Plant ontology updates

[Peter Stevens]

>Ummm, I think Homer nodded.  As  far as I can work out, differences 
>between young roots in monocots and BLAs, certainly in eudicots, has 
>to do more with the number of protoxylem poles than anything else; 
>BLAs are 1-few, monocots tend to be many (and to have a pith, too, 
>although this is certainly at least sporadic in BLAs).  Furthermore, 
>roots don't really have vascular bundles at all, so the term should 
>not be used here; the aylem and phloem poles alternate regularly 
>around the circumference of the stele.  So the vascular system of 
>the root consists of the vascular tissue, initially alternating 
>xylem and phloem, which may take up the whole of the central part of 
>the root - or not.  The stele can be clearly recognised, unlike in 
>many stems (strictly speaking, 'stele' and 'vascular system' are not 
>synonyms, although they have been treated as such).  Incidentally, 
>the direction of development of the xylem in the root and stem 
>differs; the root is exarch, the stem endarch; this is true of all 
>seed plants.


What goes on in the stem is roughly what Toby described; most 
monocots and things like Piperaceae tend to have scattered vbs; 
Ranunculaceae Cucurbitaceae Asteraceae (e.g.) have initially a ring 
of separate bundles, whether or not later joined by vascular cambium, 
while other BLAs have a ring of vascular tissue from the beginning - 
but I am not sure of the distribution of this latter feature.

P.





>The difficulty with the root terms is created by the differences in root
>anatomy.  In monocots plus a few of the early-diverging angiosperms
>(e.g. Piperaceae), the vascular system of the root is made up of
>vascular bundles scattered all over the place as seen in cross section,
>and not organized into a central cylinder.  In eudicots, the term root
>vascular bundle doesn't have much meaning, since the stele is a
>cylindrical unit without separate bundles.  Thus for monocots and
>Piperaceae, you'd need the terms root vascular bundle and root vascular
>system (all the bundles as a group), whereas in eudicots and other of
>the early diverging lineages you'd need stele (which would include the
>endodermis) and root vascular system, which would be the vascular tissue
>encompassed by the stele.  So the accurate definition of the terms - to
>avoid confusing the annotators - would have to include some sort of
>comment on where the terms are to be applied.
>Toby
>
>On May 3, 2005, at 7:09 PM, Katica Ilic wrote:
>
>
>>  Hi all,
>>
>>  The following changes to the Plant Structure Ontology are to be made
>>  this
>>  week:
>>
>>  I. Bringing back from the obsolete node terms 'crown root' and
>>  'seminal
>>  root', and obsoleting 'nodal root'
>>
>>  Ontology structure:
>>
>>  adventitious root
>>    % crown root ; PO:0003008
>>    % seminal root ; PO:0003009
>>
>>  Please, let me know if term 'brace root' is needed at present time.
>>
>>  II. From St Louis meeting, the following terms are to be added (which
>>  we
>>  already agreed on):
>>
>>  New term:
>>  1. stem vascular system
>>  Def: Total of the vascular tissues in their specific arrangements in
>>  the
>>  stem.
>>
>>  2. root vascular bundle (new term, requested by Pankaj)
>>  Def: A strandlike part of vascular system of root, composed of phloem,
>>
>>  xylem and associated transfusion tissue
>>
>>  3. add 'leaf vascular bundle' as a synonym of 'leaf vein'
>>
>>  NOTE: we now have three highly redundant terms: root vascular system,
>>  root
>>  stele and root vascular bundle. For a curator, it is going to be a
>>  very
>>  arbitrary decision to make on which one to use for annotation.
>>
>>  4. Renaming the term 'nodule' to 'root nodule' and adding a new
>>  structure
>>  for the term 'nodule:
>>
>>  New term: adventitious root nodule (syn. stem nodule)
>>  Def:  Enlargement or swelling on adventitious aerial roots in some
>>  legumes
>>  (e.g., Sesbania rostrata), inhabited by nitrogen-fixing bacteria.
>>  Unlike
>>  the root nodules, these contain functioning chloroplasts in the nodule
>>
>>  cortex and are therefore capable of carbon fixation. (TAIR:ki)
>  >
>>  Ontology structure:
>>
>>  root
>>   (p) root nodule
>>   (i) adventitious root
>>       (p) adventitious root nodule (synonym: stem nodule)
>>
>>
>>  IV. Corrections of typos and minor errors in the ontology file :
>>  1. Term: stem cortex
>>  Definition: The primary tissue located between the vascular system and
>>  the
>>  epidermis of the root.
>>  (It should be 'of the stem").
>>
>>  2.	Sillica cell to silica cell
>>
>>  3. Cotyledon vascular system (to correct the definition)
>>
>>  4. Also, several minor typos in the text of the following:
>>  Terms: stolon, valve, phloem, chlorenchyma, and shoot procambium.
>>
>>  Thanks,
>>
>>  Katica
>>
>>
>>  ----------------------------------------------------------------------
>>  ----
>>  Katica Ilic            		katica at acoma.stanford.edu
>>  The Arabidopsis Information Resource	Tel: (650) 325-1521 ext. 253
>>  Carnegie Institution of Washington	FAX: (650) 325-6857
>>  Department of Plant Biology		URL: http://arabidopsis.org/
>>  260 Panama St.
>>  Stanford, CA 94305
>>  U.S.A.
>>  ----------------------------------------------------------------------
>>  ----
>>
>>
>>
>>
>Elizabeth A. Kellogg
>E. Desmond Lee and Family Professor of Botanical Studies
>Department of Biology
>University of Missouri-St. Louis
>St. Louis, MO 63121
>Tel: 314-516-6217
>FAX: 314-516-6233
>http://www.umsl.edu/divisions/artscience/biology/Kellogg/Kellogg/home.ht
>ml