Difference between revisions of "POC Conf. Call 4-12-11"

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=New terms for Physcomitrella and related taxa (continued)=
 
=New terms for Physcomitrella and related taxa (continued)=
−
==[https://sourceforge.net/tracker/index.php?func=detail&aid=3132600&group_id=76834&atid=835555 Sporangium]==
 
  
−
We currently have the class '''sporangium''' (PO:0025094), which is a cardinal organ part.
+
==Cardinal organ parts==
 +
Terms requested by MO:
  
−
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?
+
* '''[https://sourceforge.net/tracker/?func=detail&aid=3234979&group_id=76834&atid=835555 calyptra]'''
  
−
Current def: A hollow cardinal organ part in which spores are produced. [source: ISBN:0716710072]
+
Moss Ontology definition: A membranous or hairy cap or hood that forms from the wall of the archegonium and protects the embryonic sporophyte. It is formed from the archegonium by mitotic divisions, and hence it is haploid. Bill and Nancy Malcolm (2006): Mosses and other Bryophytes, an illustrated glossary, second edition and altered from David Cove.
  
−
Comment: May be multicellular or unicellular. In bryophytes, particularly in mosses, a sporangium is referred to as a capsule
+
We also have a request (from PJ) for calyptra, which encloses the fruit in Eucalyptus. That term should be named '''perianth calyptra''' (see below under operculum), and this term should be named '''spore capsule calyptra''', to distinguish them.
  
 +
'''Proposed name and def.: spore capsule calyptra:''' A cardinal organ part that develops from the wall of an archegonium and surrounds a sporangium.
  
−
We also have:
+
Comment: Found in bryophytes and pteridophytes (''according to Parihar''). The calyptra ia a membranous or hairy cap or hood composed of gametophytic tissue that protects the embryonic sporophyte within the archegonium. In some species, the calyptra may persist after the sporophyte develops and gets carried upward as the seta elongates.
  
−
'''megasporangium''' (PO:0025201): A sporangium in which megaspores are produced. [source: ISBN:0716710072]
+
participates_in gametophytic phase, develops_from venter (more specific) or archegonium (more general)?
  
−
'''microsporangium''' (PO:0025202): A sporangium in which microspores are produced. [source: ISBN:0716710072]
+
subsets for bryophytes, pteridophytes
  
−
'''nucellus''' (PO:0020020): A megasporangium in a seed plant, composed of fleshy subepidermal tissue inside an ovule and surrounding a megasporocyte. [source: POC:rw]
+
[From Smith p. 39: calyptra develops from venter in Corsiniaceae (also has an involucre); also p. 52, p. 67, See picture on p. 77
  
−
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]
+
* '''[https://sourceforge.net/tracker/?func=detail&aid=3234981&group_id=76834&atid=835555 venter]'''
  
−
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.
+
This term was not suggested by Moss Ontology, but perhaps we should add it.
  
 +
'''proposed def.:''' A cardinal organ part that is the enlarged basal part of an archegonium and has an egg cell located in it.
  
−
'''Proposed def. nucellus:''' A megasporangium in a seed plant, composed of fleshy subepidermal tissue ''located in'' an ovule and surrounding a megasporocyte.
+
part_of archegonium
  
−
'''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]
+
subsets for bryophytes, pteridophytes, gymnosperms
  
−
(comments stay the same)
 
  
−
We could continue to use the more general part_of relation for located_in
+
*'''[https://sourceforge.net/tracker/?func=detail&aid=3234985&group_id=76834&atid=835555 archegonium neck]'''
  
−
==Sporangium parts==
+
This term was not suggested by Moss Ontology, but perhaps we should add it.
  
−
This is continued from our discussion at the [[POC_Conf._Call_3-8-11]]
+
'''proposed def.:''' A cardinal organ part that is the elongated apica part of an archegonium.
  
−
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).
+
Comment: Early in development, the neck is occluded by a single row of neck canal cells. At maturity, the neck canal cells disintegrate, creating a canal for the sperm to enter the archegonium.
  
−
From Smith:
+
part_of archegonium
  
−
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).
+
(can also add term for neck canal cell when we deal with cells)
  
−
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.
+
subsets for bryophytes, pteridophytes, gymnosperms
  
−
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.
+
*'''[https://sourceforge.net/tracker/?func=detail&aid=3241725&group_id=76834&atid=835555 base]'''
  
−
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
+
'''Proposed name and def.: sporangium base''': A cardinal organ part that is the basal part of a sporangium.
  
