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. 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.
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.
Sporangium parts
This is continued from our discussion at the POC_Conf._Call_3-8-11
Currently classes like exothecium, endothecium, primary parietal cell layer and tapetum are part of anther wall (PO:0000002). However, these layers and their constituent cell types can be part of any sporangium, not just an anther. Proposed making them part of a general class sporangium wall (as we did for parts of leaf).
From Smith:
Liverworts: Embryo divides to form outer layer (ampithecium) that gives rise to jacket layer and inner mass (endothecium) that gives rise to archesporium (cells of which divide to produce sporocytes and nurse cell, may also produce elators).
Hornworts: Embryo divides to form ampithecium that gives rise to jacket layer and primiary sporogenous layer, and endothecium that gives rise to sterile columella in all but one species (where it gives rise to sporagenous tissue). Jacket layer is 4-6 cells thick, and outer layer develops into epidermis. Sporagenous tissue gives rise to sporocytes and filaments of sterile cells called pseudoelators.
Sphagnum: Upper tier of cells in the embryo divides to form endothecium that gives rise to sterile columella and ampithecium that gives rise to outer sterile layer and inner archesporium. Archesporium gives rise to sporogenous layer two to four cells thick. Outer sterile layer gives rise to jacket layer 3 or 4 cells thick.
Eubrya: Early division of capsule gives rise to multilayered ampithecium and endothecium (with ampithecial cells and endothecial cells). Endothecium (usually) gives rise to archesporium and columella. Columella cells adjacent to archesporium remain small and develop into inner spore sac. Ampithecium develops into a multilayered structure, including layers with and without chloroplasts and an epidermis.
Psilophyta: Paired sporangia (a synangium or maybe a reduced sporangiophore) develop from a single cell. First cell division leads to a jacket initial and an archesporial (primary sporogenous) cell. Repeated periclinal divisions of jacket initial lead to jacket layer four or five cells thick and divisions of archesporial cell lead to many sporogenous cells. No tapetum develops. Near maturity, irregular clumps of sporogenous tissue divide to give rise to spore mother cells, remainder disintegrate
Lycopods: Sporangia borne on sporophylls. Early cell division leads to a layer of jacket initials and an archesporium, which divides to form a mass of sporogenous tissue. Nearly all cells in this tissue function as spore mother cells that divide to for tetrads of megaspores. Tapetum is formed from innermost layer of jacket cells and outer layer of sporogenous tissue. Unlike most pteridophytes, tapetum does not break down during sporogenesis.
Selaginellaceae: Has microsporanigia and megasporangia borne on microsporophylls and megasporophylls that are always in strobili (maybe in same or different strobili). Development of mega- and microsporangia is the same up to sporocyte stage. One or multiple cells divide to form outer jacket initial(s) and inner archesporial cell(s). Inner cells develop into mass of sporogenous tissue while outer develop into jacket layer two cells thick, outer layer with thick-walled cells and inner layer with thin-walled cells. A distinct tapetum develops from the outer layer of sporogenous cells.
Isoetaceae: Each sporophyll bears a single flattened sporangia between the ligule and the leaf base, which is covered by a membranous outrgrowth from the epidermis just below the ligule called a 'velum. Early development of mega- and microsporangia is similar. Several cells divide to form jacket jacket initials and archesporial cells. Archesporial cells divide to form mass of sporogenous tissue. Later in development, this is divided into blocks of fertile cells divided by sterile cells. The sterile cells mature into trabeculae, that incompletely divide the sporangium chamber. Sporogenous cells adjacent to trabeculae and jacket layers form a tapetum that is generally two cells thick. Remaining sporogenous cells may become sporocytes. Jacket layer may become 3 or 4 cells thick.
Plant Cells
Terms requested by MO:
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 gives rise to a sporocyte.
Comment: May be part of an 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. 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: Male archesporial cell may undergo 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
brachycyte
chloronema cell - done
caulonema cell - done
tmema cell
jacket layer cell
axillary hair terminal cell
axillary hair base cell
neck canal cell
side branch initial
Other cell types, not requested by MO:
hyrdoid
leptoid
rhizoid initial
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 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
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."
Proppsed 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 bristle: A stipule that has a brush-like appearance.
Alternative is to suggest bristled to PATO
Proppsed def: A leaf in which there is no normal lamina development, but instead the petiole or petiole plus rachis is laminar.
Banner (as in a legume flower) - suggest using name 'banner petal'
Proppsed 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'
Proppsed 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
proposed def: A short, enlarged storage stem in which the internodes do not elongate. Comment: usually underground.
child of stem (PO:0009047).
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:
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.
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)
Should probably be a synonym of strobilus (PO:0025083). Narrow or exact?
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
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
