Difference between revisions of "Sporulation Meeting Notes"

From GO Wiki
Jump to: navigation, search
m (Meeting summary)
Line 104: Line 104:
 
Some existing definitions should be rewritten. Two that I've had a stab at so far:
 
Some existing definitions should be rewritten. Two that I've had a stab at so far:
  
sporulation GO:0030436<br>
+
:updated earlier draft; see Definitions below
def: The process by which a relatively unspecialized cell acquires the specialized features of a spore. [can include general description of features shared by all spores]
 
 
 
ascospore formation GO:0030437<br>
 
def: The process by which a diploid cell undergoes meiosis, and the meiotic products acquire the specialized features of an ascospore [include ascospore features here].
 
  
 
Additional comments:
 
Additional comments:
Line 132: Line 128:
 
Changes we did decide on:
 
Changes we did decide on:
  
*Create two child terms, for spores produced by mitosis (= asexual) and by meiosis (sexual), The definitions probably need work; any other comments also welcome.
+
*Create two child terms, for spores produced by mitosis (= asexual) and by meiosis (sexual), The definitions probably need work; any other comments also welcome. Definitions below.
<pre>
 
id: GO:new
 
name: asexual sporulation
 
def: "The formation of spores derived from the products of mitosis." [GOC:mah; PMID: 9529886]
 
synonym: "asexual spore formation" EXACT []
 
synonym: "mitotic sporulation" EXACT []
 
synonym: "mitotic spore formation" EXACT []
 
is_a: GO:0030435 ! sporulation
 
 
 
id: GO:new
 
name: sexual sporulation
 
def: "The formation of spores derived from the products of meiosis." [GOC:mah]
 
synonym: "meiotic sporulation" EXACT []
 
synonym: "meiotic spore formation" EXACT []
 
synonym: "sexual spore formation" EXACT []
 
is_a: GO:0030435 ! sporulation
 
 
 
Note: any of the synonyms could be used as the term name, if you prefer.
 
</pre>
 
 
*For types of sporulation observed in bacteria, Debby will look up distinguishing features that can be used in definitions; Midori will help convert that information into GO-definition-friendly sentences. See below ...
 
*For types of sporulation observed in bacteria, Debby will look up distinguishing features that can be used in definitions; Midori will help convert that information into GO-definition-friendly sentences. See below ...
 
*Rename 30437 to ascospore formation, and improve definition; also rename 30476 to ascospore wall assembly.
 
*Rename 30437 to ascospore formation, and improve definition; also rename 30476 to ascospore wall assembly.
Line 200: Line 177:
 
-- --[i] ascospore wall formation GO:0030476 (renamed)<br>
 
-- --[i] ascospore wall formation GO:0030476 (renamed)<br>
 
-- --[other new terms as needed, e.g. as in Feb. 14 draft above]<br>
 
-- --[other new terms as needed, e.g. as in Feb. 14 draft above]<br>
 +
 +
===Definitions===
 +
(Feb. 26; Midori)
 +
 +
<pre>
 +
id: GO:0030436
 +
name: sporulation
 +
def: "The process by which a relatively unspecialized cell acquires the specialized features
 +
of a spore, a cell form that can be used for dissemination, for survival of adverse conditions
 +
because of its heat and dessication resistance, and/or for reproduction.Spores are usually
 +
unicellular and may develop into vegetative organisms or gametes.  They may be produced
 +
asexually or sexually and are of many types." [GOC:mah; ISBN:0072992913]
 +
 +
id: GO:new
 +
name: asexual sporulation
 +
def: "The formation of spores derived from the products of mitosis." [GOC:mah; PMID: 9529886]
 +
synonym: "asexual spore formation" EXACT []
 +
synonym: "mitotic sporulation" EXACT []
 +
synonym: "mitotic spore formation" EXACT []
 +
is_a: GO:0030435 ! sporulation
 +
 +
id: GO:new
 +
name: sexual sporulation
 +
def: "The formation of spores derived from the products of meiosis." [GOC:mah]
 +
synonym: "meiotic sporulation" EXACT []
 +
synonym: "meiotic spore formation" EXACT []
 +
synonym: "sexual spore formation" EXACT []
 +
is_a: GO:0030435 ! sporulation
 +
 +
Note: any of the synonyms could be used as the term name, if you prefer.
 +
 +
id: GO:0030437
 +
name: ascospore formation
 +
def: "The process by which a diploid cell undergoes meiosis, and the meiotic products
 +
acquire the specialized features of ascospores. Ascospores are generally found in clusters
 +
of four or eight spores within a single mother cell, the ascus, and are characteristic of the
 +
ascomycete fungi (phylum Ascomycota)." [GOC:mah; PMID:16339736]
 +
is_a: GO:new ! sexual sporulation
 +
 +
id: GO:new
 +
name: basidiospore formation
 +
def: "The process by which spores form outside a specialized end cell known as a basidium.
 +
Basidia are characteristic of the basidiomycete fungi (phylum Basidiomycota), and give rise to
 +
spores that each contain a haploid nucleus that is the product of meiosis. The spores are
 +
usually attached to the basidium by short spikes called sterigmata (singular: sterigma). In
 +
most basidiomycetes there are four sterigmata (and four spores) to a basidium." [GOC:mah,
 +
GOC:ds, http://www.ilmyco.gen.chicago.il.us/Terms/basid133.html,
 +
http://www.gsbs.utmb.edu/microbook/ch073.htm]
 +
is_a: GO:new ! sexual sporulation
 +
 +
id: GO:new
 +
name: zygospore formation
 +
def: "The process by which zygospores are formed. Zygospores are characteristic of the
 +
zygomycete fungi (phylum Zygomycota) thick-walled and darkly colored, and usually heavily
 +
ornamented as well, with many spines or ridges. It is formed between two specialized organs
 +
called suspensors, which are themselves usually heavily ornamented, one from each mating
 +
partner. The zygospore forms between them and then breaks away." [GOC:mah, GOC:ds,
 +
http://www.ilmyco.gen.chicago.il.us/Terms/zygos581.html]
 +
is_a: GO:new ! sexual sporulation
 +
 +
</pre>

