POC Conf. Call 4-26-11
POC meeting, Webex Conference Call; Date: Tuesday Apr 26th, 2011 10am (PDT)
In attendance:
POC members:
Absent:
Collaborators:
Acceptance of the minutes from the POC_Conf._Call_4-19-11?
Issues arising from last week's meeting:
Sporangium
We currently have the class sporangium (PO:0025094), which is a cardinal organ part.
Current def: A hollow cardinal organ part in which spores are produced. [source: ISBN:0716710072]
Comment: May be multicellular or unicellular. In bryophytes, particularly in mosses, a sporangium is referred to as a capsule
In bryophytes, the sporangium is a plant organ. In seed plants, it is a cardinal organ part (part of a sporophyll). In ferns, it grows on the surface of a leaf and in other pteridophytes is grows on the surface of a sporophyll. Would it be legitimate to say that in seed plants, the sporangium is a reduced organ that is located in another organ? If so, could change the parent to plant organ.
Is it really hollow? It is full of sporocytes or spores.
Proposed definition: A plant organ in which spores are produced.
Comment: In bryophytes, particularly in mosses, a sporangium is referred to as a capsule. In seed plants, a sporangium is located in a sporophyll. In pteridophytes, a sporangium is located on the surface of a sporophyll or fertile leaf or borne on a sporangiophore. May unicellular in some algae.
We also have:
megasporangium (PO:0025201): A sporangium in which megaspores are produced. [source: ISBN:0716710072]
microsporangium (PO:0025202): A sporangium in which microspores are produced. [source: ISBN:0716710072]
nucellus (PO:0020020): A megasporangium in a seed plant, composed of fleshy subepidermal tissue inside an ovule and surrounding a megasporocyte. [source: POC:rw]
Comment: In seed plants, the megaspores and megagametophyte are retained within the nucellus.
pollen sac (PO:0025277): A microsporangium that is part of a sporophyll where the pollen grains developed and are contained after they develop. [source: POC:curators]
Comment: A pollen sac is a microsporangium in seed plants. In angiosperms, a single, unfused pollen sac may contain an anther locule or several pollen sacs may fuse so they contain a single anther locule.
Proposed def. nucellus: A megasporangium in a seed plant, composed of fleshy subepidermal tissue located in an ovule and surrounding a megasporocyte.
Proposed def. pollen sac: A microsporangium that is located in a sporophyll and where the pollen grains developed and are located after they develop. [source: POC:curators]
(comments stay the same)
We could continue to use the more general part_of relation for located_in, if we don't want to add a new relation.
Plant Cells
Terms requested by Moss Ontology:
archesporial cell
We have the terms:
female archesporial cell (PO:0006015): In the majority of flowering plants including Arabidopsis, the female archesporial cell elongates and polarizes longitudinally, and directly differentiates into the megasporocyte or megaspore mother cell (MMC). In some flowering plants, it undergoes a periclinal division, and subsequently the inner cell differentiates into the megasporocyte. [source: PMID:10465788]
male archesporial cell (PO:0006014): It undergoes periclinal divisions, giving rise to an inner primary sporogenous cell (PSC) layer and an outer primary parietal cell (PPC). [source: GR:pj, PMID:10465788]
Suggest new term for archesporial cell (for homosporous plants), plus revised definitions of male and female archesporial cell.
Proposed definitions:
archesporial cell A plant cell that divides to gives rise to a sporocyte and is part of a sporangium.
Comment: May also give rise to sterile cells such as elators (in liverworts) or tapetal cells. In most species outside seed plants, multiple archesporial cells are part of an archesporium (=sporogenous tissue).
synonym: sporogenous cell (part of sporogenous tissue or archesporium)
female archesporial cell (PO:0006015): A plant cell that is part of a megasporangium and divides to give rise to a megasporocyte.
Comment: Found in heterosporous ferns and seed plants. May also give rise to sterile cells. In the majority of flowering plants, including Arabidopsis, the female archesporial cell elongates and polarizes longitudinally, and directly differentiates into the megasporocyte or megaspore mother cell (MMC). In some flowering plants, it undergoes a periclinal division, and subsequently the inner cell differentiates into the megasporocyte. [source: PMID:10465788]
male archesporial cell (PO:0006014): A plant cell that is part of a microsporangium and divides to gives rise to a microsporocyte.
Comment: Found in heterosporous ferns and seed plants. May also give rise to sterile cells. In seed plants, a male archesporial cell undergoes periclinal division, giving rise to an inner primary sporogenous cell (PSC) layer and an outer primary parietal cell (PPC). [source: GR:pj, PMID:10465788]
alar cell
Moss Ontology definition: Specialized cells at both basal corners of a moss leaf that differ from the other leaf cells in ther size, shape, color or thickness and ornamentation of their walls. Bill and Nancy Malcolm (2006): Mosses and other Bryophytes, an illustrated glossary, second edition
Proposed def.:A plant cell located at the base of a non-vascular leaf adjacent to where the leaf attaches to the stem
Comment: Found in mosses. Different in size, shape, color, thickness or ornamentation form other cells in the leaf.
is_a plant cell, part_of non-vascular leaf, part_of leaf base
other refs: Schofeld, Crum
brachycyte
Moss Ontology definition: Drought-tolerant cell with thick cell wall developed in protonemata under stress (also called brood cells). A type of gemma. Celia Knight,Pierre-François Perroud,David Cove (2009): The moss Physcomitrella patens. The Annual Plant Review 36, Glossary
Proposed def.: A plant cell that develops from cell in a protonema and has a thick cell wall.
