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Vascular tissues and cell types

leaf vein, primary vein, mid vein

These changes have been made to the obo file.

• leaf vein (PO:0020138)

May want to rename "leaf lamina vein".

current definition: A strand of vascular tissue in the leaf blade.

revised definition, leaf lamina vein (PO:0020138): A vascular bundle that is part of a leaf lamina vascular system.

part_of leaf lamina vascular system

synonym: leaf lamina vascular bundle

• primary leaf vein (new term)

proposed def'n: A leaf vein (PO:0020138) that connects directly to a petiole vascular system (PO:0000052) or a shoot axis vascular system (PO:0000039).

Comment: Generally the largest and most prominent of the leaf veins. A leaf may have more than one primary vein. The central primary vein is the midvein (PO:0020139). Vein orders only apply to hierarchically branching vein patterns, not to dichotomously branching vein patterns, as in some ferns and gymnosperms.

• midvein (PO:0020139)

revised def'n: A primary leaf vein (PO:0025413) that is the central vein of a vascular leaf (PO:0009025).

Comment: Often the most prominent vein of a vascular leaf. See costa (PO:0030072) for the central conductive strand of a non-vascular leaf (PO:0025075).

broad synonyms: mid rib, midrib, mid-rib; exact synonym: vascular leaf midvein; related synonym: costa, Hickey and Peterson 1978 doi:10.1139/b78-128

We already have terms for secondary, tertiary, quaternary, and higher order veins.

Primary and secondary growth, etc.

request has been made to GO.

proposed terms for GO

primary growth (new term):

proposed definition: Growth of a plant structure from the time of its initiation by an apical meristem until its expansion is completed. Ref: Esau (ISBN:0471245208 or 9780471245209)

comment: Has its inception in the apical meristems (PO:0020144) and continues in their derivative meristems - protoderm (PO:0006210) and procambium (PO:0025275) - even in older tissues. Primary and secondary growth can occur simultaneously in the same organism.

is_a growth (GO:0040007)

secondary versus lateral growth

GO currently defines secondary growth as: Increase in plant girth due to the activity of lateral meristems (vascular and cork cambium). Source: PMID:19074290

Secondary growth from the vascular cambium does not occur in monocots, but there is a secondary thickening meristem that may be discontinuous from apical meristem that can contribute to another kind of secondary growth. See paper by Rudall et al. in Botanical Review (JSTOR:4354165).

I suggest that GO add a general term for lateral growth (to mirror PO, see below), with specific subtypes for growth from the vascular cambium and growth from other types of lateral meristems.

lateral growth (GO:new term): Growth of a plant axis (shoot axis or root) that originates from a lateral meristem (PO:0020145).

Comment: Includes thickening of plant axes (PO:0025004) due to the activity of a cambium (PO:0005597), known as secondary growth and found in most gymnosperms and dicotyledons, a primary thickening meristem (PO:0005039) as found in many monocotyledons, some ferns and some cycads, or secondary thickening meristem, (PO:0025414) as found in some monocotyledons.

proposed new def., secondary growth (GO:0080117): Lateral growth of a plant axis (PO:0025004, shoot axis or root) that is an increase in thickness resulting from formation of secondary vascular tissues by the vascular cambium (PO:0005598). Ref: Esau (ISBN:0471245208 or 9780471245209)

Comment: Occurs in vascular plants, including gymnosperms and most dicotyledons. Commonly supplemented by activity of the cork cambium or phellogen (PO:0005599). Monocotyledons do not have secondary growth, but may undergo primary thickening (GO:xxx) or secondary thickening (GO:xxx), which can give the appearance of secondary growth. Primary and secondary growth can occur simultaneously in the same organism.

Add exact synonym "cambial secondary growth", which is makes the meaning clearer.

secondary thickening (GO:new term): Lateral growth of a plant axis (PO:0025004, shoot axis or root) that is an increase in thickness resulting from formation of tissue from a secondary thickening meristem (PO:0025414).

comment: Occurs in shoot axes in some monocotyledons such as Dracaena, and rarely in roots of monocotyledons. Distinct from primary thickening, because it is distant from and generally discontinuous with the apical meristem.

