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?

New terms for Physcomitrella and related taxa (continued)

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.

The only differences below are substituting located in for other words.

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 or sporogenous tissue.

synonym: sporogenous cell

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: 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. Alar cells occur in an area at the base of a leaf that may be triangular, ovate or rectangular, and is sometimes called the alar region. They are 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, Lars Hedenas The Bryologist 100(1), pp. 65-88.

Blurry image of alar cells at the base of a moss leaf

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 a cell in a protonema and has a thick cell wall.

Comment: Found in mosses. A brachycyte is a drought tolerant cell that can act as a gemma and may give rise to a new plant. Cells of a protonema may develop into brachycytes under stress. May form a chain or be separated by tmema cells.

Synonym: brood cell (from Crum)

chloronema cell (PO:0030001) and caulonema cell (PO:0030002)

Already added at the POC_Conf._Call_3-8-11.

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 gemma or brood cell, see also brachytmema and dlichotmema

Proposed def.: A plant cell at the base of a gemma or adjacent to a brachycyte that breaks down to allow abscission of the gemma or brachycyte.

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 sporangium wall exists, we can add this cell term now.

Proposed def. for sporangium wall cell:A plant cell that is part of a sporangium wall.

Comment: The sporangium wall is also known as the jacket layer.

Synonym: sporangium jacket layer cell

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 base

Lars Hedenas The Bryologist 100(1), pp. 65-88.

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.

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

From Parihar: sterile, slender filaments accompanying reproductive organs.

From Schofeld: filamentous sterile structures intermixed with the sex organs of most mosses

Proposed def.: A portion of plant tissue that is a slender, usually uniseriate hair-like structure that grows intermixed with the gametangia.

Comment: Found in bryophytes and pteridophytes, especially in mosses.

adjacent_to gametangium, plural: paraphyses

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

Is it a type of trichome?

Proposed def.: A trichome (or portion of plant tissue) consisting of one long terminal cell atop a basal stalk that grows in the leaf axil of a non-vascular leaf.

Comment: Found in pleurocarpous mosses.

synonym: club-hair

rhizoid

Moss Ontology definition: Filamentous tissue protruding from the gametophore stem with a rooting function.

Rhizoids may also grow from thalli. They arise from the epidermis, and so are like trichomes. Like trichomes, they may be uni- or multicellur

Proposed def.: A trichome that grows from the epidermis of a plant in the gametophytic phase.

Comment: Found in bryophytes and pteridopytes growing from a gametophore or thallus. May be muticellular or unicellur. May anchor the plant to the substrate.

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 separate agenda item for parts of sporangium.

sporogenous tissue or archesporium