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Vascular tissues and cell types
companion cell
Background:
"Minor vein companion cells may also be grouped on the basis of morphological specialization. In some species, they are "transfer cells" with wall ingrowths (Pate and Gunning, 1969), while in others they are "intermediary cells" with especially numerous and unevenly branched plasmodesmata linking them to the bundle sheath (Turgeon, 1996). Companion cells without such specialized features, regardless of the number of plasmodesmata, are often called "ordinary" companion cells."
From Adams et al. 2007:
"In species that load exclusively through the apoplast, plasmodesmata (cell wall pores that permit direct movement of substances between adjacent cells) connecting the minor vein phloem to surrounding cells are few in number (Gamalei 1989, 1991)"
"In these species (symplastic loaders), the minor vein companion cells are very distinctive, with extremely abundant, highly branched and narrowed plasmodesmata joining them to the bundle sheath. Such anatomically specialized companion cells are known as intermediary cells, and these cells carry out the key step in concentrating sugars in the phloem of symplastic loaders."
From Turgeon 2006:
"The specialization referred to here is the presence of elaborate wall thickenings that increase the surface area of the plasma membrane and the uptake capacity from the apoplast (Amiard et al. 2004). These specialized companion cells are called transfer cells (figure 4c). On the other hand, many species of apoplastic loaders have no such wall elaborations. Their companion cells are often referred to as “ordinary” (figure 4d). Why some apoplastic loaders have transfer cells (e.g., Pisum sativum), while others have ordinary minor vein companion cells (e.g., Nicotiana tabacum and A. thaliana), is unclear. Confusing the issue even more is the fact that several type 1 species load apoplastically (Goggin et al. 2001, Turgeon and Medville 2004)."
(In other words, the type of companion cell cannot always predict the type of phloem loading.)
"(In symplastic loaders) Intermediary cells have dense cytoplasm, small vacuoles, and proplastids rather than chloroplasts. The plasmodesmata that link them to the bundle sheath are not only plentiful but highly branched, more so on the intermediary cell side... The other distinguishing characteristic of species with intermediary cells is that they translocate high concentrations of raffinose-family oligosaccharides (RFOs; raffinose and stachyose)... Indeed, all species known to have intermediary cells use RFOs as their primary transport sugars, and all species known to use RFOs as their primary transport sugars have intermediary cells... All plants with intermediary cells have standard (“ordinary”) companion cells in the minor vein phloem as well."
The following references confirm that intermediary cells, transfer cells, and ordinary companion cells are types of companion cells: Turgeon et al. 2001, Flora and Madore 1996, Turgeon et al. 1991, Adams et al. 2007 (uses "regular companion cell" instead of "ordinary"),
Transfer cell (PO:0000078) is also a general term for cells with many cell wall invaginations.
(See Offler et al. 2003.)
A good figure showing the different types of companion cells and phloem loading:
http://www.bioone.org/action/showFullPopup?doi=10.1641%2F0006-3568%282006%29056[0015%3APLHLGT]2.0.CO%3B2&id=i0006-3568-56-1-15-f04
proposed terms and definitions:
companion cell (PO:0000400): A parenchyma cell (PO:0000074) that is adjacent to a sieve-tube element (PO:0000289) and arises from the same phloem mother cell (PO:0000400) as the sieve tube element.
comment: Companion cells are connected to sieve tube elements through plasmodesmata and may participate in phloem sucrose loading (GO:0009915). A sieve tube element may have one or more or no companion cells associated with it. This term should not be used for other types of phloem parenchyma cells or mesophyll cells (PO:0004006) that do not arise from the same phloem mother cell as a sieve tube element. Companion cells are found in angiosperms while albuminous cells (PO:0025412) are found in non-angiosperm vascular plants. Companion cells may be specialized as transfer companion cells (PO:id), intermediary companion cells (PO:id), or ordinary companion cells (PO:id). Multiple types of companion cells may be found in the same plant.
adjacent_to sieve tube element, part_of phloem
synonym: minor vein companion cell
Need to look at definition of phloem mother cell. I think it can be used for primary phloem too. Also, phloem mother cell and xylem mother cell are not initial cells.
transfer companion cell (new term): A companion cell (PO:0000400) that is a transfer cell (PO:0000078) with many cell wall invaginations.
Comment: Plasmodesmata between a transfer companion cell and adjacent mesophyll cells may be few in number. Transfer companion cells are found in plants that use apoplastic phloem loading.
syn: transfer cell (broad)
is_a companion cell and is_a transfer cell. No way to set up transfer cell as a cross-product, so must have dual parentage for now.
ordinary companion cell (new term): A companion cell (PO:0000400) that lacks cell wall invaginations and has few or no plasmodesmata connecting it to adjacent mesophyll cells.
