Parentage of germination pore GO:0043677

[rachhuntley]

The definition of this term is "A small pore in the outer wall of a mycelial spore through which the germ tube exits upon germination. It can be apical or eccentric in its location. "

It is currently an is_a extracellular matrix component. Judging by the definition, should it instead be part_of GO:0031160 spore wall and is_a GO:0044426 cell wall part?

Any comments from the fungal curators? @ValWood @srengel @marekskrzypek

[ValWood]

I have no idea.... pombe don't have this. The conjugation tubes from opposite mating type cells fuse plasma membranes like so: https://www.pombase.org/archive/spotlight (research spotlight 2).

So I guess this is specific to mycelia forming fungi?

[ValWood]

If it really is a pore, wouldn't it be a membrane part rather than a cell wall part. I agree that matrix sounds wrong.

[ValWood]

Ah got it, it is talking about the conjugation tube emerging from the spore rather than connecting to another yeast.

I don't know anything about this either. Pombe don't do this either. The conjugation tube formation is really just a cell ' cone shaped outgrowth'. It doesn't originate from a pore.

[rachhuntley]

OK, thanks Val. I know even less than you, so we'll wait for comments from the other curators.

[marekskrzypek]

Hi all,

I am not familiar with this term, either from Candida or Aspergillus literature. Both produce spores that germinate into a germ tube at some point in their lives. Either I don't remember, or Ascomycetes don't make germ pores as recognizable structures. In any case, the definition clearly says this is a part of spore wall, NOT extracellular matrix. So, "part_of GO:0031160 spore wall and is_a GO:0044426 cell wall part" sounds right to me.

I don't think this germ pore would ever be a hole in the membrane, so it wouldn't be a membrane part.

Cheers, Marek

On Jul 16, 2018, at 5:30 AM, Rachael Huntley notifications@github.com<mailto:notifications@github.com> wrote:

The definition of this term is "A small pore in the outer wall of a mycelial spore through which the germ tube exits upon germination. It can be apical or eccentric in its location. "

It is currently an is_a extracellular matrix component. Judging by the definition, should it instead be part_of GO:0031160 spore wall and is_a GO:0044426 cell wall part?

Any comments from the fungal curators? @ValWoodhttps://github.com/ValWood @srengelhttps://github.com/srengel @marekskrzypekhttps://github.com/marekskrzypek

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/geneontology/go-ontology/issues/16086, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AVeuT1wpnMJjtOwdtuskZNe67Utw4be6ks5uHF0bgaJpZM4VQ0MQ.

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Marek S. Skrzypek, Ph.D. Senior Biocuration Scientist, Candida Genome Database Saccharomyces Genome Databases Department of Genetics Stanford University School of Medicine Stanford, CA 94305 marek.skrzypek@stanford.edumailto:marek.skrzypek@stanford.edu ORCID: 0000-0001-6749-615X http://www.candidagenome.org/ http://www.yeastgenome.org/

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[ValWood]

maybe obsoletion is better unless a supporting publication can be found. Then it would be placed properly if it were ever required?

[ukemi]

A quick literature search implies that they are in mushrooms.

[ValWood]

I think we acknowledged that this occurs in some fungi, but the term is odd.

if kept rename "fungal germination mycelium pore" place under cell wall

However, It is difficult to imagine which gene products could be annotated to a "hole" in a cell wall though! so obsoletion might be best, even if this structure (or hole) does exist, and can be seen by light microscopy.

We probably shouldn't create terms until we have gene products to annotate to them.....

[pgaudet]

The reference cited is the wikipedia stub: https://en.wikipedia.org/wiki/Germ_pore Which links to this: http://www.mushroomthejournal.com/greatlakesdata/Terms/germp704.html

And there are no annotations. I'd be in favor of obsoletion.