new terms under gametogenesis ; GO:0007276

gocentral commented 21 years ago

Please can I have some new terms under gametogenesis. I've tried to make them as non-sensu as poss. Hopefully they shouldn't cause any true-path violations, tho' I don't know much about gametogenesis (including nomenclature) in non-Drosophila so hopefully someone who does can verify this.

gametogenesis ; GO:0007276 --<germ-cell development ; GO:0007281 ----<germ-line stem cell division ------%female germ-line stem cell division ------%male germ-line stem cell division ----<germ-line cyst formation ------%female germ-line cyst formation (sensu Insecta ????) --------<cystoblast cell division ; GO:0007282 (sensu Insecta ???) ------%male germ-line cyst formation --------<spermatogonial cell division ; GO:0007284 --------<primary spermatocyte growth ; GO:0007285 --------<spermatocyte cell division --<germ-line cyst encapsulation ----%female germ-line cyst encapsulation (sensu Insecta ???) ----%male germ-line cyst encapsulation

--%spermatogenesis ; GO:0007283 ----<male germ-line stem cell division ----<male germ-line cyst formation ----<male germ-line cyst encapsulation

--%oogenesis ; GO:0007292 ----<female germ-line stem cell division ------%female germ-line stem cell division (sensu Insecta)

Proposed Definitions:

NB: the proposed defs for the female cyst terms are insect-specific (see point 4). If there's non-insect instances of female germ-line cyst formation, these can be altered accordingly.

germ-line stem cell division extra parent: asymmetric cytokinesis ; GO:0008356 Division of a germline stem cell to produce a daughter stem cell and a daughter germ cell, which will divide to form the gametes. ref: PMID:2279698

male germ-line stem cell division Division of a germline stem cell in the male gonad, to produce a daughter stem cell and a daughter germ cell, which will divide to form the male gametes.

female germ-line stem cell division Division of a germline stem cell in the female gonad, to produce a daughter stem cell and a daughter germ cell, which will divide to form the female gametes.

spermatogonial cell division ; GO:0007284 The mitotic divisions undergone by a gonial cell (the daughter of the germ-line stem cell) to produce a cyst of diploid primary spermatocytes. ref: ISBN:0-87969-423-8

!! NB !! There is variation in the literature as to whether a spermatogonial cell is the PGC or the daughter of the PGC. Different organisms also have different nomenclature. There's no annotations to this term at the moment so I'm proposing a definition assuming its the child of the PGC.

spermatocyte cell division The meiotic divisions undergone by the primary and secondary spermatocytes to produce a cyst of haploid spermatids. ref: ISBN:0-87969-423-8 NB: Is this nomenclature ok for non-insects?

germ-line cyst formation Formation of a cluster of germ-line cells derived from a single founder cell. ref: PMID: 10370240

female germ-line cyst formation (sensu Insecta ??) Formation of a cluster of germ-line cells, in the female gonad [of an insect] , derived from a single [cystoblast] founder celll.

male germ-line cyst formation Formation, in the male gonad, of a cluster of germ-line cells derived from a single founder cell. A cyst of spermatocytes is produced by mitotic divisions of the founder cell. The spermatocytes then divide meiotically resulting in a cyst of spermatids.

cyst encapsulation extra parent: morphogenesis of follicular epithelium ; GO:0016333 Formation of a single follicular epithelium around the germ-line derived cells of a cyst. ref: PMID:11591336

female cyst encapsulation (sensu Insecta??) Formation of a single follicular epithelium around the germ-line derived cells of a cyst formed in the female gonad [of an insect].

male cyst encapsulation Formation of a single follicular epithelium around the germ-line derived cells of a cyst formed in the male gonad.

primary spermatocyte growth ; GO:0007285 The phase of growth and gene expression that male germ cells undergo as they enter the spermatocyte stage. The cells grow in volume and transcribe most of the gene products needed for the morphological events that follow meiosis. ref: ISBN:0-87969-423-8

female germ-line stem cell division (sensu Insecta) additional parent (isa) female germ-line stem cell division The asymmetric division, in the insect ovary, of a germline stem cell to produce a new stem cell and a cystoblast.

I think cystoblast cell division ; GO:0007282 and spermatogonial cell division should be removed as children of germ-line stem cell renewal ; GO:0042078. The PGC divides to form a stem cell daughter and a spermatogonial/cystoblast cell. Therefore I'd take the initial PGC division step to be the renewal step.

