POC Conf. Call 4-28-11

POC meeting, Webex Conference Call; Date: Thursday April 28th, 2011 10am (PDT)

In attendance:

POC members:

Absent:

Collaborators:

Acceptance of the minutes from the POC_Conf._Call_4-26-11?

Items arising from previous meetings:

Plant cell and sperm cell

Most sperm cells do not have a plasma membrane (as should be so per definition of cell by GO).

We should add a comment to antheridium sperm cell (PO:0025120) and plant cell (PO:0009002): "Motile sperm cells (antheridium sperm cells?) do not have a plasma membrane."

New terms for Physcomitrella and related taxa (continued)

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

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

Additional organ related moss terms:

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 is 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:

• calyptra

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 (PO:0030037): A cardinal organ part that develops from the wall of an archegonium and surrounds a sporangium.

Comment: Found in bryophytes and pteridophytes. The calyptra is 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 archegonium

subsets for bryophytes, pteridophytes

• venter (PO:0030038)

This term was not suggested by Moss Ontology, but 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

• archegonium neck(PO:0030039)

This term was not suggested by Moss Ontology, but we should add it.

proposed def.: A cardinal organ part that is the elongated apical 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

• base

Proposed name and def.: sporangium base (PO:0030040): A cardinal organ part that is the basal part of a sporangium.

Comment: Term used in mosses and other bryophytes and some 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, pteridophytes

• theca

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. We should call that anther theca and call this term sporangium theca:.

Proposed name and def.: sporangium theca (PO:0030041): A cardinal organ part that is the main body of a sporangium and has spores located in it.

Comment: Term used for bryophytes and pteridophytes.

part_of sporangium

subsets for bryophytes, pteridophytes

• peristome (PO:0030042)

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 (PO:0030043)

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?

• lid/operculum

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 (PO:0030044): 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 top 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.

Other related terms for mosses, not from Moss Ontology

• spore capsule mouth

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

• epiphragm

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

• pseudopodium

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

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 trichome 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 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 trichome 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

• hydroids and leptoids

See separate agenda item for [POC_Conf._Call_4-28-11#Conductive_cells_and_tissues conductive cells and tissues]

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

These are a kind of trichome

Proposed def.: A multicellular trichome 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; particpates_in gametophytic phase

axillary 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

This is a type of trichome. Axillary trichomes may also be found in angiosperms, so suggest we specify that this for hair son gametophores.

Proposed def., gametophore axillary hair: A multicellular trichome 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; part_of gametophore

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

Their definition defines a cell type, but they have tmema as a tissue type. It would be the tissue composed of tmema cells

Proposed def.: A portion of plant tissue composed of tmema cells.

Comment: Found in bryophytes at the base of a gemma or a brachycyte that will act as a gemma. Participates in abscission of the gemma.

archesporium, amphithecium, endothecium, jacket layer

See separate agenda item for parts of sporangium.

sporogenous tissue or archesporium