plant gametogenesis 2

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This is to follow on from [ 800444 ] Plant gametogenesis https://sourceforge.net/tracker/index.php? func=detail&aid=800444&group_id=36855&atid=440764 which is getting quite long.

Reported by: jenclark

Original Ticket: "geneontology/ontology-requests/1537":https://sourceforge.net/p/geneontology/ontology-requests/1537

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Hi Jen,

My goodness, you have been busy this morning! It's taken me till now (it's 10:20 here) to catch up to all of the discussions!

In the last exchange, you said:

>I see, yes, that sounds similar. In that case would you be >happy for me to call it 'eight-nucleate embryo sac >formation'? That's what I would have done in the first place >really since the only change is the number of nuclei.

I agree. This is much better than the previous 'differentiation term' and it sounds much more like what I would actually search for.

I've also had a look at the files you attached have a few comments:

1. Overall, it looks great! Good work!

2. The term 'male gametophyte development (s. M.)' is missing as a child of 'male gamete generation (s.M.)' and parent of the current terms under 'male gamete generation (s.M.).' Is this intentional?

3. Would you say that 'pollen tube growth', 'pollen tube nucleus disintegration','pollen tube nucleus migration', and 'germination of the pollen grain' are part of 'male gametophyte development'? From the definition of mgd :"...into mature gametophytes containing the gametes (pollen)", it doesn't sound like those terms belong here.
   Perhaps they are better off as children of 'post-pollination', where 'pollen tube growth' is currently. Does pollen grain germination occur outside of pollination?

4. 'male gametophyte initial cell differentiation' - should this be part of spore development? With its children, 'differentiation of vegetative cell' and 'differentiation of generative cell', I'm not too sure.

5. Should 'mega-' and 'microsporogenesis' be isa children of spore development instead of partof children?

Those are my comments for now. I think Sue should have a look at this too since she has more experience than I do in this area.

Cheers,

Tanya

Original comment by: tberardini

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Hi Tanya,

Thanks, I'm glad you like it. Thank you for all your comments, especially about the post-pollination terms. They've given me lots of good pointers for how to sort this tree out and fit it better into the rest of the DAG. I'm currently having a good think about the post-pollination terms so I'll wait a bit before coming back with a new draft. I've fixed the things you pointed out in no.2 &5.

Once I get things straightened out a bit more I'll e-mail Sue as well so she can look at it.

Ta.

Jen

Original comment by: jenclark

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I Tanya,

I have been looking at the post-pollination terms.

--%physiological process ; GO:0007582 ---%organismal physiological process ; GO:0050874 ----%reproductive physiological process ; GO:0050876 -----%post-pollination ; GO:0009856 ------%compatible pollen-pistil interaction ; GO:0009858 -------<pollen adhesion ; GO:0009876 -------<pollen hydration ; GO:0009859 -------<pollen recognition ; GO:0009857 -------<pollen tube adhesion ; GO:0009865 ------<pollen germination ; GO:0009846 ------<pollen tube growth ; GO:0009860 ------%pollen tube guidance ; GO:0010183

There are two possible places to put sexual reproduction terms:

1)

%physiological process ; GO:0007582 def: Those processes specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. %reproductive physiological process ; GO:0050876 def: The processes pertinent to the reproductive function of an organism.

-%physiological process ; GO:0007582 --%organismal physiological process ; GO:0050874 ---%reproductive physiological process ; GO:0050876

2)

%development ; GO:0007275 def: Biological processes specifically aimed at the progression of an organism over time from an initial condition (eg. a zygote, or a young adult) to a later condition (eg. a multicellular animal or an aged adult). reproduction ; GO:0000003 def: The production by an organism of new individuals that contain some portion of their genetic material inherited from that organism.

%development ; GO:0007275 -%reproduction ; GO:0000003

.....................

I will have a look at the terms I have, and the ones under post- pollination, and try to work out the logic of which ones are physiological or developmental.

Thanks,

Jen

Original comment by: jenclark

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Hi Jen,

I must admit I'm a little confused as to the difference between 'reproductive physiological process' and 'reproduction.' From the children terms, it seems that all of the gamete generation bits fall under 'reproduction' while related, post-fertilization processes (mostly) are under 'reproductive physiological process'. On the other hand, 'lactation' and 'menstrual cycle' don't seem to belong, or do they? I can kind of convince myself that 'menstrual cycle' belongs but 'lactation'? Actually, even 'dehiscence' has me wondering.