References: Fahn 1990, ISBN:0080374903; Rudall 1991, JSTOR:4354165

primary thickening (GO:new term): Lateral growth of a plant axis (PO:0025004, shoot axis or root) that is an increase in thickness resulting from the activity of a primary thickening meristem (PO:0005039)

comment: Occurs in shoot axes and rarely in roots in many monocotyledons.

Ref: JSTOR:4354165, Rudall 1991; and Esau ISBN:0471245208

diffuse secondary thickening (GO:new term): Lateral growth of the older parts of a stem that occurs when the central parenchyma cells and the not yet fully differentiated fiber cells of the bundle sheaths continue to undergo cell division and expansion for a long period of time, leading to an increase in girth of the stem.

comment: Occurs in the stems (PO:0009047) of some Arecaceae (palms).

Ref.: Fahn 1990, ISBN:0080374903

PO terms for lateral meristems

These edits have been done in the obo file, except as noted below.

See Items_for_future_meetings#Primary_and_secondary_growth.2C_etc. for more details on terms that will be requested in GO.

The PO has a general term for lateral meristem, of which cambium is a subtype:

lateral meristem (PO:0020145)

revised def'n: A portion of meristem (PO:0009013) tissue located parallel to the circumference of a plant organ (PO:0009008).

comment: Participates in lateral growth (request has been made for lateral growth in GO) of a plant organ, primarily shoot axes (PO:0025029) and roots (PO:0009005). Contrast with apical meristem (PO:0020144).

cambium (PO:0005597)

revised def'n: A lateral meristem that is part of a plant axis (PO:0025004) and has as part a single layer of cambial initial cells and their derivatives, arranged orderly in radial files. (Ref.: Esau)

comment: This term is applied to only two types of meristems: vascular cambium (PO:0005598) and cork cambium/phellogen (PO:0005599).

Changed cambial initial from part_of vascular cambium to part_of cambium, because that is how it was defined.

root lateral meristem (PO:0006308)

didn't do this edit yet

This is just a lateral meristem in the root, which is only the cambium (vascular cambium and phellogen). Therefore, it makes more sense to call it a root cambium.

proposed new name and def'n: root cambium: A cambium that is part of a root.

This terms has six annotations. These should be checked, because it is not obvious what some of them have to do with roots.

Suggest that we also add root vascular cambium and root cork cambium, plus shoot axis vascular cambium and shoot axis cork cambium. Set up root cambium and shoot lateral meristem as XPs, so we don't have multiple inheritance.

vascular cambium (PO:0005598)

revised def'n: A cambium (PO:0005597) that is located between and gives rise to secondary xylem (PO:0005848) and secondary phloem (PO:0005043).

comment: Vascular cambium gives off cells in both directions by periclinal division, leading to an increase in girth of a plant axis (PO:0025004).

Got rid of relation vascular cambium part_of vascular bundle.

cork cambium/phellogen (PO:0005599)

revised def'n: A cambium (PO:0005597) that is part of a shoot axis periderm (PO:0005048) and produces phellem (PO:0004003) and phelloderm (PO:0005050).

comment: Cork cambium is located between the phellem and phelloderm and produces phellem toward the outside and phelloderm toward the inside of a plant axis.

primary thickening meristem (PO:0005039)

Esau defines it as originating in the apical meristem, but Rudall's review shows that in some species, it is discontinuous with the SAM.

revised def'n: A shoot lateral meristem (PO:0006344) that is part of a stem (PO:0009047) and has a parts multiple layers of meristematic cells (PO:0004010) located near the shoot apical meristem (PO:0020148).

