POC Conf. Call 3-22-11

POC meeting, Webex Conference Call; Date: Tuesday Mar 22nd, 2011 10am (PST)

In attendance:

POC members:

Absent:

Collaborators:

Acceptance of the minutes from the POC_Conf._Call_3-15-11?

Physcomitrella terms

Gametangium, antheridium, archegonium and related terms

May want to use the name plant gametangium, to make it clear that we are not including algae.

Current definitions:

plant gametangium (PO:0025124): A cardinal organ part (or an organ?) that is part of a whole plant in the gametophytic phase and produces gametes.

antheridium (PO:0025125): A gametangium that produces antheridium sperm cells.

archegonium (PO:0025126): A gametangium that produces archegonium egg cells.

Need definitions that distinguishes gametangia from megagametophyte (embryo sac) and microgametophyte (pollen). The current definitions are circular (see definitions below of archgonium egg cell and antheridium sperm cell)

Current definitions of--

megagametophyte (PO:0020092): A gametophyte that produces female gametes.

microgametophyte (PO:0020091): A gametophyte that produces pollen sperm cells.

-This would be a good place to introduce the "only in taxon" and/or "never in taxon" relations

We also have the terms:

archegonium egg cell (PO:0025122): An egg cell that is produced by an archegonium.

embryo sac egg cell (PO:0025123): An egg cell that is produced by a megagametophyte.

antheridium sperm cell (PO:0025120): A sperm cell that is produced by an antheridium.

pollen sperm cell (PO:0025121): A sperm cell that is produced by a microgametophyte.

Having both sets of egg and sperms cells is redundant. They were put in to satisfy the part_of relations. We could get around this by using has_part relations.

Here is an image of the current PO, showing only female parts:

-Maybe having reciprocal part_of and has_part relations is causing a problem?

Here is how it would look using has_part relations:

In this image, archegonium egg cell and embryo sac egg cell have been merged with egg cell. May also want to merge embryo sac with female gametophyte. It is the only child of female gametophyte, suggesting they are redundant.

Proposed definitions:

apical cell

Moss Ontology has requested the term apical cell.

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." Suggest renaming PO:0004000 embryonic apical cell for clarity. The embryonic apical cell can also be found in non-angiosperms.

Growth in mosses (and other bryophytes) results from divisions of a single apical cell. Branches or leaves form from division and differentiation of sub-apical cells. The moss apical meristem may differ from that of vascular plants, but it is still possible to call it an apical meristem.

Apical cell is consistent with the definition of meristematic cell (synthesizing protoplasm and producing new cells by division and with only a primary cell wall). Meristematic cell is part_of meristem, and a meristem is a portion of tissue and therefore two or more cells. We do not need to add apical cell part of apical meristem, but logically it will be part of a meristem.

Non-seed vascular plants can also have an apical cell, similar to bryophytes. Suggest we add separate terms for sporophytic apical cell and gametophytic apical cell.

Proposed def. of gametophytic apical cell: A meristematic cell at the apex of a gametophore or non-vascular leaf.

Comment: Occurs in mosses and other bryophytes. Something about how it divides.

Proposed def. of sporophytic apical cell: A meristematic cell at the apex of a shoot apical meristem that ...something about being distinct from other cells at the apex and/or about being a single cell rather than an indistinguishable group of cells.

Comment: Occurs in lycopods and ferns (what about Psilotum?).

Moss ontology also requested shoot apical cell and phyllid apical cell.

Proposed definitions:

gametophore apical cell: A gametophytic apical cell at the apex of a gametophore.

Comment: Divides to produces leaf initial cells and other stem tissues.

phyllid apical cell: A gametophytic apical cell at the apex of a phyllid

Comment: Divides to produce phyllid tissues. (C. Jill Harrison et al. (2009): Local Cues and Asymmetric Cell Divisions Underpin Body Plan Transitions in the Moss Physcomitrella patens.)

Collective plant structures:

gametophore

Def'n 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'n.: A shoot system that consists of the shoot axes and non-vascular leaves of a plant in the gametophytic phase. participates_in gametophytic phase

Comment: A gametophore is the leafy part of a moss gametophyte, without the protonema. Antheridia and archegonia arise on the gametophore.

gametophore bud

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 bud on a protonema that develops into a gametophore. participates_in gametophytic phase

Comment: Occurs in mosses.

Plant organs:

cauloid

- This is the term used for the gametophore stem or axis.

Suggest using gametophore axis as primary name, cauloid as synonym.

Proposed def'n: A plant axis that is part of a gametophore. is_a plant axis, part_of gametophore, participates_in gametophytic phase

Synonyms: cauloid, gametophyte axis

Also suggest adding terms for gametophore stem and gametophore branch (similar to stem and branch).

perigonial bract

- 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.

Additional 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 may as well add them now.

perichaetal bract

Proposed def'n: A bract that subtends and archegonium. part_of gametophore, participates_in gametophytic phase.

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

Proposed def'n: A collective phyllome structure that consists of two or more of the most distal parachaetal bracts on a gametophore axis that are fused laterally and surround the calyptra.