−
Lycopods: Sporangia borne on sporophylls.
+
Comment: Term used in mosses and other bryophytes (what about pteridophytes?). The sporangium base is the sterile part of the sporangium below the theca. If swollen and distinct from the rest of the sporangium, it is called an apophysis or hypophysis. (ref: Bill and Nancy Malcolm (2006): Mosses and other Bryophytes, an illustrated glossary, second edition)
 +
 
 +
part_of sporangium; Synonyms: sporangium neck, apophysis, hypophysis
 +
 
 +
subsets for bryophytes
 +
 
 +
 
 +
*'''[https://sourceforge.net/tracker/?func=detail&aid=3241737&group_id=76834&atid=835555 theca]'''
 +
 
 +
Moss Ontology definition: The main body (urn) of a sporangium. Altered from Bill and Nancy Malcolm (2006): Mosses and other Bryophytes, an illustrated glossary, second edition
 +
 
 +
We already have the term theca (PO:0009069) to describe paired microsporangia in angiosperms. Maybe we should call that '''anther theca''' and call this term '''sporangium theca:'''.
 +
 
 +
'''Proposed name and def.: sporangium theca:''' A cardinal organ part that is the main body of a sporangium and has spores located in it.
 +
 
 +
Comment: Term used in mosses and other bryophytes (what about pteridophytes?)
 +
 
 +
part_of sporangium
 +
 
 +
subsets for bryophytes, maybe pteridophytes
 +
 
 +
 
 +
*'''[https://sourceforge.net/tracker/?func=detail&aid=3241747&group_id=76834&atid=835555 peristome]'''
 +
 
 +
Moss Ontology definition: A single or double circle of teeth inside the mouth of a moss sporangium. Bill and Nancy Malcolm (2006): Mosses and other Bryophytes, an illustrated glossary, second edition
 +
 
 +
'''proposed definition:''' A cardinal organ part that is a single or double circle of teeth inside a spore capsule mouth.
 +
 
 +
Comment: The peristome is located under the operculum, if an operculum is present. Upon maturity of a capsule, the teeth of the peristome open to release the spores.
 +
 
 +
part_of sporangium
 +
 
 +
subsets for bryophytes
 +
 
 +
 
 +
*'''peristome tooth'''
 +
 
 +
Not requested by Moss Ontology, but should add it.
 +
 
 +
'''Proposed def:''' A cardinal organ part that is a single lobe or tooth of a peristome.
 +
 
 +
Comment: Peristome teeth may be simple or compound, and may be attached by their tips to the epiphragm.
 +
 
 +
part_of peristome
 +
 
 +
subsets for bryophytes
 +
 
 +
 
 +
*Add term for peristome cell? Are they dead at maturity? What kind of cells are they?
 +
 
 +
 
 +
*'''[https://sourceforge.net/tracker/?func=detail&aid=3241767&group_id=76834&atid=835555 lid/operculum]'''
 +
 
 +
Moss Ontology definition: Either the lid that blocks the capsule mouth or the apical portion of a sporangium that opens during dehiscence. Bill and Nancy Malcolm (2006): Mosses and other Bryophytes, an illustrated glossary, second edition.
 +
 
 +
We also have a request (from PJ) for operculum, which is part of the fruit in Eucalyptus. That term should be named fruit operculum, and this term should be named spore capsule operculum, to distinguish them.
 +
 
 +
'''Proposed name and def.: spore capsule operculum:''' A cardinal organ part that is the apical part of a spore capsule that separates from the rest of the capsule during dehiscence.
 +
 
 +
Comment: Found in mosses. May remain partly attached to the rest of the capsule.
 +
 
 +
Synonym: sporangium lid
 +
 
 +
part_of sporangium
 +
 
 +
subsets for bryophytes
 +
 
 +
===Also add these terms for angiosperms:===
 +
 
 +
'''[https://sourceforge.net/tracker/?func=detail&aid=3241802&group_id=76834&atid=835555 fruit operculum]:''' A cardinal organ part that is the apical part of a capsular fruit that separates from the rest of the capsule (the fruit calyptra) during dehiscence. apical part of a circumsesile fruit.
 +
part_of fruit
 +
 
 +
The top part of the bud where the perianth (petals) is fused. Leaves fruit underneath it. Operculum is underneath that
 +
 
 +
Comment: Found in Eucalyptus.
 +
 
 +
Is is a cardinal organ part (formed from a single carpel) or collective organ part structure (formed from parts of multiple carpels)?
 +
 
 +
'''[https://sourceforge.net/tracker/?func=detail&aid=3241802&group_id=76834&atid=835555 perianth calyptra]:''' A collective plant structures that is composed of fused perianth parts and located on tops of a gynoecium that contains an inferior ovary.
 +
 
