megagametogenesis/oogenesis/spore development

[gocentral]

Hi Jen,

Thought I'd start this out as a SF item right away.

After more thought and discussion over here about the whole female gametogenesis/oogenesis situation, we'd like to propose some changes to discuss before you put the current proposal into action.

Current proposal:

%gametogenesis ..%female gamete generation ....%oogenesis ......%oogenesis (sensu Insecta) ......%oogenesis (sensu Mammalia) ....%megagametogenesis ..%male gamete generation ....%spermatogenesis ......%spermatogenesis (sensu Insecta) ?? ......%spermatogenesis (sensu Mammalia) ?? ....%microgametogenesis

However,

megagametogenesis = generation of the female gametophyte (NOT the female gamete). There is a term that is a child of megagametogenesis, 'GO:0009560 : female gametophyte egg cell differentiation' that could go under female gamete generation, if necessary.

Here's a proposal:

%sexual reproduction ..%gametophyte development (was gametogenesis (s.M.)) ....%megagametogenesis (and children) ....%microgametogenesis (and children) ..%gametogenesis ....%female gamete generation NEW ......%oogenesis (s.I.) ......%oogenesis (s.M.) ......%female gametophyte egg cell differentiation ....%male gamete generation NEW ......%spermatogenesis ......%male gametophyte sperm cell differentiation NEW ..%spore development (sensu Magnoliophyta)?? ....%microsporogenesis ....%megasporogenesis

Question: where does 'sporulation' fall in all this?
Should it be a part of sexual reproduction?

I know you've been reading up on this as well. Do you have some other ideas?

Cheers,

Tanya

Reported by: tberardini

Original Ticket: "geneontology/ontology-requests/980":https://sourceforge.net/p/geneontology/ontology-requests/980

[gocentral]

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Hi Tanya -

I wouldn't put the general 'sporulation' (GO:30435) term as a child of 'sexual reproduction' because 'sporulation (sensu Bacteria)' (GO:30436) is a child of 'sporulation' and bacterial sporulation isn't considered to be sexual reproduction. It would be okay to put 'sporulation (sensu Fungi)' (GO:30437) under 'sexual reproduction'.

I think Chandra was proposing to move GO:30435 out of the 'cell growth/maintenance' branch to the 'cell differentiation' branch. (I think that was it, I can't seem to find my email about it but I'll check with her). Would you then put 'spore development (sensu Mag)' as a child of 'GO:30435'? Would this work for you?

eurie

Original comment by: eurie

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As far as Dictyostelium is concerned (as well as bacteria and yeast I believe), sporulation is NOT a form of sexual reproduction. Therefore if sporulation should go under sexual reproduction it should have a "sensu" term.

Pascale

Original comment by: pgaudet

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Just FYI.

In plants, spore development results in the formation of haploid mega- and microspores which develop into the female and male gametophytes in heterosporous plants. This is clearly not the case in bacteria or fungi.

However, since sporulation is currently defined as "The formation of spores." I thought I'd bring up the issue. This definition is broad enough that we could put 'spore development (sensu Magnoliophyta) under it, although I don't think one would say that plants are sporulating (maybe you would for ferns?). Anyway, here's an idea:

%cell growth and/or maintenance ..%sporulation ....%spore development (sensu Magnoliophyta) NEW ....%sporulation (sensu Fungi) ....%sporulation (sensu Bacteria)

We could leave all current sporulation terms out of sexual reproduction (except for the Fungi one, see Eurie's email) and implement the spore development (sensu Magnoliophyta) in the place I suggested in the original email.

Comments?

Tanya

Original comment by: tberardini

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Hi Tanya -

So Chandra did propose to move 'sporulation' to be a child of 'cell differentiation'. see:

https://sourceforge.net/tracker/index.php?func=detail&aid=763419& group_id=36855&atid=440764

When she does this, will the parentage be okay for 'spore development (sensu Mag)'?