comment: Contributes to primary thickening of a stem (PO:0009047), adventitious (shoot-borne) root (PO:0000042) formation, and formation of linkages between shot axis (PO:0000039), leaf (PO:0000036), and root (PO:0003011) vascular systems. Contiguous with the shoot apical meristem (PO:0020148) in some species, but not all. Produces more or less distinct vascular bundles (PO:0005020) surrounded by ground tissue (PO:0025059), as opposed to the more or less continuous xylem (PO:0005352) and phloem (PO:0005417) produced by a vascular cambium (PO:0005598). A primary thickening meristem is a multi-layered structure, compared to the single layer of a cambium. Found in many monocotyledons.

secondary thickening meristem (new term)

proposed def'n: A shoot lateral meristem (PO:0006344) that is part of a stem (PO:0025029) not contiguous with the shoot apical meristem (PO:0020148) and has a parts multiple layers of meristematic cells (PO:0004010).

comment: Contributes mainly to formation of the body of a stem (PO:0009047), but may also produce adventitious (shoot-borne) roots (PO:0000042). May be continuous or discontinuous with the primary thickening meristem (PO:0005039). Found in some monocot species of the Liliales and Asperigales.

Other types of lateral meristems

didn't do these edits yet

PO has the terms shoot lateral meristem (PO:0006344), inflorescence lateral meristem (PO:0009105), ear lateral meristem (PO:0009110) and tassel meristem (PO:0009107), plus their subtypes.

Shoot lateral meristem is okay, but inflorescence lateral meristem and all the others are misleading. Inflorescence branches develop from apical meristems, not a lateral meristem.

There are three annotations on shoot lateral meristem and two on inflorescence lateral meristem that should be moved to shoot apical meristem.

Shoot lateral meristem should be set up as an xp, so subtypes and be inferred, just like root lateral meristem. Same for root meristem and shoot meristem.

inflorescence lateral meristem (PO:0009105)

current def'n: The meristem which gives rise to the lateral structures of the inflorescence and contributes to their apical growth.

This should be called inflorescence branch meristem, and be a subtype of inflorescence meristem (PO:0000230), which should in turn be an apical meristem.

ear lateral meristem (PO:0009110)

This should be called ear inflorescence branch meristem, and be a subtype of inflorescence branch meristem (PO:0009105). Will need to add XP definitions to the different types of meristems so that they don't have dual parentage (e.g., ear inflorescence meristem XP of is_a inflorescence meristem and part_of ear inflorescence).

revised def'n: An inflorescence branch meristem that gives rise to the branches of an ear inflorescence.

conductive and related cell types

Current parent: axial cell

Existing structure:

axial cell (PO:0000081)

>sieve tube member (PO:0000289, alt: PO:0000286)

>phloem fiber (PO:0004519)

>xylem element (PO:0000273)

>>tracheary element (PO:0000273)

>>>tracheid (PO:0000301)

>>>vessel member (PO:0002003)

>>xylem fiber (PO:0000274)

>>>fiber tracheid (PO:0000355)

>>>libriform fiber (PO:0004520)

>>>septate fiber (PO:0004521)

axial cell

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 axial cell, and the current definition, describe a particular type of vascular cells found in wood. This is not appropriate as the parent for xylem and phloem cells. Also, the term axial cell is not widely used. "Axial system" is widely used to describe the vascular tissue in wood (in contrast to the radial system).

Suggest that we obsolete this term, possibly replace with new terms for axial system and radial system.

See Items for future meetings#other wood terms, below.

New proposed hierarchy (children of plant cell):

plant cell

>sieve element (new term)

>>sieve tube member (syn.: sieve tube element)

>>sieve cell (new term)

>tracheary element

>>tracheid

>>vessel member

>ground tissue cell (PO:0025030)

>>sclerenchyma cell (PO:0000077)

>>>sclerid (new term)

>>>fiber cell (new term)

>>>>phloem fiber cell

>>>>xylem fiber cell

>>>>other kinds of fiber cells?

New definitions - sieve elements

Definitions from Esau's Anatomy of Seed Plants

sieve element (new term)

From Esau (glossary): The cell in the phloem tissue concerned mainly with longitudinal conduction of food materials. Classified into sieve cell and sieve tube member.

