart shaped or almost filamentous. Although there are no distinct organs, there may be tissue differentiation and dichotomous branching.
Add prothallium as a broad synonym of thallus and as a narrow synonym of whole plant.
Other gametophyte terms
We need to keep in mind terms for other types of gametophytes, such as the subterranean, heterotrophic gametophytes of some ferns. RW, DWS, and MAG will maintain a list of terms that we don't need to add yet, but may want to add as time allows or need demands. Can use this list, for example, for writing a renewal of things that still need to be done.
apical cell
Moss Ontology has requested the term apical cell. Apical growth in byrophytes is via division of a single cell at the tip of the shoot apical meristem. They also requested shoot apical cell and phyllid apical cell.
Non-seed vascular plants can also have an apical cell, that is, a single dividing cell at the apex of a root or shoot.
We already have the term apical cell (PO:0004000), which is an embryonic cell: "An embryonic plant cell that is the uppermost cell formed after the first division of the zygote." The embryonic apical cell can also be found in non-angiosperms. Suggest obsoleting PO:0004000 and replacing it with the new termembryonic apical cell for clarity, and using the name apical cell for the general class of apical cells described below.
Definition of apical cell from Esau: The single initial cell in an apical meristem of root or shoot. Characteristic of many lower vascular plants.
Definition of apical cell from Crum: A single cell at the tip of a stem, leaf, leaf or other structure that divides repeatedly to form new cells; also known as an apical intial.
Is apical cell more consistent with meristematic cell (A cell synthesizing protoplasm and producing new cells by division and with only a primary cell wall) or with initial cell (A meristematic cell that by division gives rise to two cells, one of which remains meristematic, while the other is added to the plant body)? Probably meristematic cell, because the apical cell can give rise to more than two cells (because it can have three or four cutting faces).
Proposed def. of apical cell (PO:0030007): A single meristematic cell at the tip of a shoot axis apex, leaf apex, root apex, or thallus apex.
Comment: Occurs in bryophytes and some pteridophytes, where apical growth results from division of a single meristematic cell located at the tip of an apical meristem or plant organ, rather than from a population of meristematic cells located at the tip of an apical meristem. May be tetrahedral shaped, with three (in shoots) or four (in roots) cutting faces, or wedge shaped with two cutting faces (in non-vascular leaves or thalli). An apical cell maybe established upon germination of a spore or upon the first cell division of an embryo or later.
-note: the last sentence of the comment allows us to classify an embryonic apical cell as an apical cell.
Suggested ontology structure for the children of apical cell:
The dotted lines represent relations inferred by the reasoner.
Includes two ways of classifying: by structure and by gametophyte/sporophyte. Structural relations are asserted as is_a relations. The relations to gametophyte or sporophyte are inferred by the intersection_of terms.
New terms and definitions for apical cells
gametophytic apical cell (PO:0030014): An apical cell that is part of a whole plant in the gametophytic phase.
Comment: Occurs bryophytes and pteridophytes.
intersection_of: is_a apical cell, intersection_of: participates_in gametophytic phase
sporophytic apical cell (PO:0030015): An apical cell that is part of a whole plant in the sporophytic phase.
Comment: Occurs in pteridophytes and the sporophyte of bryophytes.
intersection_of: is_a apical cell, intersection_of: participates_in sporophytic phase
thallus apical cell (PO:0030025): An apical cell that is part of a thallus.
part_of thallus
root apical cell (PO:0030008): A sporophytic apical cell that is part of a root apical meristem.
comment: Occurs in the sporophytic phase of pteridophytes.
part_of root apical meristem
shoot apical cell (PO:0030009): An apical cell that is part of a shoot system.
comment: May occur in shoot axes or leaves of bryophytes or ferns.
part_of shoot system
gametophore apical cell (PO:0030019): A shoot apical cell that is part of a gametophore.
comment: Occurs in the non-vascular shoot system of the gametophyte of mosses.
intersection_of: is_a shoot apical cell, intersection_of: part_of gametophore
leaf apical cell (PO:0030011): A shoot apical cell that is part of a leaf apex.
comment: Occurs in the non-vascular leaves of bryophytes and the vascular leaves of some ferns. Only in plants where leaf growth is apical.