I'm thinking that the terms you've developed will largely fall under development, under reproduction, since they do deal more with the generation of gametes.

My thoughts for now,

Tanya

Original comment by: tberardini

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latest draft as at 24/3/4

Original comment by: jenclark

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Hi,

I have adjusted the terms so they are better distributed between development and the post-pollination parent that is now called 'Interaction between male gametophyte and female floral organs'.

Would it be possible to have a look at what I've done? The file is uploaded below in obo format.

Thanks,

Jen

Original comment by: jenclark

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By the way I have made a little snapshot ontology in that file just so you can see the plant gametogenesis terms side-by-side with the post- pollination ones. In reality the two groups of terms would just be under sexual reproduction ; GO:0019953 and 'Interaction between male gametophyte and female floral organs' that used to be 'post-pollination' ; GO:0009856. The terms in my file that are parents to these terms are just there to allow the two sets to be displayed together and are made up.

Thanks,

Jen

Original comment by: jenclark

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Here's a radical idea:

How about merging 'pollen-pistil interaction' and 'post- pollination' and just retaining the string 'pollen-pistil interaction'?

Looking at the defs, it seems like they are describing very similar if not identical things.

PPI: The interaction between a pollen grain and pistil.

PP: Post-pollination involves interactions between the female tissues (stigma, style and ovary) and the male gametophyte or the pollen tube cell, which contains the sperm cells.

Original comment by: tberardini

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we can't merge PP and PPI, because PPI is a very short lived event whereas PP goes up until the fertilization is about to happen.

I suggested a new definition for PP in the morning on go mailing list.

pankaj

Original comment by: jaiswalp

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OK, point well taken. Not such a brilliant idea after all.

Are you referring to:

It involes all the processes involving male gametophyte and female floral organs of an angiosperm plant starting from the pollen pistil interaction up until the fertilization is about to happen.

How about a slight modification (of term name and def)?

name: male gametophyte/female floral organ interaction def: Processes involved in the interaction between the male gametophyte and floral female organs of an angiosperm plant beginning with pollen-pistil interaction and ending just prior to fertilization.

Tanya

Original comment by: tberardini

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Hi Jen,

Just had a look at the OBO file you attached below. Here are my comments:

1. You'll probably update this a little so that instead of compatible pollen-pistil interaction, the term will now be 'pollen-pistil interaction' with the changes you just implemented in the SF item about pistil interaction changes, right?

2. What did you think of my idea of modifying the term name of "Interaction blah, blah..." in my last comment in this SF item? What about the definition?

3. Don't forget 'pollen tube guidance' as a child of the 'interaction...' term. Or should that go somewhere else?

Otherwise, this looks fine to me. BTW, do you know of any of the online GO browsers that are updated on a daily basis?

Cheers,

Tanya

Original comment by: tberardini

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Jen,

What was wrong with 'post-pollination' in the first place? I think the name of the term you replaced is horrid. I don't see anything wrong with "post-pollination process".

Original comment by: syrhee

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from tanya How about a slight modification (of term name and def)?

name: male gametophyte/female floral organ interaction def: Processes involved in the interaction between the male gametophyte and floral female organs of an angiosperm plant beginning with pollen-pistil interaction and ending just prior to fertilization.

The name sounds a bit awkward, plus its more than just interaction. Is there a harm in keeping the existing one. Post pollination process..

Original comment by: jaiswalp

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Hi,

It seems to me that it would be good first of all to sort out what this term is trying to represent.

if it's everything that happens between pollination and fertilization as pankaj suggests:

A) def: It involes all the processes involving male gametophyte and female floral organs of an angiosperm plant starting from the pollen pistil interaction up until the fertilization is about to happen.

1) 'all the processes involving male gametophyte': Does this include all the processes involved in male gametophyte development, independent of it's interaction with the female floral organs?

2)'starting from the pollen pistil interaction': Does this say that it includes pollination?

Pankaj's def is a bit different from the definition of the current term:

post-pollination: B) current def: Interactions between the female tissues (stigma, style and ovary) and the male gametophyte or the pollen tube cell, which contains the sperm cells. These processes begin after pollination and end with fertilization.

This clearly starts after polination and finishes before fertilization and it only covers the actual interactions between the male gametophyte and female floral organ tissues as far as I can see. It doesn't actually include things like male gametophyte development.