Also from Esau (in text): Their principal morphological characteristics are sieve areas (modified pits) in their walls and the absence of nuclei in mature protoplasts.

proposed def.: A plant cell that is part of a portion of phloem tissue, has sieve areas (modified pits) in its walls, and lacks a nucleus in its mature protoplast.

Comment: Sieve cells function mainly in longitudinal conduction of organic solutes. Classified into sieve cells and sieve tube members based on the presence of sieve plates and specialization of sieve areas in different parts of the cell. Develops from either a cambial initial or a cell of the procambium.

part_of phloem, participates_in sporophyte stage

sieve cell (new term)

proposed def.: A sieve element in which the sieve areas are not aggregated into sieve plates.

Comment: Sieve areas in sieve cells generally have narrow pores and thin connecting strands, and they are not highly specialized, but instead are fairly uniform throughout the cell wall. Typical of gymnosperms and non-seed vascular plants. Differ from sieve tube members, which have sieve plates and more pronounced specialization of sieve areas.

sieve tube member (PO:0000289)

current def.: One of the series of cells that make up a sieve tube; it shows a more or less pronounced differentiation between sieve plates (wide pores) and lateral sieve areas (narrow pores).

comment: Also sieve tube element and the obsolete sieve tube segment. Occurs in the sporophytic phase of a plant life cycle.

proposed def.: A sieve element that is part of a sieve tube and has sieve areas aggregated into sieve plates.

Comment: Sieve tube members have sieve areas that are specialized into those with wide pores in sieve plates and those with with narrow pores in lateral sieve areas. Sieve tube members may have inclined end walls with compound or simple sieve plates. Typical of angiosperms. Differ from sieve cells, which have less pronounced specialization of sieve areas and no sieve plates.

syn.: sieve tube element, sieve tube segment

part_of sieve tube (new term)

See below for companion cells and other parenchyma cells found in vascular tissue.

New term for sieve tube

sieve tube, proposed definition: A portion of phloem tissue that has as parts a series of sieve tube members arranged end to end and interconnected through sieve plates.

Comment: A sieve plate (GO:0097218) is part of a sieve tube member.

New terms for GO

These subcellular components have been added to GO:

• GO:0097217 sieve area
• GO:0097218 sieve plate
• GO:0097219 compound sieve plate
• GO:0097220 simple sieve plate

sieve area: A cell wall part that is a pit-like area in a plant-type cell wall of a sieve element and has as parts pores lined with callose and occupied by strands of protoplasmic material that interconnect the protoplasts of contiguous sieve elements.

is_a cell wall part (GO:0044426), part_of plant-type cell wall (GO:0009505); part_of sieve element (PO:xxxx) - may have to go in comment

sieve plate: A cell wall part that is the part of a wall of a sieve tube member that bears one or more highly specialized sieve areas.

comment: Typical of angiosperms.

is_a cell wall part (GO:0044426), part_of plant-type cell wall (GO:0009505), has_part sieve area (GO:xxxx); part_of sieve tube member (PO:xxxx).

Could add the relation callose deposition in phloem sieve plate (GO:0080165) inheres_in sieve plate.

compound sieve plate: A sieve plate that has as parts several specialized sieve areas in either a scalariform or reticulate arrangement.

comment: Often located on an end wall of a sieve tube member. Unspecialized sieve areas may occur on other parts of the cell.

is_a sieve plate

simple sieve plate: A sieve plate that has as part a single specialized sieve area.

comment: Often located on an end wall of a sieve tube member. Unspecialized sieve areas may occur on other parts of the cell.

New definitions - tracheary elements

These edits are done in the obo file.

xylem element (PO:0000273): A cell making up xylem tissue.

Currently, this is parent of tracheary element and xylem fiber. I suggest we obsolete it and make xylem fiber cell a child of fiber cell. Xylem element could be a broad synonym of tracheary element and xylem fiber.

tracheary element (PO:0000290)

current def.: General term for any water conducting cell, tracheid or vessel member.