Comment: Found in plants that use apoplastic phloem loading.
syn.: regular companion cell, standard companion cell
intermediary companion cell (new term): A companion cell (PO:0000400) that has dense cytoplasm, a small vacuole, proplastids rather than chloroplasts, and abundant and highly branched plasmodesmata linking it to mesophyll cells.
Comment: Intermediary companion cells translocate high concentrations of raffinose-family oligosaccharides and are found in plants that use symplastic phloem loading.
syn.: intermediary cell
References:
PMID:21669666 (Turgeon et al. 2001, AJB)
PO_REF:00011 (Turgeon 2006, BioScience)
Need to get synonyms from Gamalei's classification paper.
New definitions - tracheary elements
Moved to POC Conf. Call 2-28-12
New definitions - ground tissue cells
sclerenchyma cells
Moved to POC Conf. Call 2-28-12
parenchyma cells in phloem tissue
Moved to POC Conf. Call 2-21-12
fiber cells
Moved to POC Conf. Call 2-28-12
other wood terms
Wood parenchyma cells and tissues
wood parenchyma (PO:0004532):
Current def.: Parenchymatous tissue occurring in the wood.
Currently is_a secondary xylem. Should be is_a parenchyma.
Proposed def.: A portion of parenchyma (PO:0005421) tissue that is part of a portion of secondary xylem (PO:0005848) and has as parts wood parenchyma cells (PO:0004525).
part_of secondary xylem
Should this be part_of secondary vascular tissue instead, if it can be found in secondary phloem as well.?
axial wood parenchyma (PO:0004533):
Current def.: Parenchyma tissue in the axial system of secondary xylem.
Proposed def.: A portion of wood parenchyma (PO:0004532) that is part of an axial system (PO:0025410) and has as parts axial wood parenchyma cells (PO:0004526).
part_of axial system
ray wood parenchyma (PO:0004534):
Current def.: Radially oriented parenchyma tissue in secondary xylem.
Proposed def.: A portion of wood parenchyma (PO:0004532) that is part of a ray system (PO:0025411) and has as parts ray wood parenchyma cells (PO:0004527).
comment: Occurs in bands or rays of variable width and height that extend radially in the secondary xylem (PO:0005848) and secondary phloem (PO:0005043) of a plant axis (PO:0025004).
part_of ray system
synonym: ray (broad)
wood parenchyma cell (PO:0004525):
Current def.: Parenchyma cell occurring within secondary xylem.
Proposed def.: A parenchyma cell (PO:0000074) that is part of a portion of wood parenchyma (PO:0004532).
comment: Found in secondary xylem (PO:0005848) or secondary phloem (PO:0005043).
part_of wood parenchyma
ray wood parenchyma cell (PO:0004527):
Current def.: Parenchyma cell of a ray in secondary xylem.
Proposed def.: A parenchyma cell (PO:0000074) that develops from a ray initial (PO:0000082) and is part of a portion of ray wood parenchyma (PO:0004534).
part_of ray wood parenchyma, develops_from ray initial
upright wood ray parenchyma cell (PO:0004528)
Current def.: Ray cell in secondary xylem oriented axially (vertically in the axis) with its longest dimension.
Proposed def.: A ray wood parenchyma cell (PO:0004527) that is oriented with its longest dimension parallel to the plant axis (PO:0025004) in which it is found.
procumbent wood ray parenchyma cell (PO:0004529)
Suggest naming it "procumbent ray wood parenchyma cell".
Current def.: Ray cell within secondary xylem having its longest axis in radial direction.
Proposed def.: A ray wood parenchyma cell (PO:0004527) that is oriented with its longest dimension radial to the plant axis (PO:0025004) in which it is found.
axial wood parenchyma cell (PO:0004526)
Current def.: Parenchyma cell in the axial system of secondary xylem.
Proposed def.: A wood parenchyma cell (PO:0004525) that is part of a portion of axial wood parenchyma (PO:0004533).
part of axial wood parenchyma, develops from fusiform initial.
Also see tile cell (PO:0004530) and sheath cell (PO:0004531).
wood types
sapwood (PO:0004513):
Current def.: Outer part of the wood of stem or root containing living cells and reserves and in which conduction of water takes place. Generally lighter colored than the heartwood.
From Esau: Wood that in the living tree contains living cells and reserve materials.