Revision as of 10:01, 26 February 2008

August 2007 - January 2008

sporulation (sensu Bacteria)
sporulation (sensu Fungi)
spore development (sensu Magnoliophyta)

People:

Val
Maria Costanzo
Michelle
Midori
Pascale
Jen
Jim Hu
Tanya
Debby Siegele

Questions:
What are the distinguishing features of sporulation in different species?

Plan:

Michelle speaking - I see from below the "sporulation" terms still have sensu designations - didn't we talk once about making terms that were "reproductive sporulation" and "stress-induced sporulation" or something along those lines? If so, could we carry that into these terms? I fear that there might be so much heterogeneity in spore wall structures (even within bacteria) that getting good defs based on that may be hard. But I need to do more checking.... that was just a first thought.

Eurie is to be included in one of these calls so she can get up to speed on editing techniques.

Debby Siegele (Texas A&M) (Nov 25): I think that the child terms for sporulation (GO:0030435) need to be reorganized. The current organization is shown below. A proposed reorganization is shown following my discussion of the current terms.

  • GO:0030435: sporulation
    • GO:0030436: sporulation (sensu Bacteria)
      • GO:0042243: spore wall assembly (sensu Bacteria)
    • GO:0042173: regulation of sporulation
    • GO:0042244: spore wall assembly
    • GO:0048622: reproductive sporulation (def: "The formation of reproductive spores." [GOC:jic])
      • GO:0030437: sporulation (sensu Fungi)
        • GO:0048315 : conidium formation
        • GO:0031321 : prospore formation
        • GO:0030476 : spore wall assembly (sensu Fungi)


The term for sporulation (sensu Bacteria) and spore wall assembly (sensus Bacteria) should be eliminated because there are multiple types of bacterial spores (e.g. endospores, exospores, myxospores, and akinetes) and therefore multiple types of spore cell walls and assembly pathways. The term GO:0055030: peptidoglycan-based spore wall (a child term of spore wall) could be retained as it refers to a specific type of spore wall.

I would make the same argument for eliminating the term for sporulation (sensu Fungi) as different groups of fungi make spores differently. (In fact, the synonyms listed for sporulation (sensu Fungi) are specific for formation of ascospores, which excludes fungi outside the Ascomycetes.) I suspect that the terms spore wall (sensu Fungi) (GO:0005619) and spore wall assembly (sensu Fungi) should also be eliminated, since there probably isn't a common spore wall present in all fungal spores, but I don't know enough about this.

I don't know is meant by a reproductive spore. Does this refer to the spore being formed by a sexual process? or that the spores themselves are gametes (as is the case with some fern spores)? or simply that the spores will rise to a new organism? If the first is correct, then GO:0048315 shouldn't be a child term of reproductive spore, since conidia are asexual spores and the true path rule isn't followed.