Also, I'm going to take back what I said about the sensu fungi sporulation. I was reminded that asexual sporulation happens in non- yeastie fungi and we don't have terms right now to cover that. So it's probably better to leave the 'sporulation (sensu Fungi)' terms out of sexual reproduction for now. Sorry for the confusion!

eurie

Original comment by: eurie

[gocentral]

• milestone: --> TermGenie
• assigned_to: nobody --> jenclark

Original comment by: jenclark

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Yes, I think that

%cell differentiation --%sporulation ----%spore development (sensu Mag)

would be ok.

Original comment by: tberardini

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Yes that seems fine to me. One suggestion I would make is that we help people out a bit with the gametogenesis confusion by making synonyms e.g.

%gametophyte development, synonym:gametogenesis (sensu Magnoliophyta)

%female gametophyte development, synonym: megagametogenesis

%male gametophyte development, synonym: microgametogenesis

That way we avoid chopping and changing between the gametogenesis and gametophyte development terminology. I'm quite inclined to have the 'gametogensis'-style phrases as the synonyms since they are not anything like as widely used as plain 'gametophyte development'.

Would that suit you?

Jen

Original comment by: jenclark

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Hi,

This may be rather unfortunate timing, but I was also working on a whole lot of child terms for this section of the ontology and had just finished fitting my new terms in with the old ones when I got to this sourceforge item. I've put my new terms below for people to have a look at. If everyone's happy with the new structure we've discussed in this sourceforge item, shall I commit those changes first? Then I can reintegrate my new child terms so we can discuss those separately.

$sexual reproduction ; GO:0019953 -%fertilization ; GO:0009566 --<chemiattractant secretion by synergid cells to attract pollen tube GO:new PMID: 12495749 --<pollen tube entry into micropyle GO:new --<pollen tube penetration of layers of nucellar cells GO:new --<pollen tube entry to embryo sac GO:new --<pollen tube tip rupture. GO:new --%double fertilization (sensu Magnoliophyta) ; GO:0009567 ---<zygote formation (sensu Magnoliophyta) GO:new ----<fusion of sperm cell nucleus and egg cell nuclei (sensu Magnoliophyta) GO:new ----<entry of sperm to egg cell (sensu Magnoliophyta) GO:new ---<formation of primary endosperm cell GO:new ----<entry of sperm to endospore mother cell GO:new ----<fusion of sperm cell nucleus and polar nuclei GO:new --<antipodal cell disintegration GO:new --<synergid cell disintegration GO:new -%gametogenesis ; GO:0007276 --%gametogenesis (sensu Magnoliophyta) ; GO:0009552 ---<megagametogenesis ; GO:0009553 ----<mature embryo sac formation -----<megagametophyte nuclear division ; GO:0009561 synonym: mitotic divison of the megaspore ------<two-nucleate-embryo sac formation ------<four-nucleate embryo sac formation ------<eight-nucleate embryo sac formation ----<mature embryo sac development -----<megagametophyte nuclear migration ; GO:0009562 ------%migration of two nuclei to opposite poles of the embryo sac ------%migration of one nucleus from each pole to the center of the embryo sac -----<endosperm mother cell differentiation ; GO:new ------<regulation of endosperm mother cell differentiation ; GO:new -------%negative regulation of endosperm mother cell differentiation ; GO:new -------%positive regulation of endosperm mother cell differentiation ; GO:new -----<antipodal cell differentiation ; GO:0009557 ------<regulation of antipodal cell differentiation ; GO:0045688 -------%negative regulation of antipodal cell differentiation ; GO:0045689 -------%positive regulation of antipodal cell differentiation ; GO:0045690 -----<cellularization of megagametophyte ; GO:0009558 -----<female gametophyte central cell differentiation ; GO:0009559 ------<regulation of female gametophyte central cell differentiation ; GO:0045691 -------%negative regulation of female gametophyte central cell differentiation ; GO:0045692 -------%positive regulation of female gametophyte central cell differentiation ; GO:0045693 -----<egg apparatus differentiation ; GO:new -------<regulation of egg apparatus differentiation ; GO:new --------%negative regulation of egg apparatus differentiation ; GO:new --------%positive regulation of egg apparatus differentiation ; GO:new -------<female gametophyte egg cell differentiation ; GO:0009560 --------<regulation of female gametophyte egg cell differentiation ; GO:0045694 ---------%negative regulation of female gametophyte egg cell differentiation ; GO:0045695 ---------%positive regulation of female gametophyte egg cell differentiation ; GO:0045696 -------<synergid cell differentiation ; GO:0009563 --------<regulation of synergid cell differentiation ; GO:0045697 ---------%negative regulation of synergid cell differentiation ; GO:0045698 ---------%positive regulation of synergid cell differentiation ; GO:0045699 ---<megasporogenesis ; GO:0009554 ----<ovule primordium formation GO:new ----<ovule primordium development GO:new ----<megasporocyte formation GO:new ----<meiotic division of the megasporocyte GO:new ---<microsporogenesis ; GO:0009556 ----<pollen formation GO:new -----<pollen generative cell formation (to replace 'formation of generative and vegetative cell ; GO:0009564') -----<pollen tube cell formation (to replace 'formation of generative and vegetative cell ; GO:0009564') ---<microgametogenesis ; GO:0009555 ----<germination of the pollen grain GO:new ----<pollen tube growth GO:new ----<pollen sperm cell formation GO:new ----<pollen generative cell division GO:new ----<pollen sperm cell migration GO:new ----<pollen tube nucleus migration GO:new ----<pollen tube nucleus disintegration GO:new --<germ-cell development ; GO:0007281 --<germ-cell migration ; GO:0008354 --%oogenesis ; GO:0007292 ---<oocyte construction ; GO:0007308 ----<oocyte axis determination ; GO:0007309 -----<oocyte anterior/posterior axis determination ; GO:0007314 -----<oocyte dorsal/ventral axis determination ; GO:0007310, GO:0008072 ------<oocyte nucleus positioning ; GO:0030722 -------<oocyte nucleus anchoring ; GO:0042070 -------<oocyte nucleus migration ; GO:0007312, GO:0008102 -----<oocyte microtubule cytoskeleton polarization ; GO:0008103-< oocyte microtubule cytoskeleton organization ; GO:0016325 ----<oocyte microtubule cytoskeleton organization ; GO:0016325 -----<oocyte microtubule cytoskeleton polarization ; GO:0008103-< oocyte axis determination ; GO:0007309 ---%oocyte differentiation ; GO:0009994 ----<oocyte maturation ; GO:0001556 ---<oocyte growth ; GO:0001555 ---<ovulation ; GO:0030728 --<pole cell development ; GO:0007277 ---<pole cell fate determination ; GO:0007278 ---<pole cell formation ; GO:0007279 --%spermatogenesis ; GO:0007283