Proposed def.: A portion of secondary xylem (PO:0005848) that has as parts living wood parenchyma cells (PO:0004525).
comment: Sapwood contains reserve materials and is where the conduction of water takes place. It is generally lighter colored than the heartwood (PO:0004512) and is located between the heartwood the vascular cambium (PO:0005598) of a plant axis (PO:0025004).
heartwood ; PO:0004512
Current def.: The inner layers of secondary xylem that have largely ceased to function in storage and conduction and in which reserve materials have been removed or converted into heartwood substances; generally darker colored than the functioning sapwood.
Proposed def.: A portion of secondary xylem (PO:0005848) that lacks living wood parenchyma cells (PO:0004525).
comment: Heartwood has ceased to function in storage and conduction, and the reserve materials have been removed or converted into heartwood substances. It is generally darker colored than sapwood (PO:0004513) and is found in the center of a plant axis (PO:0025004), interior to the sapwood.
early wood ; PO:0004515
Current def.: The wood formed in first part of a growth ring and characterized by a lower density and larger cells than the late wood.
Proposed def.: A portion of secondary xylem (PO:0005848) that has lower density and larger cells than late wood (PO:0004516) and is formed in the first part of a growing season. The transition from early wood to late wood may be gradual and is not always easy to distinguish.
part_of growth ring
synonym: spring wood
late wood ; PO:0004516
Current def.: The secondary xylem formed in the later part of a growth ring; denser and composed of smaller cells than the early wood.
Proposed def.: A portion of secondary xylem (PO:0005848) that has higher density and smaller cells than early wood (PO:0004515) and formed in the later part of a growing season. The transition from early wood to late wood may be gradual and is not always easy to distinguish.
part_of growth ring
synonym: summer wood
growth ring (PO:0004514)
Current def.: A growth layer of secondary xylem or secondary phloem as seen in transection of stem or root; may be an annual ring or a false annual ring.
Proposed def.: A portion of secondary xylem (PO:0005848) that has as parts a single layer of early wood (PO:0004515) and a single layer of later wood (PO:0004516) from the same growth season and is part of a plant axis (PO:0025004).
comment: Forms a ring when viewed in transverse section. May be an annual ring or a false annual ring.
growth ring boundary (PO:0004517):
Current def.: Boundary between two growth rings.
The boundary is the transition between the outermost late wood of one growth ring and the earliest early wood of the next growth ring. This is not a portion of tissue, but an anatomical surface (CARO:0000010).
Proposed definition: A plant anatomical surface that is the boundary between the outermost (last formed) late wood (PO:0004516) of one growth ring and the innermost (earliest formed) early wood (PO:0004515) of the next growth ring (PO:0004514).
NOTE: do we need a term for reaction wood?
Unfinished items from older agendas and user requests
lobe and tooth
On 1-10-12, we added the term "sinus" and agreed to add the related terms for tooth and lobe, all part_of some margin.
We currently have organ margin (PO:0025005), phyllome margin (PO:0025018) without part of relations. Suggest that we add organ margin is part_of lamina, phyllome margin part_of phyllome lamina.
Leaf margin (PO:0020128) is already part of leaf and leaf lamina margin (PO:0025009) is part_of leaf lamina.
proposed definition, lobe: A cardinal organ part that is a rounded projection on the margin of an organ.
part_of organ margin
proposed definition, phyllome lobe: A lobe that is a rounded projection on the margin of a phyllome.
part_of leaf phyllome margin
proposed definition, leaf lamina lobe: A phyllome lobe that is a rounded projection on the margin of a leaf lamina. (Is this in vascular leaf only?)
part_of leaf lamina margin
can add other types of lobes as we want, or wait until they are requested.
proposed definition, plant organ tooth: A cardinal organ part that is a pointed projection on the margin of an organ.
part_of organ margin
proposed definition, phyllome tooth: A plant organ tooth that is a pointed projection on the margin of a phyllome.
part_of leaf phyllome margin
proposed definition, leaf lamina tooth: A phyllome tooth that is a rounded projection on the margin of a leaf lamina. (Is this in vascular leaf only? - no)
part_of leaf lamina margin
can add other types of teeth as we want, or wait until they are requested.
Be sure to add "teeth" as exact plural synonym to all.
Ref.: Harris and Harris, ISBN:0964022168.
bud areole and lamina areole
At the POC meeting on 11-8-11 we to add a term for areole, refering to a type of bud in cacti. However, this term is also used to refer to a part of a leaf (or other phyllome) lamina.
Proposed definition, bud areole (PO:0025353): An axillary bud that does not elongate, in which the leaves develop as spine leaves.