Should it be surrounds the capsule, in case no calyptra is present?

-has_part parachaetal bract, part_of gametophore, participates_in gametophytic phase, disjoint from perianth (PO:0009058)

Comment: The gametophytic perianth is not the same structure as a perianth (PO:0009058) in angiosperms.

Maybe should just add disjoint from relation.

May want to put the phrase "fused laterally" in the comment. Don't know if they are fused in all species.

seta

-The stalk of a moss sporophyte.

Suggested def'n: A plant axis that that holds up a spore capsule. participates_in sporophytic phase

Comment: Found in mosses

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 is part of the fruit in Eucalyptus. That term should be named fruit 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 an archegonium wall and surrounds the sporangium.

Comment: Found in mosses. The calyptra ia a membranous or hairy cap composed of gametophytic tissue that protects the embryonic sporophyte within the archegonium. In some species, the calyptra may persist after the sporophyte develops and be carried upward as the seta elongates.

(Definition suggests that we should add a term for archegonium wall, is_a gametangium wall)

• base (save for next week)

Moss Ontology definition: The sterile bottom of the sporangium. Also called neck or if swollen apophysis or hypophysis. Bill and Nancy Malcolm (2006): Mosses and other Bryophytes, an illustrated glossary, second edition

Need to look up if we should add separate terms for apophysis and hypophysis, or add as synonyms.

Proposed name and def.: sporangium base

Synonyms: sporangium neck

• peristome

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 sporangium mouth.

• peristome tooth

Not requested by Moss Ontology, but should add it.

Proposed def: A cardinal organ part that is a lobe or tooth of the peristome.

• theca (maybe save for next week)

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.

Proposed name and def.: sporangium theca: The main body of the sporangium.

Comment: Term used in mosses and other bryophytes (what about pteridophytes?)

• 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: 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.

Also add:

fruit operculum: A cardinal organ part that is the apical part of a capsular fruit that separates from the rest of the capsule (the fruit calyptra) during dehiscence. part_of fruit

Comment: Found in Eucalyptus.

Is is a cardinal organ part (formed from a single carpel) or collective organ part structure (formed from parts of multiple carpels)?

fruit calyptra: A cardinal organ part that is the basal part of a capsular fruit that separates from the fruit operculum during dehiscence. part_of fruit

Comment: Found in Eucalyptus. The capsule may remain attached to the plant after the fruit operculum dehisces.

• foot

Moss Ontology definition: The base of the sporophytes in mosses

Proposed name and def.: sporophyte foot: The base of the sporophyte (seta?) that attaches it to the gametophore. (From Schofeld)

Comment: The sprophyte foot serves for both attachment and absorption. The outer portion of the foot is the absorptive haustorium. (From Crum)

- Can add term for sporophyte foot haustorium when we deal with portions of plant tissue. Contains transfer cells.

Other related terms for mosses, not from Moss Ontology

• spore capsule mouth

Proposed definition: A plant anatomical space that is the opening on the distal end of a spore capsule.

Comment: The mouth is formed when the operculum separates from the capsule. The mouth may be partially covered by a peristome.

• epiphram

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 plant 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.

What kind of tissue is it?

• 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 gaemtophore tissue that pushes the sporophyte beyond the perichaetial leaves (in Andreaea and Sphagnum)."

Proposed definition: An extension of a gametophore axis on which a spore capsule is borne.

Comment: Raises the sporophyte above the perichaetial bracts. Found in Sphagnum and Andreaea.

• venter

• neck canal

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.

MO has this listed as a plant organ

Proposed definition: A phyllome/portion of plant tissue that is a small filamentous, scale-like, or leaf-like outgrowth from the epidermis between the leaves of a gametophore axis.

Comment: Paraphyllia are much smaller than leaves. Found in pleurocarpous mosses and a few leafy liverworts.

The paraphyllia are the small, dark structures between the leaves.

midrib

rhizoid

archesporium

amphithecium

endothecium

jacket layer

paraphysis

axilliary hair

tmema

Plant Cells

Terms requested by MO:

archesporial cell

apical cell

shoot apical cell

phyllid apical cell

alar cell

brachycyte

chloronema cell

caulonema cell

tmema cell

jacket layer cell

axillary hair terminal cell

axillary hair base cell

neck canal cell

side branch initial

Other terms, not requested by MO:

hyrdoid

leptoid

rhizoid initial

Continuing User requests: for PSO

- Deal with and complete the list of user requests on SourceForge-

Legume terms

submitted by Austin Mast

Several terms have already been dealt with (Taproot, Stem Hair, Prickles, Anther pore and anther slit)

fascicle The term fascicle can refer to different structures in different taxa. Suggest we use the term floral fascicle or flower fascicle in this case, to distinguish it from a "leaf fascicle," which we may want to add for describing gymnosperms.