Currently is part_of primary xylem and part_of secondary xylem.

proposed def.: A plant cell (PO:0009002O) that has a lignified cell wall with secondary thickening and bordered pits and is dead at maturity.

comment: More or less elongated and with pits of various types in the cell wall. Tracheary elements function in the conduction of water and dissolved substances such as mineral nutrients from the roots to the shoot system. Tracheary elements can be distinguished from fiber cells (PO:0025407) by the presence of bordered pits, although there are intermediate forms called fiber tracheids (PO:0000355).

participates_in sporophyte stage, part_of xylem, disjoint from hydroid

tracheid (PO:0000301)

current def.: In the xylem, a dead elongated water-conducting cell in which at least the middle lamella of the end walls remains intact.

proposed def.: A tracheary element (PO:0000290) that has no perforations in its cell wall.

comment: May have any of the kinds of secondary wall thickenings found in tracheary elements. The area of contact between two tracheids has only bordered pits, whereas in vessel members (PO:0002003) it has openings in the cell wall called perforations, organized into perforation plates (term has been requested in GO).

vessel member (PO:0002003)

current def.: One of the cellular components of a vessel, a dead cell with the wall between adjacent members being variously perforated and the walls that persist variously thickened.

proposed def.: A tracheary element (PO:0000290) that is part of a vessel (PO:0025417) and has as parts perforation plates.

Comment: The cell wall of a vessel member has openings called perforations, which are organized into perforation plates (term has been requested in GO). These are usually on the end walls of a cell, but may also be on the side walls. A perforation plate may be simple, with one perforation, or multiperforate, with more than one perforation.

syn.: vessel element, vessel segment

part_of vessel (new term)

vessel (PO:0025417)

proposed def.: A portion of xylem (PO:0005352) tissue that has as parts a tube-like series of vessel members (PO:0002003), the common walls of which have perforations.

perforation plate (for GO)

proposed def.: A cell wall part that is the part of a wall of a vessel member and bears one or more openings (perforations).

comment: Part of a vessel member (PO:0002003). May be simple, with one perforation, or multiperforate, with more than one perforation. Perforation plates are usually on the end walls of a cell, but may also be on the side walls.

Reference ISBN:0471245194 (Esau's Anatomy of Seed Plants).

New definitions - ground tissue cells

sclerenchyma cells

These edits are done in the obo file.

sclerenchyma cell (PO:0000077)

current def.: Usually dead cell variable in form and size, with more or less thick, often lignified, secondary walls.

proposed def.: A ground tissue cell (PO:0025030) with thickened secondary cell walls that are lignified.

comment: May or may not be devoid of protoplast at maturity. Not always easy to distinguish from tracheary elements (PO:0000290) or sclerified parenchyma cells (PO:0000074). Distinguishable from collenchyma cells (PO:0000075) because collenchyma cells alive at maturity. Collenchyma cells provides flexibility while sclerenchyma cells provide hardness.

Currently, sclerenchyma cell part_of sclerenchyma, but this is not always true. There can be isolated sclerenchyma cells.

sclerid (PO:0025418)

proposed def.: A sclerenchyma cell (PO:0000077) that has thick secondary walls with many pits.

comment: Usually not very elongated.

parenchyma cells in phloem tissue

These edits are done in the obo file.

companion cell (PO:0000071)

current definition: A specialized parenchyma cell associated with a sieve-tube member in angiosperm phloem and arising from the same mother cell as the sieve-tube member.

proposed definition: A parenchyma cell (PO:0000074) that is adjacent to a sieve-tube member (PO:0000289) and arises from the same initial cell (PO:0004011) as the sieve-tube member.

comment: Found in angiosperms. Compare to albuminous cells (PO:0025412), which are found in gymnosperms.

Currently part_of primary phloem and part_of secondary phloem, which can't be true. Should change to part_of phloem.

