POC Conf. Call 9-20-11

POC meeting, Webex Conference Call; Date: Tuesday Sept 20th, 2011 10am (PDT)

In attendance:

POC members:

Absent:

Collaborators: none

Acceptance of the minutes from the POC_Conf._Call_8-30-11?

Tech issues

OWL version stamp

Request from Gavin Kennedy:

"Would it be possible to add an owl:versionInfo attribute to the OWL Plant Ontology so that we can track the changes in versions. This could be the version number or a date stamp, etc."

User requests open on Source Forge: PAO

Legume terms

submitted by Austin Mast

phyllode

Last week, we looked at examples of leaves where the petiole has phyllode development, but there is normal lamina development (with leaflets) beyond the petiole. We need a term to describe this, as well as when the whole leaf develops as a phyllode.

Background:

Boke 1940 (http://www.jstor.org/stable/2436690, DOI:10.2307/2436690) uses the term phyllode to refer only to those leaves without leaflets:

"The seedling usually displays 1 even-pinnate leaf, 1 bipinnate leaf, and several transition forms. Pinnate leaves and transition forms possess an apical pointlet like that of the phyllode."

The main reference people cite for phyllodes is: D.R. Kaplan 1980, Heteroblastic leaf development in Acacia: morphological and morphogenetic implications, La Cellule 73, pp. 137–203.

Kaplan say: "The present developmental comparisons between phyllodes and pinnatifid leaves in seedlings of Acacia have demonstrated unequivically that the blade of the phyllode is the longitudinal positional homologue of the lamina of the fully pinnate leaf, at all stages of development. At no stage is the phyllode blade merely a petiolar derivative, nor is there evidence of lamina suppression in favor of petiolar elaboration as suggested in the classical developmental paradigm."

Some more contemporary uses of the term phyllode:

Gardner et al. 2005 (http://www.publish.csiro.au/view/journals/dsp_journal_fulltext.cfm?nid=150&f=SB04052):

"A phyllode usually consists of a pulvinus and photosynthetic region, although it can be sessile, decurrent with the stem, or reduced to scales. The photosynthetic region is highly variable and ranges from vertically flattened, through terete, quadrangular and triquetrous to horizontally flattened. Phyllodes usually possess at least one extra-floral nectary on the adaxial nerve, and sometimes up to five. Boughton (1981, 1985) observed three types of extra-floral nectaries. She also investigated the indumentum and found almost all species have two kinds of trichomes, one glandular and one non-glandular (Boughton 1989). According to Arber (1918), the chief anatomical feature by which phyllodes differ from true leaf laminae is the occurrence of two opposing series of vascular bundles."

and later in the paper:

"Previous approaches, such as basic anatomy and inferences from the sequence of heteroblastic leaf development in acacias, have led researchers to state that the phyllode is homologous with the petiole of a bipinnate leaf (e.g. Mann 1894; Goebel 1905; Troll 1939), or with the petiole and rachis (e.g. Bentham 1875; Reinke 1897), and make comparisons with the monocotyledonous leaf. Investigating the developmental morphology of phyllodes, Kaplan (1980) proposed a new model: that the phyllode is actually the positional homologue of the lamina of a bipinnate leaf. In essence, this suggests that the phyllode is directly comparable to a simple leaf. Kaplan’s theory does not, however, address the issue of the opposing vascular bundles found in phyllodes.

"The pattern of branching observed in the vascular bundles of A. verniciflua phyllodes suggests that the abaxial marginal nerve is homologous to the mid-rib in a simple leaf. This implies that laminar expansion occurs on both sides of the ‘mid-rib’, but vertically, and fused together. The emergence of the adaxial marginal nerve as two separate bundles, originating on opposing sides that eventually fuse rather than directly from the vascular ring found in the pulvinus, supports our interpretation and has been observed (together with other patterns) in several other Acacia species (von Wartburg 1991)."