 +
Comment: Found in Eucalyptus and other Myrtaceae. Sometimes erroneously referred to as part of a fruit.
 +
 
 +
==Other related terms for mosses, not from Moss Ontology==
 +
 
 +
*'''[https://sourceforge.net/tracker/?func=detail&aid=3241816&group_id=76834&atid=835555 spore capsule mouth]'''
 +
 
 +
'''Proposed definition:''' A plant anatomical space that is the opening on the apical end of a spore capsule.
 +
 
 +
Comment: The mouth is formed when the operculum separates from the capsule. The mouth may be covered by a peristome.
 +
 
 +
part_of sporangium
 +
 
 +
subsets for bryophytes
 +
 
 +
 
 +
*'''[https://sourceforge.net/tracker/?func=detail&aid=3241820&group_id=76834&atid=835555 epiphragm]'''
 +
 
 +
Schofeld says it is a "membranelike expansion of the columella covering most of the mouth of the sporangium in Polytrichidae (hair cap mosses)."
 +
 
 +
From Crum: "A circular membrane at the tip of the columella to which the peristome teeth of the prolytrichaceae are attached."
 +
 
 +
'''Proposed definition:''' A portion of parenchyma tissue that forms a circular membrane extending from a spore capsule collumella and attached to the ends of the peristome teeth that covers a spore capsule mouth.
 +
 
 +
Comment: Present in some moss species of the family Polytrichaceae.
 +
 
 +
Synonym: tympanum, epiphram
 +
 
 +
subsets for bryophytes
 +
 
 +
 
 +
*'''[https://sourceforge.net/tracker/?func=detail&aid=3241827&group_id=76834&atid=835555 pseudopodium]'''
 +
 
 +
From Crum: "An elongation of the gametophytic axis on which the capsule is borne in Sphagnum and Andreaea."
 +
 
 +
From Schofeld: "An elongated mass of leafless gametophore tissue that pushes the sporophyte beyond the perichaetial leaves (in Andreaea and Sphagnum)."
 +
 
 +
'''Proposed definition:''' A plant axis that is a leafless extension of a gametophore axis on which a sporophyte is borne.
 +
 
 +
Comment: Raises the sporophyte above the perichaetial bracts. Found in Sphagnum and Andreaea.
 +
 
 +
participates_in gametophytic phase
 +
 
 +
subsets for bryophytes
  
 
=Next meeting scheduled for Tues, Apr. 19th, 2011 at 10am PDT=
 
=Next meeting scheduled for Tues, Apr. 19th, 2011 at 10am PDT=

Revision as of 15:01, 6 April 2011

POC meeting, Webex Conference Call; Date: Tuesday April 12th, 2011 10am (PDT)

In attendance:

POC members:

Absent:

Collaborators:


Acceptance of the minutes from the POC_Conf._Call_4-5-11?


Items arising from last week's meeting:

New terms for Physcomitrella and related taxa (continued)

Cardinal organ parts

Terms requested by MO:

Moss Ontology definition: A membranous or hairy cap or hood that forms from the wall of the archegonium and protects the embryonic sporophyte. It is formed from the archegonium by mitotic divisions, and hence it is haploid. Bill and Nancy Malcolm (2006): Mosses and other Bryophytes, an illustrated glossary, second edition and altered from David Cove.

We also have a request (from PJ) for calyptra, which encloses the fruit in Eucalyptus. That term should be named perianth calyptra (see below under operculum), and this term should be named spore capsule calyptra, to distinguish them.

Proposed name and def.: spore capsule calyptra: A cardinal organ part that develops from the wall of an archegonium and surrounds a sporangium.

Comment: Found in bryophytes and pteridophytes (according to Parihar). The calyptra ia a membranous or hairy cap or hood composed of gametophytic tissue that protects the embryonic sporophyte within the archegonium. In some species, the calyptra may persist after the sporophyte develops and gets carried upward as the seta elongates.

participates_in gametophytic phase, develops_from venter (more specific) or archegonium (more general)?

subsets for bryophytes, pteridophytes

[From Smith p. 39: calyptra develops from venter in Corsiniaceae (also has an involucre); also p. 52, p. 67, See picture on p. 77


This term was not suggested by Moss Ontology, but perhaps we should add it.

proposed def.: A cardinal organ part that is the enlarged basal part of an archegonium and has an egg cell located in it.

part_of archegonium

subsets for bryophytes, pteridophytes, gymnosperms


This term was not suggested by Moss Ontology, but perhaps we should add it.

proposed def.: A cardinal organ part that is the elongated apica part of an archegonium.