Suggest that we add relation companion cell adjacent_to sieve tube member.

Need to check definition of phloem mother cell. Does it only differentiate into secondary phloem, or can it be for primary phloem too?

albuminous cell (new term)

proposed def.: A parenchyma cell (PO:0000074) that is morphologically and physiologically associated with a sieve cell (PO:0025415) but does is not derived from the same initial cell (PO:0004011) as the sieve cell.

comment: May be found in the ray system (PO:0025411) and sometimes the axial system (PO:0025410) of gymnosperms. Compare to companion cells (PO:0000071), which are found in angiosperms.

is_a parenchyma cell, part_of phloem, adjacent_to sieve cell.

fiber cells

These edits are done in the obo file.

fiber cell (new term, PO:0025407)

proposed def.: An elongated, tapering schlerenchyma cell (PO:0000077) with a more or less thick secondary cell wall.

comment: May or may not have lignin in the secondary wall or a living protoplast at maturity. It may be difficult to distinguish fiber cells from tracheary elements (PO:0000290).

phloem fiber cell (PO:0004519) (was called phloem fiber)

current def.: A fiber in phloem.

proposed def.: A fiber cell (PO:0025407) that is part of a portion of phloem (PO:0005417) tissue.

Made part_of phloem, instead of part_of secondary phloem.

xylem fiber cell (PO:0000274) (was called xylem fiber)

current def.: A fiber in xylem.

proposed def.: A fiber cell (PO:0025407) that is part of a portion of xylem (PO:0005352) tissue.

comment: It may be difficult to distinguish xylem fiber cells from tracheary elements (PO:0000290).

Made part_of xylem, instead of part_of secondary xylem.

libriform fiber cell (PO:0004520)

current def.: A xylem fiber commonly with thick walls and simple pits.

proposed def.: A xylem fiber cell (PO:0000274) with simple pits.

Comment: Libriform fiber cells have unbordered pits while fiber tracheids (PO:0000355) have bordered pits. Many intermediate forms exists and are generally classified as fiber tracheids. If both libriform fiber cells and fiber tracheids are present, the libriform fiber cells usually have thicker walls. Libriform fiber cells have a slit-like aperture toward the cell lumen, but no pit cavity.

fiber tracheid (PO:0000355)

current def.: A fiber-like tracheid in the secondary xylem; commonly thick walled, with pointed ends and bordered pits that have lenticular to slit-like apertures.

proposed definition: A xylem fiber cell (PO:0000274) with bordered pits with pit cavities.

comment: Commonly thick walled, with pointed ends and bordered pits that have lenticular to slit-like apertures. If both libriform fiber cells (PO:0004520) and fiber tracheids are present, the libriform fiber cells usually have thicker walls. Fiber tracheids have bordered pits with smaller pit cavities than the vessel members (PO:0002003) or tracheids (PO:0000301) of the same wood and a distinct pit cavity leading from the pit cavity to the cell lumen through the thick cell wall.

septate fiber (PO:0004521)

current def.: A fiber with thin transverse walls (septa), which are formed after the cell develops a secondary wall thickening.

Septate fibers can be found in both the xylem and the phloem. PO:0004521 is_a xylem fiber, but both tracheid-type and libriform-type xylem fibers can be septate. There are no annotations on this term, so I suggest we obsolete it, and replace it with two new terms: septate fiber tracheid and septate libriform fiber. Could also add septate phloem fiber, is_a phloem fiber.

proposed definition, septate fiber tracheid: A fiber tracheid (PO:0000355) that has as parts one or more thin internal partitions or septa.

comment: Septate fiber cells usually have a living protoplast at maturity. The septa form from mitosis within the lignified cell wall.

proposed definition, septate libriform fiber cell: A libriform fiber cell (PO:0004520) that has as parts one or more thin internal partitions or septa.

comment: Septate fiber cells usually have a living protoplast at maturity. The septa form from mitosis within the lignified cell wall.