Can you tell me first of all if you think that the current definition of this term agrees with your understanding of what the term is meant to represent? If it does, then that's fine, and if it doesn't then I can obsolete it and we can make a new one that better represents the concept in question.

I think that once we have got that straight then we will be in a better position to work out a name that is appropriate to the term.

Tanya: Thanks for pointing out the bits I missed in the file I uploaded. I'll look at that. If you want a browser that's updated every day you could try QuickGO. It's updated every day and is made to be really fast so it's useful for annotators who have to search a lot. http://www.ebi.ac.uk/ego/ I'm not sure if there are others but I can ask if you want more options. Come to think of it that should really be on the tools page shouldn't it?

Thanks,

Jen

Original comment by: jenclark

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Jen,

The current definition is fine and correct. However, it seems that the name of the term has already been changed for at least a couple of days. You can see that either in QuickGo or our local curators' version of AmiGo (http://tesuque.stanford.edu/~dyoo/amigo/htmlbrowser/cgi-bin/go.cgi?dbname=go\_daily).

You still haven't provided the motive for renaming the term. I think the term should be renamed back to 'post-pollination process'. All of the things that are under this term (GO:0009856) are OK to be there. All of these things do happen after pollination.

It would probably be good to have a term called 'pollination' (Def: transfer of pollen from the anther to the stigma of a plant) at the same node as post-pollination. I assume we didn't put it there because it's not known that this process involves genes or is a purely physical process.

I am not sure about Pankaj's suggegstion to remove 'compatible' and 'incomptible' pollen-pistal interactions. I thought these were both legitimate processes that happen in different plants.

Original comment by: syrhee

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Hi Sue,

Yes I changed the term name the other day after I wrote to the list and nobody complained. Then after you said that you weren't keen on the idea I thought I'd better stop and talk about it first rather than change it back and then end up changing it again.

I changed the name because it didn't seem to make a clear statement about what the term covers. 'post-pollination' as it was, is not a noun, and it suggests any process that occurs after pollination, e.g. seedset, fruit formation. It is very non-specific and does not give a clear idea of what this term is about. I don't want to leave the term name that I have made up either, and I agree that the name is clumsy, but I'd like to have a discussion about what we can do to make this term name clearer and then I can commit it once and solve the problem.

If you have concerns about the compatible and incompatible terms could you possibly start a new sourceforge item since this one is getting to have rather a lot of different things on it.

Thanks,

Jen

Original comment by: jenclark

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A delay of at least a week would be good before implementing any changes. That way people that are travelling/busy with other things will have a shot at catching up before any actions are taken.

term name: Post-pollination OR Post-pollination process OR Interaction between male gametophyte and female floral organs OR Male gametophyte/female floral organ interaction

Current def:

Interactions between the female tissues (stigma, style and ovary) and the male gametophyte or the pollen tube cell, which contains the sperm cells. These processes begin after pollination and end with fertilization.

My proposed def (very similar but maybe a little more specific?)

Processes involved in the interaction between the male gametophyte and floral female organs of an angiosperm plant beginning with pollen-pistil interaction and ending just prior to fertilization.

Which term name to pick? I suggest that we consider what users might enter in the search box when looking for gene products associated to this term and take it from there.

Sue, you are right in that there is no 'pollination' term because it is not clear that there are genes involved in the transfer of pollen to the stigma, it does seem to be a physical process (mediated by insects, wind...).

Tanya

Original comment by: tberardini

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Regarding the post-pollination/pollination issue. A little history- 1.term was first entered as pollination 2.Pankaj pointed out (rightly so) that pollination was the part about the birds and the bees...how the pollen gets to the stigma in the first place. 3.pollination changed to post-pollination to distingush this as the events/processes that occur once the pollen is deposited on the female reproductive organ. The endpoint is when fertilization occurs.

I think most plant scientists would expect to find the term pollination ( or post pollination) included as a process plants undergo and a thing they study. I was under the impression (well a long time ago I suppose) that the definition is the key and may reflect what how something is commonly defined. I dont think many scientists think of post pollination as encompassing all plant development- just the naughty bits after anther dehiscence up to fertilization.

So this process includes things like pollen-pistil interactions involved in self/non self recognition, pollen hydration (which in some plants requires self-non self recognition) , pollen tube germination, pollen tube guidance...

So maybe there needs to be a term 'post-germination pollen development' that is a part of male gametophyte development and an instance/part of post-pollination processes.