part_of leaf
non-vascular leaf apical cell (PO:0030013): A leaf apical cell that is part of a leaf apex of a non-vascular leaf.
comment: Occurs in the non-vascular leaves of bryophytes, which grow by division of a single, wedge-shaped apical cell with two cutting faces.
part_of non-vasucular leaf; synonym: phyllid apical cell
vascular leaf apical cell (PO:0030012): A leaf apical cell that is part of the leaf apex of a vascular leaf.
comment: Occurs in vascular leaves of some ferns in their sporophytic phase.
part_of vascular leaf
shoot axis apical cell (PO:0030010): An apical cell at the tip of a shoot apical meristem.
Comment: Divides to produces leaf initial cells and other stem tissues.
part_of shoot apical meristem
gametophore axis apical cell (PO:0030023): A shoot axis apical cell at the tip of a gametophore axis.
Comment: Occurs at the tips of the stems and branches of bryophytes.
part_of gametophore axis; synonym: cauloid apical cell, non-vascular shoot axis apical cell
vascular shoot axis apical cell (PO:0030024): A shoot axis apical cell at the tip of a shoot apical meristem in a vascular shoot system.
Comment: Occurs in some ferns in their sporophytic phase.
part_of vascular_shoot system; synonym: fern shoot axis apical cell
Also:
embryonic apical cell (PO:0025284, replaces PO:0004000): An apical cell that is part of an embryo and is the uppermost cell formed after the first division of a zygote.
Comment: For plants that grow via an apical cell in their sporophytic phase, the embryonic apical cell may remain meristematic throughout the plant's life.
Plant organs:
cauloid
- This is the term used for the gametophore stem or axis.
Suggest using gametophore axis (PO:0030020) as primary name, cauloid as synonym.
Proposed def'n: A shoot axis that is part of a gametophore.
Synonyms: cauloid, gametophyte axis, non-vascular shoot axis (broad, because it can also apply to the seta); participates_in gametophytic phase.
intersection_of: is_a plant axis, intersection_of: part_of gametophore
Add caulome as synonym of shoot axis
-Also suggest adding terms for gametophore stem and gametophore branch.
gametophore stem (PO:0030022): A stem that is part of a gametophore.
is_a stem, part_of gametophore
gametophore branch (PO:0030021): A branch that is part of a gametophore.
is_a branch, part_of gametophore
-If the intersection_of relations are asserted in the end user's version (e.g. Amigo), users will see dual parentage (is_a gametophore axis and is_a stem or branch).
perigonial bract (PO:0030028)
- The specialized phyllids surrounding the antheridia.
Ref: Bill and Nancy Malcolm (2006): Mosses and other Bryophytes, an illustrated glossary, second edition (MO definition)
A bract (PO:0009055) is defined as: A phyllome, usually different in form from the foliage leaves, subtending a reproductive structure. [source: POC:curators] Comment: Often used to refer to what is called here floral bract.
Proposed def'n: A bract that subtends an antheridium.
part_of gametophore, participates in gametophytic phase
Comment: When an antheridium occurs on a specialized lateral branch of the gametophore, all of the phyllomes on that branch are usually perigonial bracts. If an antheridium occurs on a main axis of the gametophore, usually only the terminal phyllomes are perigonial bracts.
foot
Moss Ontology definition: The base of the sporophytes in mosses
Proposed name and def.: sporophyte foot (PO:0030029): A plant organ that is the base of a whole plant in the sporophytic phase and attaches it to the gametophore. (ref: Schofeld)
Comment: Found in bryophytes and some pteridophytes. In mosses, the foot is located below the seta. In ferns, the foot is formed from the upper hypobasal quandrant of the embryo. The sporophyte foot serves for both attachment and absorption. The outer portion of the foot is composed of absorptive transfer cells. (ref: Crum)
participates_in sporophytic phase, has_part transfer cell
These were not requested by the Physcomitrella group, but they are related to the terms above and are commonly used to describe mosses, so we should add them now.
perichaetal bract (PO:0030030)
Proposed def.: A bract that subtends an archegonium. part_of gametophore
Comment: When an archegonium occurs on a specialized lateral branch of the gametophore, all of the phyllomes on that branch are usually parichaetal bracts. If an archegonium occurs on a main axis of the gametophore, only the terminal phyllomes are usually parichaetal bracts. The two or three terminal-most perichaetal bracts may fuse to form a gametophytic perianth.
gametophytic perianth (PO:0030031)
Proposed def.: A collective phyllome structure that consists of two or more of the most distal perichaetal bracts on a gametophore axis and surround a capsule.
