chorion micropyle formation - clarify if this is applicable to vertebrates, insects, or both

[cmungall]

We have ZFIN annotations to

http://amigo.geneontology.org/amigo/term/GO:0046844

id: GO:0046844
name: chorion micropyle formation
namespace: biological_process
def: "Establishment of the micropyle, a single cone-shaped specialization of the chorion that allows sperm entry into the egg prior to fertilization." [ISBN:0879694238]
is_a: GO:0003006 ! developmental process involved in reproduction
is_a: GO:0032502 ! developmental process
is_a: GO:0048646 ! anatomical structure formation involved in morphogenesis
intersection_of: GO:0048646 ! anatomical structure formation involved in morphogenesis
intersection_of: results_in_formation_of GO:0070825 ! micropyle
relationship: part_of GO:0007306 ! eggshell chorion assembly

But these should be flagged as taxon constraints (aside: where are we tracking these?)

The reasons are nuanced and there is a lot of confusion in GO with terms like eggshell/chorion/follicle:

@gouttegd from FlyBase and @paolaroncaglia are working on the underlying CL terms

• https://github.com/obophenotype/cell-ontology/issues/589
• https://github.com/obophenotype/uberon/issues/1524

[pgaudet]

Is this a question for ZFIN folks? @sramachand @doughowe

[cmungall]

I had assumed chorionic micropyle referred to the insect structure, exemplified by the FBbt term:

https://www.ebi.ac.uk/ols/ontologies/zfa/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FZFA_0000329

The definition in GO referring to cone-shaped morphology seems particular: https://pubmed.ncbi.nlm.nih.gov/32829690/#:~:text=The%20micropyle%20is%20a%20cone,the%20micropyle%20are%20remarkably%20complex.

In fact the def dbxref for the GO term is https://www.abebooks.com/9780879694234/Development-Drosophila-Melanogaster-Volume-Set-0879694238/plp (aside: I really wish when we had made taxonomic scope more explicit at time of term creation)

The teleost structure seems analogous: https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1007408

Without a recognizable acrosome reaction, sperm entry in teleosts relies entirely upon a specialized funnel-like structure, the micropyle, in the chorion, an acellular coat of the egg [4–6]. Morphological and physiological studies of the micropyle in a variety of different teleost species suggest that channel formation results from the transformation of a special micropylar cell in mid-oogenesis [7–12]. The micropylar cell is morphologically distinct from other follicle cells surrounding the oocyte. Positioned over the oocyte animal pole, the micropylar cell is bigger in size and appears like an inverted cone in shape, in contrast to the flattened appearance of follicle cells, sometimes called ‘mushroom’-like [11–13]. The unique shape of the micropylar cell is gradually achieved during oogenesis. A cytoplasmic extension from the micropylar cell expands and extends through the developing vitelline envelope, till the extension tip contacts the oocyte membrane, as the vitelline envelope grows and perforation proceeds, the cytoplasmic extension becomes slim and long [14]. Finally, the micropylar cell degenerates, leaving a narrow canal called the ‘micropyle’ between the chorion and the egg [15, 16].

I know GO is very keen on grouping analogous structures together but I think it's a mistake here. For one thing, in teleosts the micropyle is in a follice cell surrounding the egg (is it really an external encapsulating structure, as in GO?); in insects it is a channel in the external encapsulating structure of the egg itself.

[cmungall]

Also, the term "chorion-containing eggshell" in GO is odd.

id: GO:0007304
name: chorion-containing eggshell formation
namespace: biological_process
def: "The construction of a chorion-containing eggshell. An example of this is found in Drosophila melanogaster." [GOC:mah, GOC:mtg_sensu]
synonym: "eggshell formation" BROAD []
is_a: GO:0030703 ! eggshell formation
intersection_of: GO:0048646 ! anatomical structure formation involved in morphogenesis
intersection_of: results_in_formation_of UBERON:0005307 ! chorion-containing eggshell
relationship: part_of GO:0030707 ! ovarian follicle cell development

(the uberon term simply mirrors the GO term)

it looks like an attempt to make a term for insect eggshells, but having an undefined "chorion" as the differentia doesn't really help here as the analogome of chorion is large. In amniotes it's the outermost extraembryonic membrane. In teleosts the chorion is the eggshell, so the taxonomic scope of GO:0007304 is very unclear

[sramachand]

So, micropyle formation occurs in both teleosts and insects but are different processes and we should have terms subject to taxon constraints?