I haven't done the definitions yet but they're on the way.

Jen

Original comment by: jenclark

[gocentral]

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Hi Jen,

Perhaps you can integrate the changes proposed in this item first as they affect the higher level terms. Sorry for the inconvenience.

Tanya

Original comment by: tberardini

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e-mail to the list:

Hiya,

This e-mail refers to [ 780468 ] megagametogenesis/oogenesis/ spore development

It was recently explained that sensu should only be used where the text sting in the term is the same for two GO:IDs and the definition is different. I have a situation that maybe is an exception to this rule so I'm writing to check that people are happy with my plan before I go ahead.

In animals the term gametogenesis ; GO:0007276 is defined as 'The generation, maintenance, and proliferation of gametes.', whilst this term has a quite different meaning in plants. Plant gametogenesis is the process by which the gametophyte phase is generated (The gametophyte phase in flowering plants is the haploid phase in alternation of generation, and it produces gametes).

This produces the straightforward situation of:

gametogenesis (sensu Animalia) - gamete generation in animals. gametogenesis (sensu Magnoliophyta) - gametophyte generation in plants.

This can be further simplified by making the plant term

gametophyte development, synonym: gametogenesis (sensu Magnoliophyta) - gametophyte generation in plants. Comment: This term should not be confused with gamete generation in plants which is defined by term x.