-has_part parachaetal bract, part_of gametophore, disjoint_from perianth (PO:0009058)
Comment: The perichaetal bracts may fuse laterally in the gametophytic perianth. The gametophytic perianth is not the same structure as a perianth (PO:0009058) in angiosperms.
seta (PO:0030032)
-The stalk of a moss sporophyte.
Proposed def.: A plant axis that holds up a spore capsule. participates_in sporophytic phase
Comment: Found in some bryophytes, especially mosses.
antheridiophore and archegoniophore
These are stalks that hold up the antheridia or archegonia in Marchantiales (liverworts)
Proposed definitions:
antheridiophore (PO:0030033): A plant axis that bears two or more antheridia.
participates_in gametophytic phase
Comment: Antheridia are borne on a disk-shaped archegonial head. Found in Marchantiales.
archegoniophore (PO:0030034): A plant axis that bears two or more archegonia.
participates_in gametophytic phase
Comment: Archegonia are borne on an umbrella-shaped archegonial head. Found in Marchantiales.
Will also add terms for antheridium stalk (PO:0030035) and archegonium stalk (PO:0030036):
A stalk that the basal part of an antheridium/archegonium. part_of antheridium or archegonium.
Comment: Raises the antheridium/venter above the rest of the gametophyte.
Cardinal organ parts
Terms requested by MO:
Moss Ontology definition: A membranous or hairy cap or hood that forms from the wall of the archegonium and protects the embryonic sporophyte. It is formed from the archegonium by mitotic divisions, and hence it is haploid. Bill and Nancy Malcolm (2006): Mosses and other Bryophytes, an illustrated glossary, second edition and altered from David Cove.
We also have a request (from PJ) for calyptra, which encloses the fruit in Eucalyptus. That term should be named perianth calyptra (see below under operculum), and this term should be named spore capsule calyptra, to distinguish them.
Proposed name and def.: spore capsule calyptra: A cardinal organ part that develops from the wall of an archegonium and surrounds a sporangium.
Comment: Found in bryophytes and pteridophytes (according to Parihar). The calyptra ia a membranous or hairy cap or hood composed of gametophytic tissue that protects the embryonic sporophyte within the archegonium. In some species, the calyptra may persist after the sporophyte develops and gets carried upward as the seta elongates.
participates_in gametophytic phase, develops_from venter (more specific) or archegonium (more general)?
subsets for bryophytes, pteridophytes
[From Smith p. 39: calyptra develops from venter in Corsiniaceae (also has an involucre); also p. 52, p. 67, See picture on p. 77
This term was not suggested by Moss Ontology, but perhaps we should add it.
proposed def.: A cardinal organ part that is the enlarged basal part of an archegonium and has an egg cell located in it.
part_of archegonium
subsets for bryophytes, pteridophytes, gymnosperms
This term was not suggested by Moss Ontology, but perhaps we should add it.
proposed def.: A cardinal organ part that is the elongated apica part of an archegonium.
Comment: Early in development, the neck is occluded by a single row of neck canal cells. At maturity, the neck canal cells disintegrate, creating a canal for the sperm to enter the archegonium.
part_of archegonium
(can also add term for neck canal cell when we deal with cells)
subsets for bryophytes, pteridophytes, gymnosperms
Proposed name and def.: sporangium base: A cardinal organ part that is the basal part of a sporangium.
Comment: Term used in mosses and other bryophytes (what about pteridophytes?). The sporangium base is the sterile part of the sporangium below the theca. If swollen and distinct from the rest of the sporangium, it is called an apophysis or hypophysis. (ref: Bill and Nancy Malcolm (2006): Mosses and other Bryophytes, an illustrated glossary, second edition)
part_of sporangium; Synonyms: sporangium neck, apophysis, hypophysis
subsets for bryophytes
Moss Ontology definition: The main body (urn) of a sporangium. Altered from Bill and Nancy Malcolm (2006): Mosses and other Bryophytes, an illustrated glossary, second edition
We already have the term theca (PO:0009069) to describe paired microsporangia in angiosperms. Maybe we should call that anther theca and call this term sporangium theca:.