[cmungall]

the structures seem different, but are there any commonalities in the process, homologous pathways etc?

[pgaudet]

See also discussion here: https://github.com/geneontology/go-ontology/issues/18623 and https://github.com/geneontology/go-ontology/issues/18128

[raymond91125]

The author of this article PMID:32829690 states "The micropyles of fish eggs represent a remarkable case of convergent evolution with insects.". Although the level of molecular conservation is not yet known. I think it's probably best to remove narrow taxon constraints until we have a clear scheme of distinguishing between them. Also, there is a micropyle (not of chorion, I believe) in flowering plants. https://en.wikipedia.org/wiki/Ovule. Functionally micropyles allow sperm entry.

[pgaudet]

@raymond91125 I think this is y good solution, please go ahead and remove the taxon constraint (or make it a bit less restricted).

Thanks, Pascale

[raymond91125]

I believe the only existing taxon constraint (on egg chorion) is 'only in taxon' some Eumetazoa, thus OK for fly and fish. Perhaps we can close for now.

[pgaudet]

@cmungall suggests two terms, one for arthropods and one for amniotes.

[raymond91125]

I have not been able to find definitive, simple distinguishing features between teleost and insect chorion micropyle.

1. They have the same function, allowing sperm to come in contact with the oocyte through some protective layer.
2. They are both formed by follicle cells. If there is a clear way to distinguish different (egg) chorion then the micropyle can follow. Otherwise, we may have to embed taxa in the terms.

[hattrill]

Hi @pgaudet I agree with @raymond91125, I can find no meaningful difference in terms of function and construction of fish v fly micropyle (except one's an innie and one's an outie).

If we do have to have new taxon-specific terms, as long as they share a common parent, I can go with that as underlying signaling pathways spec'ing construction may well differ - but not enough characterisation for definitive answer here.

[sramachand]

I looked through some of the publications and it does not seem like there are simple distinguishing features between the fish and insect micropyles. It is possible that the signaling pathways to specify a micropylar cell could be different. I have not looked at Drosophila/insect references to know if there is evidence for this.

[pgaudet]

OK, so it seems that based on the current state of knowledge, we cannot really distinguish insect and teleost micropyle.

Although in a comment above (https://github.com/geneontology/go-ontology/issues/22603#issuecomment-1010252638), @cmungall writes

For one thing, in teleosts the micropyle is in a follice cell surrounding the egg (is it really an external encapsulating structure, as in GO?); in insects it is a channel in the external encapsulating structure of the egg itself.

So, should we consider changing the definition of micropyle, which is "An external encapsulating structure part of the chorion. A single cone-shaped specialization that forms an opening in the egg chorion that allows sperm entry into the egg prior to fertilization." to remove the description as an encapsulating structure?

Note that this structure also seems to be present in plants

[pgaudet]

One precision about my last note,

Note that this structure also seems to be present in plants

this is searching for 'micropyle'. We only have the CC micropyle, not 'chorion micropyle'. So, even if we cannot limit the taxa to which these terms are applied, we could perhaps make the ontology more consistent.

[raymond91125]

In fish, micropyle is an opening left by the micropylar cell which degenerates (PMID:30608921). Thus it is an external structure.

To include plants, we could change the label of GO:0070825 to chorion micropyle and have a new term micropyle that covers both animals and plants, perhaps defined as "An anatomical structure that is an opening of the external protective layer surrounding a female gamete, through which a male gamete can penetrate the protective layer and come in contact with the female gamete prior to fertilization."