Leonore

Original comment by: lreiser

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Hi Leonore,

Thanks, that's really very helpful. I've been thinking more about this, and it seems to me a little artificial to make a parent term that groups the events that happen chronologically between pollination and fertilization. Do you think we could try to think of a more logical way to group these things, that would accommodate the post-pollination processes that we need?

e.g. Something like:

%sexual reproduction -%sexual reproduction (sensu Magnoliophyta) --<male gametophyte development --<fertilization --<Male gametophyte/female floral organ interaction

Male gametophyte/female floral organ interaction def: Processes involved in the interaction between the male gametophyte and floral female organs of an angiosperm plant beginning with pollen-pistil interaction and ending just prior to fertilization.

This is just a suggestion and I'd be very interested to know everybody's ideas on the subject.

Thanks,

Jen

Original comment by: jenclark

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Hi again,

Can I just check with you now that I understand the term post-pollination processes to mean the same thing as you do?

'Processes involved in the interaction between the male gametophyte and floral female organs of an angiosperm plant beginning with pollen-pistil interaction and ending just prior to fertilization.'

When I read that I assume that it only covers processes that directly involve interaction between the male gametophyte and female floral organs.

for example: chemiattractant secretion by synergid cells def: The process by which the synergid cells secrete chemiattractant. The pollen tube grows toward the source of the chemiattractant and so enters the embryo sac. The synergid cell is defined by its location near the interior side of the micropyle of the embryo sac of an angiosperm.

Leonore's e-mail seems to suggest at one point that the contained processes involve interaction...

'So this process includes things like pollen-pistil interactions involved in self/non self recognition, pollen hydration (which in some plants requires self-non self recognition) , pollen tube germination, pollen tube guidance...'

She also says...

'pollination changed to post-pollination to distingush this as the events/processes that occur once the pollen is deposited on the female reproductive organ. The endpoint is when fertilization occurs.'

which seems to imply all events between pollination and fertilization regardless of whether they involve interaction or not. For example male gametophyte development and the 'post-germination pollen development' term that she suggests.

Can you clarify for me the meaning of the 'interaction' within this term definition?

Thanks,

Jen

Original comment by: jenclark

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Hi,

I have another question. When you use 'post-pollination', are you using it as a technical term from a particular field of plant science that would have an understood meaning other than that implied by the normal meanings of the two words? I have checked on pubmed and the the expression is used but seems to be in situations where and event is happening e.g. '15 days post-pollination' so there it is just a chronological marker, or else it is used to refer to all events happening after pollination until fertilization.

I was talking to Jane about this and she points out that if it's that kind of field-specific term, then as long as it's not wildly misleading then we can just make sure the definition is very clear and use synonyms to add as many names as are needed to make sure everybody can find the term.

Thanks,

Jen

Original comment by: jenclark

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I agree. This term seems to be a kind of grouping term for all the events happening after the pollen has landed on the pistil (means pollination has occurred). I also agree that there is chronological order in which the events occur but that is something beyond the scope here. My suggestion is for including everything that is happening after pollination up until the fertilization or pollen tube penetration into the embryosac, but with a word of caution that pollen germination process is not always a post-pollination process. In some monocot systems it is known to occur before pollination as in one of Sheila McCormicks review papers. I think we should invite her into the discussion as an outside expert.

More info on Sheila McCormick at http://plantbio.berkeley.edu/faculty/faculty\_pages/McCormick .html

Original comment by: jaiswalp

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Hi First- I think its a great idea to get feedback from Sheila- I'm more than happy to go over to the PGEC Wednesday when I work from home and talk to her and have her review definitions /structure. I think she'd be quite happy to give feedback on this.

Second- I think this term: <Male gametophyte/female floral organ interaction

can safely be called pollen-pistil interaction...really. I dont see any particular reason why the language has to be obtuse.

When I use post-pollination I do so reluctantly... It wasnt my choice of term.It could refer to all events from pollination to fertilization- which doesn't imply ONLY pollen pistil interactions. My bad if that is confusing. As far as temporal events. I was also under the assumption that GO was not a representation of pathways-so there was no implied 'temporal sequence'.

So in your reproduction scheme: -%sexual reproduction (sensu Magnoliophyta) --<male gametophyte development --<fertilization --<Male gametophyte/female floral organ interaction

Does female gametophyte development ALSO exist in this node? Or are you trying to include only post germination pollen development (as in is SOMETIMES a part of). Leonore

Original comment by: lreiser

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Reason I ask about the female gpt is 1) its certainly required for sexual reproduction 2) in orchids, pollination triggers megagametogenesis

among other 'post-pollination' events are floral organ abscission and sometimes ovary maturation... Leonore

Original comment by: lreiser

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Leonore you are on the right track. floral organ abscission/senescence, ovary maturation and megagametogenesis are known to occur post pollination in some plants.

