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: May be multicellular or unicellular. 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.

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 initial cell that gives rise to a rhizoid.

• hyrdoid (PO:0025032):: An elongate, water conducting cell that is dead at maturity, with tapered ends that are thin and partially hydrolyzed, that lacks specialized wall thickenings or lignin. [source: ISBN:0962073342 (Crum), ISBN:9780717810073]

Comment: Occurs in the gametophytic phase of a plant life cycle.

Proposed def.: An axial cell that is dead at maturity, with tapered ends that are thin and partially hydrolyzed, and lacking specialized wall thickenings or lignin.

Comment: Water conducting cells found mainly in the gametophytic phase, but also sometimes in the sporophytic phase, of bryopytes.

part_of hydrome

• leptoid (PO:0025033): A food conducting cell associated with hydroids that resembles the sieve elements of some seedless vascular plants. [source: ISBN:962073342, ISBN:9780717810073]

Comment: Occurs in the gametophytic phase of a plant life cycle.

Proposed def.: An axial cell that resembles the sieve elements of some seedless vascular plants.

Comment: A food conducting cell found mainly in the gametophytic phase, but also sometimes in the sporophytic phase, of bryopytes.

part_of leptome

• axial cell

We also need to address the definition of axial cell, as it was written with angiosperms in mind.

axial cell (PO:0000081): A vascular cell derived from the fusiform cambial initial and oriented with its longest diameter parallel with the main axis of stem or root. [source: ISBN:0471245208]

Comment: These cells make up the axial system, also known as vertical or longitudinal system.

The term vascular cell does not exist in the PO, and should be removed from the definition, so it can encompass hydroids and leptoids. Also, current definition does not encompass conductive cells that in leaves.

Currently has develops_from fusiform initial, which is_a cambium initial, which is part_of vascular cambium, which is part_of vascular system. This won't work for hydroids and leptoids.

Proposed def.: A plant cell that develops from a fusiform cambial initial and is oriented with its longest diameter parallel with the main axis of a plant axis.

Plant Tissues

conductive tissue

These terms were not proposed by the Physco group, but should be in the PO.

• hydrome

• leptome

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 plant organ/portion of plant 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.

midrib/costa

Moss Ontology definition: The nerve of a phyllid. Altered from Bill and Nancy Malcolm (2006)

We have term midvein (PO:0020139): The central, and usually the most prominent, vein of a leaf or leaf-like organ. [source: APWeb:Glossary] (which, by the way, should just say phyllome, instead of leaf or leaf-like organ). However, midvein is_a leaf vein, which is a portion of vascular tissue, so it cannot apply to mosses.

We should have a term that groups conductive tissue together for both vascular and non-vascular plants, kind of like we have axial cell for vascular and non-vascular conductive cells.

New child of portion of plant tissue: portion of axial tissue:

(also, we need to redefine phloem to be more like definition of xylem, and not based on function) (need to redefine axial cell so it doesn't say vascular cell)

rhizoid

archesporium

amphithecium

endothecium

jacket layer

paraphysis

axilliary hair

tmema

User requests still open on Source Forge; PGDSO

tuber growth and development stages

This item has been open on SF since 6/2009

I have a bunch of potato genes which are expressed in different tuber developmental stages (e.g. the potato pmt gene is expressed in small sprouts only (http://www.ncbi.nlm.nih.gov/pubmed/16088399).

Suggested stages:

-sprout development (does this correspond to tube axillary bud development? Should come after tuber maturation)

-tuber initiation

-tuber growth

-tuber maturation

How we work these in will depend on restructuring of PGDSO

l development in legumes (Plant Physiol, March 2003, Vol. 131, pp. 911-926

terms for seed development stages

This is a fairly new request for terms for cotton