Comment: Early in development, the neck is occluded by a single row of neck canal cells. At maturity, the neck canal cells disintegrate, creating a canal for the sperm to enter the archegonium.

part_of archegonium

(can also add term for neck canal cell when we deal with cells)

subsets for bryophytes, pteridophytes, gymnosperms


Proposed name and def.: sporangium base: A cardinal organ part that is the basal part of a sporangium.

Comment: Term used in mosses and other bryophytes (what about pteridophytes?). The sporangium base is the sterile part of the sporangium below the theca. If swollen and distinct from the rest of the sporangium, it is called an apophysis or hypophysis. (ref: Bill and Nancy Malcolm (2006): Mosses and other Bryophytes, an illustrated glossary, second edition)

part_of sporangium; Synonyms: sporangium neck, apophysis, hypophysis

subsets for bryophytes


Moss Ontology definition: The main body (urn) of a sporangium. Altered from Bill and Nancy Malcolm (2006): Mosses and other Bryophytes, an illustrated glossary, second edition

We already have the term theca (PO:0009069) to describe paired microsporangia in angiosperms. Maybe we should call that anther theca and call this term sporangium theca:.

Proposed name and def.: sporangium theca: A cardinal organ part that is the main body of a sporangium and has spores located in it.

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

part_of sporangium

subsets for bryophytes, maybe pteridophytes


Moss Ontology definition: A single or double circle of teeth inside the mouth of a moss sporangium. Bill and Nancy Malcolm (2006): Mosses and other Bryophytes, an illustrated glossary, second edition

proposed definition: A cardinal organ part that is a single or double circle of teeth inside a spore capsule mouth.

Comment: The peristome is located under the operculum, if an operculum is present. Upon maturity of a capsule, the teeth of the peristome open to release the spores.

part_of sporangium

subsets for bryophytes


  • peristome tooth

Not requested by Moss Ontology, but should add it.

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

Comment: Peristome teeth may be simple or compound, and may be attached by their tips to the epiphragm.

part_of peristome

subsets for bryophytes


  • Add term for peristome cell? Are they dead at maturity? What kind of cells are they?


Moss Ontology definition: Either the lid that blocks the capsule mouth or the apical portion of a sporangium that opens during dehiscence. Bill and Nancy Malcolm (2006): Mosses and other Bryophytes, an illustrated glossary, second edition.

We also have a request (from PJ) for operculum, which is part of the fruit in Eucalyptus. That term should be named fruit operculum, and this term should be named spore capsule operculum, to distinguish them.

Proposed name and def.: spore capsule operculum: A cardinal organ part that is the apical part of a spore capsule that separates from the rest of the capsule during dehiscence.

Comment: Found in mosses. May remain partly attached to the rest of the capsule.

Synonym: sporangium lid

part_of sporangium

subsets for bryophytes

Also add these terms for angiosperms:

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

The top part of the bud where the perianth (petals) is fused. Leaves fruit underneath it. Operculum is underneath that

Comment: Found in Eucalyptus.

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

perianth calyptra: A collective plant structures that is composed of fused perianth parts and located on tops of a gynoecium that contains an inferior ovary.

Comment: Found in Eucalyptus and other Myrtaceae. Sometimes erroneously referred to as part of a fruit.

Other related terms for mosses, not from Moss Ontology

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

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

part_of sporangium

subsets for bryophytes


Schofeld says it is a "membranelike expansion of the columella covering most of the mouth of the sporangium in Polytrichidae (hair cap mosses)."

From Crum: "A circular membrane at the tip of the columella to which the peristome teeth of the prolytrichaceae are attached."

Proposed definition: A portion of parenchyma tissue that forms a circular membrane extending from a spore capsule collumella and attached to the ends of the peristome teeth that covers a spore capsule mouth.

Comment: Present in some moss species of the family Polytrichaceae.

Synonym: tympanum, epiphram

subsets for bryophytes


From Crum: "An elongation of the gametophytic axis on which the capsule is borne in Sphagnum and Andreaea."

From Schofeld: "An elongated mass of leafless gametophore tissue that pushes the sporophyte beyond the perichaetial leaves (in Andreaea and Sphagnum)."

Proposed definition: A plant axis that is a leafless extension of a gametophore axis on which a sporophyte is borne.

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

participates_in gametophytic phase

subsets for bryophytes

Next meeting scheduled for Tues, Apr. 19th, 2011 at 10am PDT

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