Leroy and Heuret 2007 (doi:10.1016/j.crvi.2007.11.006): "The subgenera Phyllodineae... as the species are characterised by a polymorphism of vegetative characters where bi-pinnate leaves are replaced by a type of foliar organ called a phyllode." and "...the different transitional forms range from pinnate leaves to phyllodes..."

See fig. 1 in this paper. They refer a "flattened petiole" and a "flattened rachis" in transitional leaves.

Yang et al. 2008 (DOI: 10.1007/s11240-008-9424-7) use leaf as synonym for phyllode in Acacia. Refer specifically to phyllodes without any pinnate (sic) on top of them.

Forster and Bonser 2009, Annals of Botany, use the term phyllode to refer to adult leaves without leaflets: "Acacia implexa (Mimosaceae) is a heteroblastic species that develops compound (juvenile), transitional and phyllode (adult) leaves that differ dramatically in form and function."

RW did not find any contemporary papers that said that a phyllode is a petiole.

Leaves that have phyllode-type development toward the base with leaflet development toward the tip are a type of transition leaf.

Unifacial leaf as synonym? No- not exactly the same, but similar development. See Kaplan 1970 (http://www.jstor.org/stable/2485311). Might be better to make a parent term ensiform leaf which has children phyllode and unifacial leaf.

Proposed terms and definitions:

vascular leaf

>unifacial leaf

>>terete leaf (round in cross section)

>>ensiform leaf (flat in cross section)

>>>phyllode

unifacial leaf: A vascular leaf that has increased activity of either the adaxial or abaxial meristem early in development, leading to abscense of the opposite surface on the leaf. (ref: Lawrence, Kaplan 1970 fig. 1, Sajo and Rudall 1999)

Comment: A unifacial leaf may be round in cross-section (terete) or it may be laminar (ensiform), in which case lamina development is in a median plane (perpendicular to the axis), rather than a transverse plane (tangent to the axis). Unifacial leaves may be bifacial at the leaf base. Many unifacial leaves develop by reduced (or absent) activity of the marginal meristems and increased activity of the adaxial meristem early in development, leading to mature leaves with only an adaxial surface (e.g., Acacia, most monocots?). However, some develop by increased activity of the abaxial meristem early in development, leading to mature leaves with only an abaxial surface.

RW: need to check and add references for all of these

terete leaf: A unifacial leaf that is round in cross section due throughout all of part of the length of the leaf.

Comment: The surface of a terete leaf correspond to either the adaxial or abaxial surface of a normal leaf.

ensiform leaf: A unifacial leaf that is flat in cross section due to a lamina that develops in a median plane (perpendicular to the axis), rather a transverse plane (tangent to the axis) throughout all of part of the length of the leaf.(ref: Lawrence, Kaplan 1970 fig. 1, Sajo and Rudall 1999)

Comment: Common in many monocots and some dicots. Both sides of an ensiform leaf correspond to only one of either the adaxial or abaxial surface of a normal leaf.

RW: Maybe phyllode should just be a narrow synonym of ensiform leaf.

phyllode: An adult ensiform leaf with a lamina that develops in a median plane, rather a transverse plane throughout the length of the leaf and is a result of increased activity of the adaxial meristem early in develop.

Comment: Common in legumes of the genus Acacia. Similar development occurs in some monocot leaves (ensiform leaves), but they are not called phyllodes. Transitional leaves also occur, in which the basal portion of the leaf develops similar to a phyllode, but the apical portion of the leaf develops normal leaflets (see PO:xxxxxxx, phyllode-type transition leaf). In some leaves, the petiole may twist giving the appearance that the lamina is a phyllode, but it is not. Phyllodes are generally xeromorphic.

is_a ensiform leaf, is_a adult leaf

phyllode-type transition leaf: A transitional vascular leaf in which the basal portion of the leaf has lamina development is a median plane, similar to a phyllode, and the apical portion of the leaf develops leaflets similar to a juvenile leaf.