Comment: Found in Cactaceae. Appears as a cluster of spines. May be covered in trichomes. In species with tubercles, the areole is often found at the distal end of the tubercle. The areole originates in the axil of the leaf that becomes the tubercle but is displaced to the tip of a tubercle through adnation (fusion of two organs of different types).
is_a axillary bud
ref.: Bell and Bryan, ISBN:9780881928501
Suggest we add a general term for lamina areole, which will cover petals, etc., and a more specific term for leaf lamina areole.
Proposed definition for lamina areole (PO:0025391): A cardinal organ part that is the smallest part of a lamina that is completely surrounded by veins. Comment: Any order of vein can form the sides of an areole. Taken together, the areoles form a contiguous field of polygons over the area of a lamina. part_of lamina
Proposed definition for leaf lamina areole (PO:0025392): A lamina areole that is the smallest part of a leaf lamina that is completely surrounded by leaf veins. Comment: Any order of leaf vein can form the sides of an areole. Taken together, the areoles form a contiguous field of polygons over the area of a leaf lamina. Free ending veinlets (PO:0025390) may be found within a leaf lamina areole. part_of leaf lamina
Ref: ISBN:9780801475184
colony/ramet/genet
This is a request from Daniel, from the Physco group.
"The description of moss phenotypes in many cases is at the level of (clonal) colony instead of single plant (which is IMO hard to define in this case). E.g. people measure colony area, diameter, branching etc. I want to annotate phenotypes using the EQ model by linking to PATO terms."
Suggest we add the following synonyms:
to "gametophore" (PO:0030018) narrow synonym: "ramet"
to "whole plant" (PO:0000003) related synonym: "ramet", narrow synonyms: "colony", "clonal colony", "genet"
On a related note, Daniel added that "IMHO plant growth/life forms should be best integrated as an extension to PO. "
Primordia
These issues came up while we were working on new term requests for Agron-Omics.
primordium (PO:0025127): A portion of plant tissue that differentiates and develops from meristem tissue into a new plant structure. [source: POC:Curators]
Comment: The primordium is the first distinct form in the development of a plant structure.
leaf primordium: A phyllome primordium that will develop into a leaf. [source: POC:Curators]
Comment: Emerges as an outgrowth in the shoot apex (flanking the meristem).
I think we should modify this to say that it develops from the peripheral zone (PO:0000225) and is part of the shoot apex.
"The SAM consists of two zones. The cells of the central zone (CZ), which occupy the center of the SAM, are undifferentiated and divide to produce cells in the peripheral zone (PZ), a ring of cells below the CZ (21). Cells in the CZ are unable to form primordia. LPs (leaf primordia) only occur in the PZ."
General question: Do these tissues only occur in the primordium, or continue on after it becomes a young leaf? When does it stop being a primordium? If these tissues are all part of LP, then presumably the LP ends when cell stop dividing. I think usually the term primordium is used for the earliest stage of an organ's development, not all the way up until cell division ceases. Maybe better to say they develop from LP and are part_of leaf during PO:0001052 leaf expansion stage.
We felt primordium should probably be an organ. All primordia have at least two types of tissue - protoderm and ground meristem(?).
Primordium ends and leaf begins with the formation of the different meristems (adaxial, plate) that contribute to the final form of a leaf.
Problem with having different types of primordia as organs means they will all have dual parentage (is_a primordium and is_a whatever type of organ. We were trying to get rid of that when we made it is_a tissue.
promeristem as synonym of AM, not RAM
User requests open on Source Forge; PSDS
from MaizeGDB:
coleoptile emergence
Moved to POC_Conf._Call_3-6-12
tuber growth and development stages
This item has been open on SF since 6/2009
From Naama Menda: 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 PSDS
l development in legumes (Plant Physiol, March 2003, Vol. 131, pp. 911-926
User requests open on Source Forge: Plant Anatomical Entities
Cacti terms:
spinule: word for when the spines are stipules – synonym of stipule spine
In Beentje, spinule is defined as a small spine. Could be narrow synonym for stipule spine and other kinds of spines
areole
Proposed definition: An axillary bud that does not elongate, in which the leaves develop as spine leaves (PO:0025173).
Comment: Found in Cactaceae. Appears as a cluster of spines. May be covered in trichomes. In species with tubercles, the areole is often found at the distal end of the tubercle. The areole originates in the axil of the leaf that becomes the tubercle but is displaced to the tip of a tubercle through adnation (fusion of two organs of different types).
is_a axillary bud
ref.: Bell and Bryan, Plant Form
glochid
cladode and phylloclade
From Beentje:
cladode: single node or internode of stem or branch that is flattened and expanded to serve the functions of a leaf
phylloclade: portion of stem or branch (several nodes an dinternodes) flattened and expanded to serve the functions of a leaf.