Therefore maybe it should be changed to:

germ-line stem cell renewal ; GO:0042078 --<germ-line stem cell division ; GO:new

Do cysts form in non-insect females ???? From reading PMID:10370240 it sounds like cystoblasts and cysts are limited to males and higher-insect females.

If no-one disagrees with this, then can I add the term 'sensu Insecta' to cystoblast cell division ; GO:0007282 and have the following parentage:

oogenesis (sensu Insecta) ; GO:0009993 --<female germ-line stem cell division (sensu Insecta) --<female germ-line cyst formation (sensu Insecta) ----<cystoblast cell division (.github.com/u) ; --<female cyst encapsulation (sensu Insecta)

Thanks!

Becky

Reported by: beckyfoulger

Original Ticket: "geneontology/ontology-requests/863":https://sourceforge.net/p/geneontology/ontology-requests/863

gocentral commented 21 years ago

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HI Becky,

Most of this looks great. I think the cyst stuff is insect-specific, but I don't see a need for sunsu insecta beacuse the term in and of itself is specific enough. I always viewed the PGCs as germ-line stem cells that were completely non-committed. The spermatogonial cells are the daughter cells that are committed to become male germ cells. What I'm nor sure of is that if you take out a spermatogonial cell and transplant it into a female, can it contribute to the female germ line? My colleagues and I pretty sure the answer is no.

Be sure that Tanya sees this stuff so we can incorporate the plants into this part of the DAG. It may be a challenge since they don't segregate their germ line at all like animals do.

David

Original comment by: ukemi

gocentral commented 21 years ago

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Hi David,

< The spermatogonial cells are the daughter cells that are committed to become male germ cells.

ok- that makes sense to me. So I think the above proposed def is therefore ok.

< I don't see a need for sensu insecta

ok- I just added it so I could put the female terms under oogenesis (sensu Insecta) ; GO:0009993, but I agree it's fine to leave it off and only insect-people will annotate to that term anyway.

Actually, I'm not sure where the oogenesis (sensu Insecta) ; GO:0009993 came from. There's terms under it that have definitions contriubuted from non-insect databases. There's also mouse Peli2 annotated to Tl receptor signaling, which now falls under this sensu parent... I'll make a new SF item.

Becky

Original comment by: beckyfoulger

gocentral commented 21 years ago

milestone: --> TermGenie

Original comment by: jenclark

gocentral commented 21 years ago

assigned_to: nobody --> jenclark

Original comment by: jenclark

gocentral commented 21 years ago

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I've added 'female cyst encapsulation' GO:0030708 as part-of 'ovarian follicle cell development (sensu Insecta)' GO:0030707. I left out 'sensu Insecta' based on David's comments. Other relationships still to be added (will leave that for Jen).

m

Original comment by: mah11

gocentral commented 21 years ago

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After a quick look at PMID 10370240, I've decided that GO:0030708 should be 'sensu Insecta' after all.

I've now also added 'female germ-line cyst formation (sensu Insecta)' GO:0030727 as a part-of 'ovarian follicle cell development (sensu Insecta)' GO:0030707 and part-of 'egg chamber formation (sensu Insecta)' GO:0007293.

This is for two comments from SF 753304:

> female cyst formation ; GO:new [see SF: 752667 ] should be made a direct > child of egg chamber formation ; GO:0007293 instead of a direct child of > oogenesis.

> female cyst encapsulation ; GO:new [see SF: 752667 ] should be made a > direct child of egg chamber formation ; GO:0007293 and ovarian follicle > cell development ; GO:new, instead of a direct child of oogenesis.

These are both done, so female cyst encapsulation is part-of both 'ovarian follicle cell development (sensu Insecta)' GO:0030707 and 'egg chamber formation (sensu Insecta)' GO:0007293 as well.

Still to do:

make sure these terms (30708 & 30727) have all the parents they need
add generic cyst terms
the rest of this SF entry!

Original comment by: mah11

gocentral commented 21 years ago

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comments from beccy on suggested additions:

I think female cyst formation only occurs in higher insects (PMID: 10370240). So I think

female germ-line cyst formation (sensu Insecta) ; GO:0030727 and female cyst encapsulation (sensu Insecta) ; GO:0030708

are fine under egg chamber formation (sensu Insecta) and they probably dont need generic parents.