From Tucker, 2003, Flora: (in the Papilionoideae) "Pseudoracemes (Fig. 5B) differ from racemes in that two to several flowers are initiated in each bract axil rather than just one as in a raceme. The cluster of flowers at each node is called a fascicle. The order of initiation among flowers at a node (Fig. 5B, Psoralea macrostachys DC) shows the fascicle to be a short shoot topped by a second order inflorescence apical meristem. This meristem initiates flowers in a bilaterally symmetrical order: a single abaxial flower, then two lateral flowers, another median abaxial, then two more laterals. The number of flowers per fascicle depends on the duration of the axillary inflorescence apex of the short shoot, which ceases activity after initiating the few flowers in the fascicle. No flowers are initiated adaxially (toward the first order axis) on the short shoot (Tucker, 1987b; Tucker and Stirton, 1991). The short shoot in a pseudoraceme can be distinguished from a cyme in that every flower is bract subtended in a pseudoraceme."

Suggested def: A second order inflorescence in which the second order inflorescence branch bears two or more flowers but is not elongated. Comment: A fascilce appears to be a cluster of flowers in an axil of a single bract of the main inflorescence. Common in some sections of the Fabaceae.

bristle (used in key as "Stipules spinose or bristles"; might be thought of as a quality, rather than a structure)

We added the term stipule spine. Could also add the term stipule bristles: A stipule that has a brush-like appearance.

Alternative is to suggest bristled to PATO

phyllode Suggested def: A leaf in which there is no normal lamina development, but instead the petiole or petiole plus rachis is laminar.

banner, wing and keel

Banner (as in a legume flower) - suggest using name 'banner petal'

Suggested def: A petal that is the top-most petal of a corolla in some flowers of the Fabaceae. Comment: The banner is usually larger than the adjacent wing petals.

Wing (as in a legume flower) - suggest using name 'wing petal'

Suggested def: One of two petals that is adjacent to the banner petal in some flowers of the Fabaceae. Comment: The wing petals are usually much smaller than the banner petal and the corolla keel.

Keel (as in a legume flower): The keel consists of two fused petals, and is analogous to the fused collective tepal structure we made for Musa. Maybe name 'corolla keel'

Suggest three new terms:

fused petal: A petal that is fused to another petal. Comment: May be fused to two petals (one on either side). This is a phenotype that is a cross-product of PO:0009032 (petal) and PATO:0000642 (fused with).

fused corolla: A corolla in which the petals are fused. Comment: This is a phenotype that is a cross-product of PO:0025023 (collective phyllome structure) and PATO:0000642 (fused with). A corolla may consist of a combination of fused and free petals, in which case fused corolla only refers to those petals that are fused.

corolla keel: A fused corolla that consists of the two lowest petals in some flowers of the Fabaceae. Comment: The two petals of the keel may be fused at the apex but free at the base. The remaining three petals (banner and two wings) are free. The keel is boat shaped.

TraitNet requests

corm

proposed def: A short, enlarged storage stem in which the internodes do not elongate. Comment: usually underground.

child of stem (PO:0009047).

podarium

Their comment: is synonym to Tubercle

podarium (from Beentje 2010): (in cacti or other succulents) a modified leaf base functioning as the photosynthesising organ.

tubercle (from Beentje 2010): (in ball- or barrel- shaped cacti), cone-shaped protuberances that are elnarge modified leaf bases fused with adjacent stem tissue (tubercle has two other definitions as well).

proposed def:

pneumatophore

definition from Beentje (2010): erect (breathing) root protruding above the soil, encountered especially in mangroves

proposed def: A root that is erect and protrudes above the soil, found in trees that live in flooded habitats such as mangroves. Comment: Pneumatophores may provide oxygen to below ground roots growing in flooded soils.

diaspore

definition from Beentje (2010): reproductive portion of a plant, such as a seed, fruit or fragment of fruit, that is dispersed and may give rise to a new plant.

We could add this term as a kind of upper level bin term (similar to trichome)

cone

Should probably be a synonym of strobilus (PO:0025083). Narrow or exact?

sorus

from Crum (2001): a cluster of fern sporangia from Beentje (2010): (of pteridophytes) structure bearing or containing groups of sporangia.

Proposed definition: A cardinal organ part composed of a cluster of two or more adjacent sporagia on the surface of a leaf. Comment: May be enclosed by an indusium.

Part_of vascular leaf, has_part sporangium

tendril

Defintion from Beentje (2010): a slender, coiling structure derived from a branch, leaf or inflorescence and used for climbing.

tendrils can derived from multiple types of structures. Suggest we make separate terms:

branch tendril (child of branch): A branch that is slender and coiling. Comment: Aids plant in climbing.

leaf tendril (child of leaf): A leaf that is slender and coiling and lacks a lamina. Comment: Aids plant in climbing.

leaflet tendril (child of leaflet): A leaflet that is slender and coiling. Comment: Aids plant in climbing.

leaf apex tendril (child of leaf apex): A leaf apex that is slender and coiling. Comment: Aids plant in climbing.

Can add other types of tendrils if they come up or users need them.

root terms

submitted by Rich Zobel (Nov 2009)

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