Proposed name and def.: sporangium theca: A cardinal organ part that is the main body of a sporangium and has spores located in it.
Comment: Term used in mosses and other bryophytes (what about pteridophytes?)
part_of sporangium
subsets for bryophytes, maybe pteridophytes
Moss Ontology definition: A single or double circle of teeth inside the mouth of a moss sporangium. Bill and Nancy Malcolm (2006): Mosses and other Bryophytes, an illustrated glossary, second edition
proposed definition: A cardinal organ part that is a single or double circle of teeth inside a spore capsule mouth.
Comment: The peristome is located under the operculum, if an operculum is present. Upon maturity of a capsule, the teeth of the peristome open to release the spores.
part_of sporangium
subsets for bryophytes
- peristome tooth
Not requested by Moss Ontology, but should add it.
Proposed def: A cardinal organ part that is a single lobe or tooth of a peristome.
Comment: Peristome teeth may be simple or compound, and may be attached by their tips to the epiphragm.
part_of peristome
subsets for bryophytes
- Add term for peristome cell? Are they dead at maturity? What kind of cells are they?
Moss Ontology definition: Either the lid that blocks the capsule mouth or the apical portion of a sporangium that opens during dehiscence. Bill and Nancy Malcolm (2006): Mosses and other Bryophytes, an illustrated glossary, second edition.
We also have a request (from PJ) for operculum, which is part of the fruit in Eucalyptus. That term should be named fruit operculum, and this term should be named spore capsule operculum, to distinguish them.
Proposed name and def.: spore capsule operculum: A cardinal organ part that is the apical part of a spore capsule that separates from the rest of the capsule during dehiscence.
Comment: Found in mosses. May remain partly attached to the rest of the capsule.
Synonym: sporangium lid
part_of sporangium
subsets for bryophytes
Also add these terms for angiosperms:
fruit operculum: A collective organ part structure that is the apical part of a circumsesile capsular fruit that separates from the rest of the capsule during dehiscence.
Comment: Develops from the apical portion of a gynoecium. Found in Eucalyptus and other Myrtaceae.
part_of fruit
Is is a cardinal organ part (formed from a single carpel) or collective organ part structure (formed from parts of multiple carpels)?
perianth calyptra: A perianth that is composed of fused perianth parts and located on tops of a gynoecium that contains an inferior ovary.
Comment: May be composed of fused petals, sepals or tepals, but is generally formed from fused petals in Eucalyptus and other Myrtaceae. May separate from the plant at maturity, exposing the capsular fruit and fruit operculum. Sometimes erroneously referred to as part of a fruit.
Proposed definition: A plant anatomical space that is the opening on the apical end of a spore capsule.
Comment: The mouth is formed when the operculum separates from the capsule. The mouth may be covered by a peristome.
part_of sporangium
subsets for bryophytes
Schofeld says it is a "membranelike expansion of the columella covering most of the mouth of the sporangium in Polytrichidae (hair cap mosses)."
From Crum: "A circular membrane at the tip of the columella to which the peristome teeth of the prolytrichaceae are attached."
Proposed definition: A portion of parenchyma tissue that forms a circular membrane extending from a spore capsule collumella and attached to the ends of the peristome teeth that covers a spore capsule mouth.
Comment: Present in some moss species of the family Polytrichaceae.
Synonym: tympanum, epiphram
subsets for bryophytes
From Crum: "An elongation of the gametophytic axis on which the capsule is borne in Sphagnum and Andreaea."
From Schofeld: "An elongated mass of leafless gametophore tissue that pushes the sporophyte beyond the perichaetial leaves (in Andreaea and Sphagnum)."
Proposed definition: A plant axis that is a leafless extension of a gametophore axis on which a sporophyte is borne.
Comment: Raises the sporophyte above the perichaetial bracts. Found in Sphagnum and Andreaea.
participates_in gametophytic phase
subsets for bryophytes