Similarly: cystoblast cell division ; GO:new vs cystoblast cell division ; GO:0007282

I think cystoblast is also an insect term, so I don't think a non-generic term is needed. (I would double-check but my netscape has gone down temporarily).

3.

> --%oogenesis ; GO:0007292 > ----<female germ-line stem cell division ; GO:new > ------<female germ-line cyst formation ; GO:new > --------<cystoblast cell division ; GO:new > ------<female cyst encapsulation ; GO:new

I think this will be corrected if the female cyst terms are insect specific anyway but female germ-line cyst formation ; GO:new and female cyst encapsulation ; GO:new should be siblings of female germ-line stem cell division ; GO:new rather than a child (it's correct under gametogenesis ; GO:0007276).

Original comment by: jenclark

gocentral commented 21 years ago

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hiya,

I think better keep the generic female cyst formation term because the article that you cited:

"Do cysts form in non-insect females ???? From reading PMID:10370240 it sounds like cystoblasts and cysts are limited to males and higher-insect females. "

seems to suggest that female cyst formation happens in many other
species.

Original comment by: jenclark

gocentral commented 21 years ago

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that's that last relationship bit laid out properly:

--%oogenesis ; GO:0007292 ----<female germ-line stem cell division ; GO:new ----<female germ-line cyst formation ; GO:new ----<female cyst encapsulation ; GO:new ----%oogenesis (sensu Insecta) ; GO:0009993 ------%female germ-line stem cell division (sensu Insecta) ; GO:new ------<female germ-line cyst formation (sensu Insecta) ; GO:0030727 --------<cystoblast cell division (sensu Insecta) ; GO:0007282 ------<female cyst encapsulation (sensu Insecta) ; GO:0030708

Original comment by: jenclark

gocentral commented 21 years ago

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Should I change this definition?

Currently: female germ-line cyst formation (sensu Insecta) ; GO:0030727 Formation of a cluster of germ-line cells, in the female gonad of an insect, derived from a single founder cell (cystoblast).

change to:

female germ-line cyst formation (sensu Insecta) ; GO:0030727 Formation of a cluster of germ-line cells, in the female gonad, derived from a single founder cell (cystoblast), as in Insecta.

Original comment by: jenclark

gocentral commented 21 years ago

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Here's the plan as it currently stands:

Generic terms to be added:

gametogenesis ; GO:0007276 --<germ-cell development ; GO:0007281 ----<germ-line stem cell division ; GO:new ------%female germ-line stem cell division ; GO:new ------%male germ-line stem cell division ; GO:new ----<germ-line cyst formation ; GO:new ------%female germ-line cyst formation ; GO:new --------%female germ-line cyst formation (sensu Insecta) ; GO:0030727 --------<cystoblast cell division (sensu Insecta) ; GO:0007282 ------%male germ-line cyst formation ; GO:new --------<spermatogonial cell division ; GO:0007284 --------<primary spermatocyte growth ; GO:0007285 --------<spermatocyte cell division ; GO:new --<germ-line cyst encapsulation ; GO:new ----%female germ-line cyst encapsulation ; GO:new ------%female germ-line cyst encapsulation (sensu Insecta) ; GO:0030708 ----%male germ-line cyst encapsulation ; GO:new

--%spermatogenesis ; GO:0007283 ----<male germ-line stem cell division ; GO:new ----<male germ-line cyst formation ; GO:new ----<male germ-line cyst encapsulation ; GO:new

--%oogenesis ; GO:0007292 ----<female germ-line stem cell division ; GO:new ----<female germ-line cyst formation ; GO:new ----<female cyst encapsulation ; GO:new ----%oogenesis (sensu Insecta) ; GO:0009993 ------%female germ-line stem cell division (sensu Insecta) ; GO:new ------<female germ-line cyst formation (sensu Insecta) ; GO:0030727 --------<cystoblast cell division (sensu Insecta) ; GO:0007282 ------<female cyst encapsulation (sensu Insecta) ; GO:0030708

germ-line stem cell renewal ; GO:0042078 --<germ-line stem cell division ; GO:new

Additional parents:

----<female germ-line stem cell division ; GO:new ------%female germ-line stem cell division (sensu Insecta) ; GO:new

------<female germ-line cyst formation ; GO:new ---------<female germ-line cyst formation (sensu Insecta) ; GO:0030727