Comment: Common in seedlings of legumes of the genus Acacia. May also occur later, after the plant has begun to produce phyllodes.

is_a transitional leaf, is_a vascular leaf

bristle

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

At the 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.

New children of calyptra perianth

This was raised at the POC meeting POC_Conf._Call_8-23-11

Existing terms:

• fruit operculum (PO:0025298): A collective organ part structure that is the apical part of a circumsessile capsular fruit that separates from the rest of the capsule during dehiscence. [source: POC:curators]

Comment: Develops from the apical portion of a gynoecium. Found in Eucalyptus and other Myrtaceae.

and

• calyptra perianth (PO:0025299): A perianth that is composed of fused perianth parts and located on top of a gynoecium that contains an inferior ovary. [source: POC:curators]

Comment: May be composed of fused petals, sepals or tepals, but is generally formed from fused petals in Eucalyptus and other Myrtaceae. Sometimes erroneously referred to as part of a fruit. Not the same structure as a spore capsule calyptra.

Synonyms: related: floral operculum; exact: angiosperm calyptra; exact: floral calyptra (suggest we add flower operculum as related and flower calyptra as exact)

Proposed changes: More specific terms for calyptra

At least week's meeting, there was a request for more specific terms for calyptras formed of fused petals or fused sepals.

In Eucalyptus, there may be one or two calyptras: an inner operculum or calyptra composed of fused petals and an outer operculum or calyptra composed of fused sepals. In many species, the sepals to do not fuse, and there is no outer operculum.

Our current definition of calyptra perianth includes fused tepals, which would encompass the existing term "fused collective tepal structure" (PO:0025138), but to my knowledge, tepals are not present in Eucalyptus. (The ANBG provides EUCLID, an excellent resource for description of Eucatypus morphology.)

Suggest adding a new term "fused perianth", that is consistent with our other terms such as "fused collective tepal structure". This would be a more general term, and could include perianths that are partially fused.

Proposed new terms and ontology structure:

• need to open a SF tracker for these

perianth

> fused perianth (new)

>> fused collective tepal structure (PO:0025138)

>> calyptra perianth (flower operculum) (PO:0025299)

>>> calyptra calyx (outer operculum) (new)

>>> calyptra corolla (inner operculum) (new)

• Should we also add terms for fused petal and fused sepal (already have fused tepal)?

terms and definitions

• fused perianth: A perianth that is composed of two or more fused perianth parts (sepals, petals or tepals).

Comment: Perianth parts may be partially or wholly fused.

• calyptra perianth (PO:0025299): A fused perianth that is composed of fused sepals or petals and located on top of a gynoecium that contains an inferior ovary.

Comment: Found in Eucalyptus and other Myrtaceae. The petals are generally completely fused. Sometimes erroneously referred to as part of a fruit. Not the same structure as a spore capsule calyptra or fruit operculum. Use the more specific term (calytra corolla or calytra calyx) if possible. Species of the subgenera Monocalyptrus have only a calyptra corolla (inner operculum) while in most other species, a calyptra calyx is also present, at least early in flower development.

Synonyms: flower operculum, floral operculum, floral calyptra; angiosperm calyptra

• calyptra calyx: A calyptra perianth composed of fused sepals.

Comment: Sometimes found in Eucalyptus and other Myrtaceae, covering an inner operculum or calyptra corolla. The sepals are generally completely fused.

Synonyms: outer operculum, calyx operculum

• calyptra corolla: A calyptra perianth composed of fused petals.

Comment: Often found in Eucalyptus and other Myrtaceae. The petals are generally completely fused. If an outer operculum (calyptra calyx) is present, it covers the inner operculum (calyptra corolla).

Synonyms: inner operculum, corolla operculum

• fused collective tepal structure (PO:0025138), calyptra calyx and calyptra corolla all have dual parentage (is_a fused perianth and is_a collective tepal structure, calyx, or corolla. If we were to import PATO:0000642 (fused with), we could make cross product definitions and infer one of the relations.