I think we should wait until we get a feedback from Sheila.

Pankaj

Original comment by: jaiswalp

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Well I am not so sure about that---(the being on the right track part) I think what matters is that people get the expected results from a query. So how about this- I'll ring up sheila and she if she has time to talk on Wednesday and if she does- pull out the relevant structures and definitions and Ill talk them over with her.

Original comment by: lreiser

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sheila is out of town til the 11th of April. -Leonore

Original comment by: lreiser

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Great. I hope it works.

Original comment by: jaiswalp

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Hi,

Thanks for all those comments. They are really helpful. I think that's a great idea to get input from Sheila. Would it be possible for you to show her the DAG that I have uploaded at the bottom of this sourceforge item? It loads into DAG-Edit and is in OBO format.

Thanks,

Jen

Original comment by: jenclark

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Yes- I should be able to once i update my DagEdit version. I will send Sheila an email and ask if she can meet after she returns from where ever. -Leonore

Original comment by: lreiser

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So Tanya and I are going to meet Sheila McCormick tomorrow at about 1:30. I loaded the OBO file and it seems to be fine (using 1.409). Its the first time I have looked at this and I have afew questions myself.

1) Female gamete generation as a parent of female gametophyte development. Id say the female gametophyte development is the parent-then forming the gametes (eggs and sperm) is some thing the female gpt does.

2) Female gamete generation. Can we use another term, like megagametogenesis? As a plant biologist my first thought is OOOH alternation of generations.

3) Speaking of real words how about using terms like Polygonium-type
megasporogenesis/gametogenesis... this refers to what you describe as sensu Magnoliophyta - and while about 70% of flowering plants do it this way- 30% do not.

4)Then there are all these terms about egg apparatus differentiation which given your definition should have some synergid cell differentiation as a part of this as well.

5) then there is megasporogenesis as an instance of gametogenesis...sort of odd dontcha think? And includes ovule development as a part of megasporogenesis? Is there another relationship type I am missing that would have this make sense (e.g. ovule primordium initiation is REQUIRED for megasporogenesis). I noticed that anther development is not a part of male gametogenesis- be good to be consistant- Id leave it out.

6)Then I think there is the potential for semi weirdness in a query.

For example the gene BELL1 is required for normal ovule development. True, they are sterile and mesporogenesis is affected, but I wouldnt necessarily expect to see BEL in a query for genes involved in megasporogenesis because th pattern of ovule development is abnormal.

(BTW- I feel sort of odd with the term primordium differentiation...its sort an oxymoron).

7) Might also help to take this opportunitiy to make the terms more interanally consistant like pick between female gametophyte or megagametophyte and use one throughout (make the other term a synonym if need be)

Well probably just cover the pollination/post pollination fertilization angle tomorrow. These just some random thoughts I had when looking at the file.

Original comment by: lreiser

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Leonore and I consulted Sheila McCormick about the pollination/post-pollination/.... section of GO. I will open a new SF item with the heading 'pollination' and attach our meeting summary to that. I think this would be a good place to start the discussion on this topic from a fresh perspective.

Original comment by: tberardini

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The pollination issue has now been resolved and we are back to dealing with plant gametogenesis. There is information on the pollination sourceforge item that is useful for the gametogenesis issue so anybody who want to comment here might like to have a look at that too.

[ 944692 ] pollination https://sourceforge.net/tracker/?func=detail&atid=440764&aid=944692&group\_id=36855

Thanks,

Jen

Original comment by: jenclark

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I'm going to split this sourceforge item into smaller parts so it's a bit more manageable.

The first is [ 1003916 ] female gametophyte development https://sourceforge.net/tracker/index.php?func=detail&aid=1003916&group\_id=36855&atid=440764

Thanks,

Jen

Original comment by: jenclark

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Hi,

This item has been open for a long time. Please comment to let us know whether you would like it to remain assigned to you, or would prefer it to be reassigned. (You don't necessarily have to work on it immediately if you keep it; we just need to know whether it's still on your list.)

Thanks, Midori & David Ontology development group managers

Original comment by: mah11

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• status: open --> closed-accepted

Original comment by: jenclark