proposed definition, septate phloem fiber cell: A phloem fiber cell (PO:0004519) that has as parts one or more thin internal partitions or septa.

comment: Septate fiber cells usually have a living protoplast at maturity. The septa form from mitosis within the lignified cell wall.

other kinds of fiber cells?

gelatinous fiber: A xylem fiber cell in which the inner-most layer of the secondary wall contains abundant alpha-cellulose and is poor in lignin.

comment: Commonly found in reaction wood in dicots. The inner layer of the cell wall, or G-layer, can absorb much water and swell and is relatively porous and less compact than the outer layers of the cell wall.

ref: Fahn

synonym: mucilaginous fiber

other wood terms

Wood is a synonym for secondary xylem (PO:0005848) -- see definition above.

New terms

Do we want to define axial system and ray system as any portion of tissue, or the entirety of tissue in a plant structure?

Should these terms be part_of secondary xylem?

axial system (new term):

Does this definition distinguish axial system from primary vascular tissue?

proposed definition: A portion of plant tissue that has as parts cells derived from the fusiform cambial initials and oriented with their longest diameter parallel to a root or shoot axis.

comment: Includes portions of secondary xylem tissue and axial wood parenchyma tissue.

synonyms: vertical system, longitudinal system

ray system (new term):

proposed definition: A portion of plant tissue that develops from ray initials and extends radially in the secondary xylem and phloem of a plant axis and has as part ray wood parenchyma.

comment: May include ray tracheids, as in Pinaceae and some Cupressaceae.

synonyms: radial system (exact), horizontal system (exact), ray (broad)

Existing terms

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 tissue that is part of a portion of secondary xylem and has as parts wood parenchyma cells.

axial wood parenchyma (PO:0004533):

Current def.: Parenchyma tissue in the axial system of secondary xylem.

Proposed def.: A portion of wood parenchyma that is part of an axial system and has as parts axial wood parenchyma cells.

part_of axial system

ray wood parenchyma (PO:0004534):

Current def.: Radially oriented parenchyma tissue in secondary xylem.

Proposed def.: A portion of parenchyma tissue that is part of a ray system and has as parts ray wood parenchyma cells.

comment: Occurs in bands or rays of variable width and height that extend radially in the secondary xylem and phloem of a plant axis.

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 that is part of a portion of wood parenchyma.

comment: Found in secondary xylem.

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 that is part of a portion of ray wood parenchyma. develops from ray initials

part_of ray wood parenchyma

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 that is oriented with its longest dimension parallel to the axis 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 that is oriented with its longest dimension radial to the axis 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 that is part of a portion of axial wood parenchyma.

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 that has as parts living wood parenchyma cells.

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:xxx) of a plant axis.

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 (wood) which lacks living wood parenchyma cells.

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, 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 (wood) that is characterized by a lower density and larger cells than late wood and is formed in the first part of a growing season.

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 (wood) that is characterized by a higher density and smaller cells than early wood and formed in the later part of a growing season.

growth ring ()

growth ring boundary (PO:0004517):

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

coleoptile emergence

This was discussed at the NYBG Meeting, on Sunday_Sept_11th,_2011

We don't need to deal with all of this before the release, because Mary will use radicle emergence stage instead of coleoptile emergence.

From MS (MaizeGDB): It would be more useful for maize if the definition for coleoptile emergence PO:0007045 were altered to be: Emergence of coleoptile from the seed. (rather than above ground)

This could compare well to the radicle definition (PO:0007015 radicle emergence): The stage at which the radicle or root emerges from seed.

At the POC meeting on Sunday_Sept_11th,_2011, we agreed to keep the existing terms that reference emergence from the soil, but rename them as stages, and add new terms for emergence from seed coat. Need to copy over list of existing synonyms to new emergence terms.

Furthermore, shoot emergence is part_of seedling growth, but has no is_a parent, and seedling growth has no is_a parent. Imbibition (sibling of shoot emergence) also has no is_a parent.

current structure:

Shoot emergence (stage) should be is_a seedling growth (stage). Seedling growth (stage) should be is_a vegetative growth stage.