I saw that one of the parent terms for reproductive sporulation is GO:0022413: reproductive process in single-celled organism. Does "single-celled" refer to spore itself? or to the organism that produces the spores?

A possible reorganization would be

  • GO:0030435: sporulation
    • GO:0042173: regulation of sporulation
    • GO:0042244: spore wall assembly
    • new GO term: formation of asexual spores
      • GO:0048315: conidium formation
      • new GO term: endospore formation
    • new GO term: formation of sexual (meiotic) spores (or redefinition/clarification of GO:0048622: reproductive sporulation?)
      • GO:0030437: redefined as ascospore formation

In AmiGO, the only genes annotated to GO:0030437: sporulation (sensu Fungi) are from S. cerevisiae and S. pombe. These are both Ascomycetes, so the change in definition wouldn't affect these annotations. Among the model organism databases, the only other organism I found with genes annotated to GO:0030437 is Dictyostelium discoidium. DictyBase has 4 genes (geneDDB0230045, geneDDB0234013, rasC, and rasD) annotated to sporulation (sensu Fungi). The annotations were inferred from electronic annotation.

Midori (Jan. 4, 2008): I have implemented the changes to fungal-type cell wall and spore wall terms as described in the notes from Nov. 2. (I have not tried to mess with the sporulation process terms, but Debby's suggestions sound reasonable. I lean toward renaming GO:0030437 and rewording its definition such that it refers to ascospore formation, because that's been the implicit meaning given who worked on it, what we were thinking of, and how it's been used.)

Feb. 14, 2008

Midori (very) rough draft of possible structure:

Please comment on this -- should any more terms be included, or anything shown be left out? I fully expect more than one round of comments before it's resolved!

sporulation GO:0030436
[i] reproductive sporulation GO:0048622 (rename 'formation of sexual (meiotic) spores'? should we add any children, such as these:
--[i] fern-type sporulation?
--[i] moss-type sporulation?
[i] ascospore formation GO:0030437 (renamed)
--[p] ascospore wall formation GO:0030476 (renamed)
--[p] prospore formation GO:0031321 (may need to be renamed because the definition seems more specific than the name, but I haven't thought of a new name yet)
[i] (a term for basidomycete sporulation) GO:new
[i] conidium formation GO:0048315
--[p] conidium wall assembly GO:new (or "formation" instead of "assembly")
[i] endospore formation GO:new
--[p] endospore wall assembly GO:new
[i] exospore formation GO:new
--[p] exospore wall assembly GO:new
[i] myxospore formation GO:new
--[p] myxospore wall v GO:new
[i] akinete formation GO:new
--[p] akinete wall assembly GO:new
[p] spore wall assembly GO:0042244
--[i] ascospore wall formation GO:0030476 (renamed)
--[i] conidium wall assembly GO:new
--[i] endospore wall assembly GO:new
--[i] exospore wall assembly GO:new
--[i] myxospore wall v GO:new
--[i] akinete wall assembly GO:new
[p] regulation of sporulation GO:0042173

We can also add "xx spore wall" terms to the cellular component (CC) ontology.

note: we have "peptidoglycan-based spore wall" in CC (GO:0055030); does it correspond to any of the wall types listed above?

To be made obsolete:

- sporulation (sensu Bacteria) GO:0030436
- spore wall assembly (sensu Bacteria) GO:0042243

Some existing definitions should be rewritten. Two that I've had a stab at so far:

updated earlier draft; see Definitions below

Additional comments:

  • Reproductive sporulation
    • David: I don't think it was necessarily meant to be just meiotic. I think it means 'sporulation whose primary biological objective is reproduction' as opposed to 'sporulation whose primary biological objective is that of protection'. I think it was the fungal groups who worked on this part of the graph. Does it make sense that they would think of sporulation as primarily a reproductive process while you folks would think of it as a protective process? The latter distinction was entirely mine based on reading a textbook.
    • Midori: David remembers more of this than I do; I would have just said I don't know where the "reproductive sporulation" term came from! We should check again with fungal experts, because in S. cerevisiae sporulation occurs in diploids in response to nutrient starvation (specifically nitrogen, if I recall correctly); it's not as obviously coupled to reproduction as in ferns or some other fungi, e.g. mushrooms. Back in my lab days I tended to think of cerevisiae sporulation as more protective than reproductive, although four spores are produced so it's got a bit of reproductive character. Sporulation in ferns and mosses would certainly fit under "reproductive sporulation"; I don't know anything more about them, such as distinguishing features or whether we would need one term or more. We should discuss whether to keep the "reproductive sporulation" term; if so, whether to change its name, what (if any) children it should have, whether to add a sibling for "sporulation in response to stress", etc.
    • Pascale: I think we should use sexual and asexual to distinguish meiotic and mitotic spores. As far as I know, all spoulation is a form of reproduction. Plus there are no direct associations to 'reproductive sporulation'. This is also consistent with the definition of reproduction: 'The production by an organism of new individuals that contain some portion of their genetic material inherited from that organism.'
    • Michelle: All sporulation is not reproductive. Sporulation in bacteria does not result in a net increase in the number of organisms - one cell becomes a spore and then germinates into one cell again. Sporulation in bacteria is generally a means to survive adverse conditions. So, if asexual sporulation will refer to a reproduction process, we will still need some kind of non-reproductive sporulation term.
  • Jim: I think there is a problem with the fungal sporulation terms excluding or misrepresenting the basidomycetes by being marked as synonymous with ascospore processes.
    Midori: I think the apparent exclusion of basidomycetes will be addressed by renaming the existing "fungal" sporulation term and adding new terms.
  • Jim: The myxospores mentioned above by Debby are made by the Myxococcales. The model organism for them is Myxococcus xanthus, and their mod is at http://xanthusbase.org. I'm trying to help them with a clade-specific cluster of MODs project right now. In an oversimplified description, myxo is sort of a bacterial version of dicty. There is social behavior followed by aggregation into a multicellular fruiting body that differentiates into spores. Some of these are quite lovely. Via googling:
http://www.mbio.ncsu.edu/MB451/lecture/deltaEpsilonPurples/lecture.html

February 20, 2008 Skype "meeting"

Present: Midori, Debby, Maria, Pascale, Val

Meeting summary

(Midori)

We discussed whether sporulation should go under reproduction; it's not resolved yet, but the other changes don't depend on the decision. If sporulation (GO:0030435) itself doesn't go under reproduction, descendants of sporulation can have reproduction as an additional parent as needed.

Changes we did decide on:

  • Create two child terms, for spores produced by mitosis (= asexual) and by meiosis (sexual), The definitions probably need work; any other comments also welcome. Definitions below.
  • For types of sporulation observed in bacteria, Debby will look up distinguishing features that can be used in definitions; Midori will help convert that information into GO-definition-friendly sentences. See below ...
  • Rename 30437 to ascospore formation, and improve definition; also rename 30476 to ascospore wall assembly.
  • Move conidium formation (GO:0048315) to is_a mitotic/asexual sporulation.
  • We agreed to make three terms obsolete:
    • reproductive sporulation GO:0048622
This term is ill defined, so much so that we don't know what it was intended to mean; it also has a parent (reproductive process in single-celled organism) that isn't consistent with the 'sporulation whose primary biological objective is reproduction' meaning (true path violation - cf ferns, mosses, mushrooms). No gene products are annotated directly to GO:0048622
  • sporulation (sensu Bacteria) GO:0030436
This is a grouping term that isn't useful -- there are several different types of spore formed by different species/genera/etc. of bacteria, and there is neither a need nor a good basis for grouping them with each other.
  • spore wall assembly (sensu Bacteria) GO:0042243
Reasons analogous to those given for GO:0030436 above.


Debby 2/20/08

GO:0030435 sporulation

  • Sexual or meiotic spores (child term of sporulation)
    • Ascospores (meiotically produced spores form by Ascomycetes)
    • Basidiospores (is a reproductive spore produced by Basidiomycete fungi. Basidiospores typically each contain one haploid nucleus that is the product of meiosis, and they are produced by specialized fungal cells called basidia. From Wikipedia)
    • Zygospores (Zygomycota, or zygote fungi, are a phylum of fungi. The name of the phylum comes from zygosporangia, where resistant spherical spores are formed during sexual reproduction. From Wikipedia)
    • Ferns
  • Asexual or mitotic spores (child term of sporulation)
    • Arthrospores (aka oidia)(Hypha fragment through splitting of the cell wall to form cells that behave as spores. Prescott ) (asexual spores formed by Basidiomycetes)
    • Blastospores (Spores produced from a vegetative mother cell by budding. Prescott) (produced by Candida, produced by fungi in the class Glomeromycota, others?)
    • Chlamydospores (Spores produced by hyphal fragmentation that are surrounded by a thick wall before separation. Prescott)
    • Conidia (Spores produced at the tips or sides of a hyphae, but are not enclosed in a sac. Prescott) (asexual spores formed by Ascomycetes)
    • Sporangiospores (Asexual Spores that develop with a sac (sporangia) at a hyphal tip. Prescott) (A spore that is formed by a cleavage process following karyogamy and mitosis in a sporangium. Dr. Fungus) (produced by fungi in the class Chytridiomycota, differ from conidia in being surrounded by a second wall) Sporangium (pl. sporangia): An asexual sac-like cell that has its entire content cleaved into sporangiospores.
    • Dictyostelium - forms spores inside fruiting bodies
    • Endospore (Dormant, highly resistant spore with a thick wall that forms within another cell, produced by some low G+C Gram-positive bacteria)
    • Akinete (An akinete is a thick-walled dormant cell derived from the enlargement of a vegetative cell.[1] It serves as a survival structure. It is a resting cell of cyanobacteria and unicellular and filamentous green algae. [2] Under magnification, akinetes appear thick walled with granular-looking cytoplasms.)
    • Myxospore
    • Actinomycetes (High G+C Gram-positive bacteria that form spores)