Comment: Found in mosses. Cells of a protonema may develop into brachycytes under stress. A brachycyte is a drought tolerant cell that can act as a gemma and may give rise to a new plant.
Synonym: brood cell (from Crum)
chloronema cell (PO:0030001) and caulonema cell (PO:0030002)
already added
tmema cell
Moss Ontology definition: An abscission cell at the base of a gemma (vegetative propagule). Bill and Nancy Malcolm (2006): Mosses and other Bryophytes, an illustrated glossary, second edition
From Crum: An abscission cell at the base of a geem or brood cell, see also brachytmema and dlichotmema
Proposed def.: A plant cell (or an abscission cell) at the base of a gemma or adjacent to a brachycyte.
Should we have class for abscission cell? Is this the same type of cell that is part of a separation layer ( PO:0006211): A portion of plant tissue that is part of an abscission zone and contains cells that develop an abnormal wall chemistry and swelling resulting in their easily being pulled apart along the pectin-rich middle lamella. [source: ISBN:0122151704] Comment: Directly involved in the weakening process of abscission
jacket layer cell
Moss Ontology definition: From the unistratose wall of an antheridium. Bill and Nancy Malcolm (2006): Mosses and other Bryophytes, an illustrated glossary, second edition
We can address the definition of jacket layer (aka sporangium wall) when we deal with the parts of a sporangium but assuming that the jacket layer exists, we can add this cell term.
Proposed def.:A plant cell that is part of a sporangium jacket layer (or sporangium wall).
axillary hair cells
See below, under portions of tissue, for definition of axillary hair.
- axillary hair terminal cell
Moss Ontology definition: A long terminal cell in an axil filament atop a basal stalk. Bill and Nancy Malcolm (2006): Mosses and other Bryophytes, an illustrated glossary, second edition
Proposed def.: A plant (epidermal?) cell that is the long terminal cell of an axillary hair.
part_of axillary hair
- axillary hair base cell
Moss Ontology definition: Basal stalk of an axil filament consisting of two to a dozen cells. Bill and Nancy Malcolm (2006): Mosses and other Bryophytes, an illustrated glossary, second edition
This actually defines the base of an axillary hair, not a cell. Suggest adding two terms:
Proposed def., axillary hair base: A portion of plant (epidermal?) tissue that is the basal part of an axillary hair, below the axillary hair terminal cell.
Comment: Consists of two to a dozen cells.
part_of axillary hair
Proposed def., axillary hair basal cell: A plant (epidermal?) cell that is part of an axillary hair base.
part_of axillary hair
neck canal cell
Moss Ontology definition: Cells in the neck of an immature archegonium neck (also called canal cells)
From Crum: The axial row of cells in the neck of an archegonium
Proposed def.: A plant cell that is one of the axial row of cells in an immature archegonium neck.
Comment: As the archegonium matures, the neck canal cells dissintegrate to form the neck canal
part_of archegonium neck, synonym: canal cell
Also suggest adding term for neck canal: A canal that in the center of an archegonium neck.
part_of archegonium neck.
side branch initial
Moss Ontology definition: A single cell produced by the division of sub-apical cells of protonemata. Side branch initials may develop into chloronemata, caulonemata, buds and hence gametophores, or may not divide further. David Cove
Proposed def.: An initial cell that is produced by division of a sub-apical cell of a protonema.
Comment: May give rise to a chloronema, a caulonema, a gametophore buse, or may not divide further.
part_of protonema
Other cell types, not requested by MO:
- rhizoid initial
Proposed def.: An epidermal initial cell that gives rise to a rhizoid. [PMID: 12917289]
part_of gametophore epidermis
Plant Tissues
paraphyllium
Tiny filaments, scales or leaf-like structures scattered on the stems of some leafy bryophytes. Bill and Nancy Malcolm (2006): Mosses and other Bryophytes, an illustrated glossary, second edition (MO definition)
Crum defines them as "Small green outgrowths formed between the leaves on stems and branches of some pleurocarps (mosses that produce archegonia and sporophytes laterally, rather than on the tips of their axes) and a very few leafy liverworts."
Schofield describes paraphyllia as outgrowths of the epidermis, but he also describes leaves that way.
Moss Ontology has paraphyllium listed as a plant organ, but they do not arise from the SAM as phyllomes do.
Proposed definition: A portion of epidermal tissue that is a small outgrowth from the epidermis between the leaves of a gametophore axis.
Comment: Paraphyllia are much smaller than leaves and may be filamentous, scale-like, or leaf-like. Found in pleurocarpous mosses and a few leafy liverworts.
The paraphyllia are the small, dark structures between the leaves.
rhizoid
Moss Ontology definition: Filamentous tissue protruding from the gametophore stem with a rooting function.
Proposed def.:
paraphysis
Moss Ontology definition: Sterile, septate, usually uniseriate hairs intermixed with sex organs. Bill and Nancy Malcolm (2006): Mosses and other Bryophytes, an illustrated glossary, second edition
Proposed def.:
axilliary hair
Moss Ontology definition: A small filament in an axil consisting of one long terminal cell atop a basal stalk (also called club-hair). Bill and Nancy Malcolm (2006): Mosses and other Bryophytes, an illustrated glossary, second edition
Proposed def.:
tmema
Moss Ontology definition: An abscission cell at the base of a gemma (vegetative propagule). Bill and Nancy Malcolm (2006): Mosses and other Bryophytes, an illustrated glossary, second edition
Proposed def.:
archesporium, amphithecium, endothecium, jacket layer
See agenda item for parts of sporangium.