The problem arises when we make a term to define gamete generation in plants. We cannot call it gametogenesis (sensu magnoliophyta), and we can't call it plain 'gamete generation', because that would be confused with generic gametogenesis. The obvious way to solve the problem is to create the term:

gamete generation (sensu Magnoliophyta) - generation of gametes in flowering plants. Comment: This term has been given sensu status to distinguish it from gametogenesis. It cannot be called 'gametogenesis (sensu Magnoliophyta) because gametogenesis refers to a different process in flowering plants (see gametophyte development ; GO:xxxxxxx).

This use of sensu does not follow the normal rule but seems like a sensible way to deal with the problem. Would everybody be happy for me to implement it?

N.B. Appologies to Tanya for the time this SourceForge item is taking but when I started editing in our new terms today I realised that: gametogenesis (sensu Magnoliophyta) ; GO:0009552 def: The generation, maintenance, and proliferation of gametes in flowering plants. was mis-defined, and in fixing that I unearthed all these other problems.

To fix gametogenesis (sensu Magnoliophyta) ; GO:0009552 I am planning to avoid obsoleteing the term by just changing the term name to 'gamete generation (sensu Magnoliophyta)' as specified above. That will preserve the 50-ish annotations already made to this term.

That's all. Are people happy with this non-standard use of 'sensu'?

Thanks,

Jen

-- EMBL - European Bioinformatics Institute and Wolfson College, Cambridge. http://www.ebi.ac.uk/~jenclark/

Original comment by: jenclark

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regenerating the e-mail for formatting

Original comment by: jenclark

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I've spent some time working out the practical details of the proposal that has already be agreed in principal. What do you think of this?

%sexual reproduction --%gametophyte development ; GO:new, synonym:gametogenesis (sensu Magnoliophyta) ----%female gametophyte development, synonym: megagametogenesis (and children) ----%male gametophyte development, synonym: microgametogenesis
(and children) --%gametogenesis ; GO:0007276 ----%female gamete generation, synonym: oogenesis ; GO:0007292 ------%oogenesis (sensu Insecta) ------%female gamete generation (sensu Magnoliophyta), synonym: oogenesis (sensu Magnoliophyta) ; GO:new -------%female gametophyte egg cell differentiation ; GO:new
----%male gamete generation ; GO:new def: Generation of the haploid male gamete. ------%spermatogenesis ; GO:0007283 -------%spermatogenesis (sensu Magnoliophyta) ; GO:new --------%male gametophyte sperm cell differentiation ; GO:new -----%male gamete generation (sensu Magnoliophyta) ; GO:new ------%spermatogenesis (sensu Magnoliophyta) ; GO:new -------%male gametophyte sperm cell differentiation ; GO:new GO:0048222 ---%gamete generation (sensu Magnoliophyta) ; GO:0009552 was Gametogenesis (sensu Magnoliophyta) ------%female gamete generation (sensu Magnoliophyta), synonym: oogenesis (sensu Magnoliophyta) ; GO:new -------%female gametophyte egg cell differentiation ; GO:new ------%male gamete generation (sensu Magnoliophyta) ; GO:new -------%spermatogenesis (sensu Magnoliophyta) ; GO:new --------%male gametophyte sperm cell differentiation ; GO:new --%spore development (sensu Magnoliophyta) ; GO:new
----%microsporogenesis ; GO:0009556 ----%megasporogenesis ; GO:0009554

%cell differentiation --%sporulation ----%spore development (sensu Mag)

Original comment by: jenclark

[gocentral]

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Hi Jen,

I think the indentation in your last message may have been a little off. I'm having a hard time distinguishing which terms are siblings and which terms have a parent-child relationship.
Would it be possible for you to throw this into DAGedit and email the new structure? Sorry about the extra work.

I'm not convinced that we need the synonyms 'spermatogenesis (sensu Mag)' and 'oogenesis (sensu Mag)' or even 'oogenesis' for 'female gamete generation'. Didn't we discuss that these terms are NOT used to describe the analogous processes in plants? Would this be for searching purposes, maybe?

Thanks,

Tanya

Original comment by: tberardini

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This is getting quite long so I'll continue on a new sourceforge item:

[ 798477 ] plant gametogenesis cont.

Original comment by: jenclark

[gocentral]

• status: open --> closed-later

Original comment by: jenclark