Midori: Current draft of the proposed ontology structure (Feb. 20):

sporulation GO:0030436
[i] asexual sporulation GO:new
--[i] conidium formation GO:0048315
--[new terms as needed, e.g. as in Feb. 14 draft above]
[i] sexual sporulation GO:new --[i] ascospore formation GO:0030437 (renamed)
-- --[p] ascospore wall formation GO:0030476 (renamed)
-- --[p] ascospore-type prospore formation GO:0031321 (renamed; suggestions welcome for nicer new name)
--[other new terms as needed, e.g. as in Feb. 14 draft above]
--[p] spore wall assembly GO:0042244
-- --[i] ascospore wall formation GO:0030476 (renamed)
-- --[other new terms as needed, e.g. as in Feb. 14 draft above]

Definitions

(Feb. 26; Midori)

id: GO:0030436
name: sporulation
def: "The process by which a relatively unspecialized cell acquires the specialized features 
of a spore, a cell form that can be used for dissemination, for survival of adverse conditions 
because of its heat and dessication resistance, and/or for reproduction.Spores are usually 
unicellular and may develop into vegetative organisms or gametes.  They may be produced 
asexually or sexually and are of many types." [GOC:mah; ISBN:0072992913]

id: GO:new
name: asexual sporulation
def: "The formation of spores derived from the products of mitosis." [GOC:mah; PMID: 9529886]
synonym: "asexual spore formation" EXACT []
synonym: "mitotic sporulation" EXACT []
synonym: "mitotic spore formation" EXACT []
is_a: GO:0030435 ! sporulation

id: GO:new
name: sexual sporulation
def: "The formation of spores derived from the products of meiosis." [GOC:mah]
synonym: "meiotic sporulation" EXACT []
synonym: "meiotic spore formation" EXACT []
synonym: "sexual spore formation" EXACT []
is_a: GO:0030435 ! sporulation

Note: any of the synonyms could be used as the term name, if you prefer.

id: GO:0030437
name: ascospore formation
def: "The process by which a diploid cell undergoes meiosis, and the meiotic products 
acquire the specialized features of ascospores. Ascospores are generally found in clusters 
of four or eight spores within a single mother cell, the ascus, and are characteristic of the 
ascomycete fungi (phylum Ascomycota)." [GOC:mah; PMID:16339736]
is_a: GO:new ! sexual sporulation

id: GO:new
name: basidiospore formation
def: "The process by which spores form outside a specialized end cell known as a basidium. 
Basidia are characteristic of the basidiomycete fungi (phylum Basidiomycota), and give rise to 
spores that each contain a haploid nucleus that is the product of meiosis. The spores are 
usually attached to the basidium by short spikes called sterigmata (singular: sterigma). In 
most basidiomycetes there are four sterigmata (and four spores) to a basidium." [GOC:mah, 
GOC:ds, http://www.ilmyco.gen.chicago.il.us/Terms/basid133.html, 
http://www.gsbs.utmb.edu/microbook/ch073.htm]
is_a: GO:new ! sexual sporulation

id: GO:new
name: zygospore formation
def: "The process by which zygospores are formed. Zygospores are characteristic of the 
zygomycete fungi (phylum Zygomycota) thick-walled and darkly colored, and usually heavily 
ornamented as well, with many spines or ridges. It is formed between two specialized organs 
called suspensors, which are themselves usually heavily ornamented, one from each mating 
partner. The zygospore forms between them and then breaks away." [GOC:mah, GOC:ds, 
http://www.ilmyco.gen.chicago.il.us/Terms/zygos581.html]
is_a: GO:new ! sexual sporulation