[pgaudet]

What I meant is that we have

• GO:0070825 micropyle (CC)
• GO_0046844 chorion micropyle formation (BP) Ideally we'd have both or a single one, but the current situation (two different ways to refer to the micropyle) leads to confusion.

---

The paper you cite says "The micropyle forms by penetration of the vitelline envelope by a single specialized follicle cell, the micropylar cell." -> I dont see how that makes this an external encapsulating structure (external seems OK)

[hattrill]

I would say that for fish and flies, the micropyle is part of the chorion - the difference is whether the hole goes in or pokes out of the chorion. Both are not just holes, but part of the structure of the chorion, which is the relation to egg chorion in GO.

The plant micropyle is fundamentally different in the functions it performs (lets pollen tube in and water in) and not part of a chorion. There are no annotations to plant for either the cc or the bp term, so as it is not used in plant annotation, we don't need to make a special term for this unless requested.

So, I think we just need a name change and a tweak of the def to make it ok for fish and flies and ontologists:

GO:0070825 chorion micropyle (CC)

And change def to "A single cone-shaped specialization that forms an opening in the egg chorion that allows sperm entry into the egg prior to fertilization."

(I think cone-shaped is ok - one is a cone that goes in and one is a cone that goes out).

[pgaudet]

Thanks @hattrill

[raymond91125]

We still have the issue of taxon constraint chorion micropyle SubClassOf 'in taxon' some insecta. This is because chroion micropyle formation subClassOf 'part of' some 'eggshell chorion assembly'; and eggshell chorion assembly is defined as "Construction of the chorion portion of the eggshell, which comprises the channels for gas exchange in an insect eggshell." I think we should change the relationship to eggshell chorion assembly HAS_PART some chroion micropyle formation. Any objections or suggestions?

[cmungall]

That’s a decent approach, but let’s look in more detail

If the chorion micropyle is indeed similar enough to warrant a grouping across fish and insects, shouldnt that similarity propagate up?

Shouldn’t chorion be generic too?

On Wed, Oct 5, 2022 at 2:16 PM Raymond Lee @.***> wrote:

We still have the issue of taxon constraint chorion micropyle SubClassOf 'in taxon' some insecta. This is because chroion micropyle formation subClassOf 'part of' some 'eggshell chorion assembly'; and eggshell chorion assembly is defined as "Construction of the chorion portion of the eggshell, which comprises the channels for gas exchange in an insect eggshell." I think we should change the relationship to eggshell chorion assembly HAS_PART some chroion micropyle formation. Any objections or suggestions?

— Reply to this email directly, view it on GitHub https://github.com/geneontology/go-ontology/issues/22603#issuecomment-1268985834, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAAMMOLYEB52TR3XNRLXN23WBXV3PANCNFSM5KOLH4HQ . You are receiving this because you were mentioned.Message ID: @.***>

[raymond91125]

GO:0042600 egg chorion is generic. We could make micropyle part of that.

[cmungall]

but we're talking about the assembly terms here...?

[raymond91125]

Of course. What we have is egg shell chorion assembly (fly) results_in_assembly_of egg chorion (Uberon, fly and fish). Perhaps we should change "egg shell chorion assembly" to "egg chorion assembly", and remove the fly specification in the definition. And then "chorion-containing eggshell formation" has_part "egg chorion assembly". Fish eggs don't have a shell.

[raymond91125]

@pgaudet Please advise what else needs to be done. Thanks.

[pgaudet]

You proposed to

Perhaps we should change "egg shell chorion assembly" to "egg chorion assembly", and remove the fly specification in the definition. And then "chorion-containing eggshell formation" has_part "egg chorion assembly".

Do you want to implement that?

[raymond91125]

I have already. https://github.com/geneontology/go-ontology/commit/83d5a6c0b83af932127e2a87c0b8d534d94310c5

[pgaudet]

Ah ok !! thanks