FNA lists cladode, phylloclade, and cladophyll as exact synonyms: A stem segment that functions as a leaf; often more or less compressed.
proposed definition:
cladode: A shoot axis that is flattened and expanded.
comment: Has an increased surface area for photosynthesis and may function similar to a leaf in plants that have no or small leaves, such as cacti. Consists of one to several internodes and nodes.
synonyms: phylloclade, cladophyll
Need to open a SF tracker for these
Should also add 'rib' for cacti and other plants
root terms
Submitted by Rich Zobel (Nov 2009).
Still need to work on definitions for these terms.
Legume terms
All trackers are now closed. Leaving notes about bristle here for when we are ready to describe phenotypes.
bristle
(used in key as "Stipules spinose or bristles"; might be thought of as a quality, rather than a structure)
Meeting of RW, MAG and DWS on 8/29/11: we felt this would be better left as a phenotypic descriptor. Should add terms needed to PATO.
At the POC meeting on 9-27-11, it was decided that bristled stipules should best be handled as a phenotype term. Leaving these notes here for when we start to add phenotypic descriptors.
We have the term stipule spine. Could also add the term stipule bristle: A stipule that has a brush-like appearance.
A bristle is a single thing, like a stiff hair, but many things can be bristled. Better to add bristled as an adjective in PATO (like ovate or acute).
There are two meanings for bristled:
!. Stiff and sharp (e.g., a bristled trichome)
2. Bearing bristles (e.g, a bristled leaf bears many bristle-like hairs)
Suggest two new phenotype descriptors (for PO phenotype branch or for PATO):
1. bristle-like:
This is a combination of two PATO descriptors:
Something describing the shape:
PATO:0001954 (subulate, awl-shaped, needle-shaped): A shape quality inhering in a bearer by virtue of the bearer's being linear, very narrow, tapering to a very fine point from a narrow base.
or
PATO:0001873 (cylindrical): A convex 3-D shape quality inhering in a bearer by virtue of the bearer's exhibiting a consistently-sized round cross section.
and/or PATO:0001154 (elongated): A quality inhering in a bearer by virtue of the bearer's length being notably higher than its width.
and something describing a quality of a substance:
PATO has:
PATO:0001544 (flexible): A physical quality inhering in a bearer by virtue of the bearer's ability of being turned, bowed, or twisted without breaking. (bendy)
PATO:0001545 (inflexibile): A physical quality inhering in a bearer by virtue of the bearer's inability of being turned, bowed, or twisted without breaking. (stiff)
A bristle is stiff but also bendy! I think in addition to flexible/inflexible, PATO needs terms for stiff or rigid/flacid, and that stiff should be a related synonym of inflexible, rather than exact.
PATO:
quality of a substance (existing)
>flexibility (existing)
>>flexible (existing)
>>inflexible (existing)
>rigidity (new)
>>rigid (new)
>>flacid (new)
2. bristle-bearing: A pilosity quality inhering in a bearer by virtue of the bearer's having structures that are bristle-like.
is_a pilosity (PATO:0000066: A texture quality inhering in a bearer by virtue of the bearer's having hair or bristles.)
Synonym: bristly (Beentje 2010: bearing stiff strong hairs or bristles).
To describe legume stipules, we may also need a term brush-like: A shape quality inhering in a bearer by virtue of the bearer's having a shape that is a cluster of bristle-like structures.
Then if we want to, we could add terms like brush-like stipule (is_a stipule) or bristle-like stipule (is_a stipule) or bristle-bearing stipule, or users could post-compose these terms on their own.
New Annotation Files
Strawberry
- Strawberry is on SVN: strawberry
Potato Annotations
LC has been in contact with the group who published the potato genome paper and they are interested in collaborating with us to assign ontology terms to the annotations.
From Dr. Richard Finker (Wageningen, The Netherlands):
"We are also interested to use trait ontologies to assist in candidate gene selection within regions of interest, I'm eager to discuss with you on the efforts of cross linking ontologies to biological relevant entities. e.g. a metabolite content trait to its e.g. chebi ontology ID, form which we could obtain info about the pathway."
This will go in the next release, do they have expression data- RNA Seq?
Annotation Guidelines
Comments from PJ from previous meeting (9-27-11): Ask MS if she can write up a small blurb on how she created the Maize annotations. Maize probe ids => gene ids methods and cut-offs, a guide for other collaborators and a page for the info. Maybe co-author it with SR
-This will also be helpful when applying for new grants
-it would be helpful to have a detailed guide on our wiki for collaborators