Imbitition (stage) should be is_a germination (stage). Will deal with definitions of imbibition and germination later.

current and proposed terms and definitions

All of the terms below originally described a single point in time. We need to figure out when the shoot emergence stage should end.

current: shoot emergence (PO:0007030): Shoot or leaf breaks through the soil surface.

proposed: shoot emergence from growth medium development stage (PO:0007030): A seedling growth stage that has as a participant a whole plant during the interval between emergence of a part of a shoot system from the growth medium and ???.

Comment: This terms is used only for seed plants.

proposed: shoot emergence from seed coat development stage (new number): A seedling growth stage that has as a participant a whole plant during the interval between emergence of a part of a shoot system from the seed coat and ???.

Comment: May occur simultaneously with shoot emergence form the growth medium. This terms is used only for seed plants.

current: coleoptile emergence (PO:0007045): Emergence of coleoptile above ground. [source: GR:ap, ISBN:3826331524]

proposed: coleoptile emergence from growth medium development stage (PO:0007045): A shoot emergence stage that has as a participant a whole plant during the interval between emergence of a coleoptile from the growth medium and ???

Comment: This terms is used only for seed plants.

proposed: coleoptile emergence from seed coat development stage (new number): A shoot emergence stage that has as a participant a whole plant during the interval between emergence of a coleoptile from the seed coat and ???

Comment: May occur simultaneously with coleoptile emergence form the growth medium. This terms is used only for seed plants.

current: cotyledon emergence (PO:0007049): Emergence of cotyledons above ground. [source: GR:ap, ISBN:3826331524]

proposed: cotyledon emergence from growth medium development stage (PO:0007049): A shoot emergence stage that has as a participant a whole plant during the interval between emergence of a cotyledon from the growth medium and ???

Comment: This terms is used only for seed plants. Cannot be used in plants with hypogeal germination.

proposed: cotyledon emergence from seed coat development stage (new number): A shoot emergence stage that has as a participant a whole plant during the interval between emergence of a cotyledon from the seed coat and ???

Comment: This terms is used only for seed plants. Cannot be used in plants with hypogeal germination. May occur simultaneously with cotyledon emergence form the growth medium.

current: epicotyl emergence (PO:0007054): Emergence of the epicotyl above ground. [source: GR:ap, ISBN:0306416875]

proposed: epicotyl emergence from growth medium development stage (PO:0007054): A shoot emergence stage that has as a participant a whole plant during the interval between emergence of an epicotyl from the growth medium and ???

Comment: This terms is used only for seed plants. During this phase, only the first true foliage leaf or pair of leaves is visible. Occurs in plants with hypogeal germination.

proposed: epicotyl emergence from seed coat development stage (new number): A shoot emergence stage that has as a participant a whole plant during the interval between emergence of an epicotyl from the seed coat and ???

Comment: This terms is used only for seed plants. During this phase, only the first true foliage leaf or pair of leaves is visible. Occurs in plants with hypogeal germination. May occur simultaneously with epicotyl emergence form the growth medium.

current: hypocotyl emergence (PO:0007043): Emergence of the hypocotyl above ground. [source: GR:ap, ISBN:0306416875]

proposed: hypocotyl emergence from growth medium development stage (PO:0007043): A shoot emergence stage has as a participant a whole plant during the interval between emergence of a hypocotyl from the growth medium and ???

Comment: This terms is used only for seed plants. Occurs in plants with epigeal germination.

proposed: hypocotyl emergence from seed coat development stage (new number): A shoot emergence stage that has as a participant a whole plant during the interval between emergence of a hypocotyl from the seed coat and ???

Comment: This terms is used only for seed plants. Occurs in plants with epigeal germination. May occur simultaneously with hypocotyl emergence form the growth medium.

Could also add terms for feeder emergence for some gymnosperms.

For all of the above terms, need to check existing synonyms and move or copy them as needed.

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

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