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NTR: ascospore release from the ascus #8088

Closed gocentral closed 9 years ago

gocentral commented 13 years ago

I would like terms for ascospore release from the ascus --endolysis of the ascospore ---extracellular polysaccharide catabolic process involved in endolysis of the ascospore <parent to extracellular polysaccharide catabolic process ---- beta-glucan catabolic process involved in endolysis of the ascospore <parent to beta-glucan catabolic process i ---- alpha-glucan catabolic process involved in endolysis of the ascospore < parent tobeta-glucan catabolic process i

Should ascospore release from the ascus go directly under "ascospore forrmation" or should it be a sibling? soes it need a differnt parent grouping term to GO:0043935 sexual sporulation resulting in formation of a cellular spore?

Reported by: ValWood

Original Ticket: geneontology/ontology-requests/7873

gocentral commented 13 years ago

I am unsure whether this would be classed as part of "spore germination" The physiological and developmental changes that occur in a spore following release from dormancy up to the earliest signs of growth (e.g. emergence from a spore wall). [source: GOC:lr]

but I feel that these should be under a grouping term for fungal-type sporulation (currently they aare separated in the graph)

Val

Original comment by: ValWood

gocentral commented 13 years ago

in all of the above substitute ascus for ascospore

change endolysis of the ascospore to ascus catabolic process def hydrolysis of the ascus wall surrounding the ascospores for release and dispersal of meiotic products

ascus wall (if we need this in componett ontology) def The ascus wall is composed of the cell wall of vegetative cells which fuse to form a diploid, composed mainly of alpha and beta glucans (need to check this is true for all orgs)

source PMID 19542306

Original comment by: ValWood

gocentral commented 13 years ago

OK final commnet. After finishing the paper I think that the process is part of sporulation (grouping term required?) it follows ascospore formation and it preceeds germination

I will ask SGD to look at this one to check

Val

Original comment by: ValWood

gocentral commented 13 years ago

Original comment by: mah11

gocentral commented 13 years ago

> change endolysis of the ascospore to > ascus catabolic process

For this I've added 'extracellular polysaccharide catabolic process involved in ascospore release from ascus', with 'ascus catabolic process' and 'ascospore endolysis' as related synonyms ('ascus' isn't a type of chemical).

> ascus wall (if we need this in component ontology)

Ascus wall may be FAO territory but I suppose we could include it under extracellular (esp. as it's not in FAO at the moment), so let me know if you need it. The part about "composed of the cell wall of vegetative cells which fuse to form a diploid" doesn't apply to all ascus-forming fungi -- some keep adding to the wall, and quite a few have more complicated mating/sporulation arrangements. So it would have to be just 'an extracellular part that consists of the wall surrounding a set of ascospores' or something to that effect. I'm skimming through a review I found by googling for epiplasm: http://dx.doi.org/10.1016/S0953-7562\(96\)80057-8

New terms so far: ascospore release from ascus GO:0071998 extracellular polysaccharide catabolic process GO:0071999 extracellular polysaccharide catabolic process involved in ascospore release from ascus GO:0072000 alpha-glucan catabolic process involved in ascospore release from ascus GO:0072316 beta-glucan catabolic process involved in ascospore release from ascus GO:0072317

Original comment by: mah11

gocentral commented 13 years ago

Hi Maria,

Glad it looks OK. I did see 'ascus' in FAO; it's 'ascus wall' I couldn't find.

cheers, Midori

Original comment by: mah11

gocentral commented 13 years ago

Ah, OK. I think 'ascus wall' is GO territory rather than FAO (somewhat analogous to hyphal cell wall), but I don't think that SGD needs this term.

Thanks, Maria

Original comment by: mariacostanzo

gocentral commented 13 years ago

OK. I'll close this. If anyone ever needs ascus wall in the future, we can add it (new item).

m

Original comment by: mah11

gocentral commented 13 years ago

Original comment by: mah11

gocentral commented 13 years ago

one more question what is the parent of this term? ascospore release from ascus GO:0071998

Original comment by: ValWood

gocentral commented 13 years ago

is_a cellular developmental process & part_of sexual sporulation resulting in formation of a cellular spore

Original comment by: mah11

gocentral commented 13 years ago

sounds good.

Should "sexual sporulation resulting in formation of a cellular spore " have the parent "reproductive process ina single-celled organism"? or does 43935 also apply to plants?

(logic, it seems like release from the ascus should have this parentage)

Original comment by: ValWood

gocentral commented 13 years ago

> or does 43935 also apply to plants?

Maybe (don't remember offhand if 43935 is the plant-spore kind of sporulation); but certainly there are a lot of multicellular ascomycete fungi, so can't add a single-celled organism parent to 43935 or 71998.

Original comment by: mah11

gocentral commented 13 years ago

Original comment by: mah11