--------<cystoblast cell division ; GO:new -----------<cystoblast cell division (sensu Insecta) ; GO:0007282

------<female cyst encapsulation ; GO:new ---------<female cyst encapsulation (sensu Insecta) ; GO:0030708

----<germ-line cyst formation ; GO:new ------%female germ-line cyst formation (sensu Insecta) ; GO:0030727

Definitions:

----<germ-line stem cell division ; GO:new extra parent: asymmetric cytokinesis ; GO:0008356 def:Division of a germline stem cell to produce a daughter stem cell and a daughter germ cell, which will divide to form the gametes. ref: PMID:2279698

------%female germ-line stem cell division ; GO:new def:Division of a germline stem cell in the female gonad, to produce a daughter stem cell and a daughter germ cell, which will divide to form the female gametes.

------%male germ-line stem cell division ; GO:new def:Division of a germline stem cell in the male gonad, to produce a daughter stem cell and a daughter germ cell, which will divide to form the male gametes.

----<germ-line cyst formation ; GO:new def:Formation of a cluster of germ-line cells derived from a single founder cell. ref: PMID: 10370240

------%female germ-line cyst formation ; GO:new def:Formation of a cluster of germ-line cells, in the female gonad, derived from a single founder cell.

------%male germ-line cyst formation ; GO:new def:Formation of a cluster of germ-line cells, in the male gonad of an insect, derived from a single founder cell (cystoblast).

--------<spermatocyte cell division ; GO:new def:The meiotic divisions undergone by the primary and secondary spermatocytes to produce a cyst of haploid spermatids. ref: ISBN:0-87969-423-8

--<germ-line cyst encapsulation ; GO:new extra parent: morphogenesis of follicular epithelium ; GO:0016333 def:Formation of a single follicular epithelium around the germ-line derived cells of a cyst. ref: PMID:11591336

----%female germ-line cyst encapsulation ; GO:new extra parent: morphogenesis of follicular epithelium ; GO:0016333 def:Formation of a single follicular epithelium around the germ-line derived cells of a cyst formed in the female gonad. ref: PMID:11591336

----%male germ-line cyst encapsulation ; GO:new extra parent: morphogenesis of follicular epithelium ; GO:0016333 def:Formation of a single follicular epithelium around the germ-line derived cells of a cyst formed in the male gonad. ref: PMID:11591336

----<male germ-line stem cell division ; GO:new def:Division of a germline stem cell in the male gonad, to produce a daughter stem cell and a daughter germ cell, which will divide to form the male gametes.

----<male germ-line cyst formation ; GO:new def:Formation, in the male gonad, of a cluster of germ-line cells derived from a single founder cell. A cyst of spermatocytes is produced by mitotic divisions of the founder cell. The spermatocytes then divide meiotically resulting in a cyst of spermatids.

----<female germ-line stem cell division ; GO:new def:Division of a germline stem cell in the female gonad, to produce a daughter stem cell and a daughter germ cell, which will divide to form the female gametes.

------<female germ-line cyst formation ; GO:new def:Formation of a cluster of germ-line cells, in the female gonad, derived from a single founder cell (cystoblast).

------<female cyst encapsulation ; GO:new def:Formation of a single follicular epithelium around the germ-line derived cells of a cyst formed in the female gonad.

------%female germ-line stem cell division (sensu Insecta) ; GO:new def:The asymmetric division, in the insect ovary, of a germline stem cell to produce a new stem cell and a cystoblast. additional parent: (isa) female germ-line stem cell division GO:new

--<germ-line stem cell division ; GO:new extra parent: asymmetric cytokinesis ; GO:0008356 Division of a germline stem cell to produce a daughter stem cell and a daughter germ cell, which will divide to form the gametes. ref: PMID:2279698

Add definition for currently undefined term: primary spermatocyte growth ; GO:0007285 The phase of growth and gene expression that male germ cells undergo as they enter the spermatocyte stage. The cells grow in volume and transcribe most of the gene products needed for the morphological events that follow meiosis. ref: ISBN:0-87969-423-8

Remove: cystoblast cell division ; GO:0007282 and spermatogonial cell division as children of germ-line stem cell renewal ; GO:0042078.

change defintion?

Currently: female germ-line cyst formation (sensu Insecta) ; GO:0030727 Formation of a cluster of germ-line cells, in the female gonad of an insect, derived from a single founder cell (cystoblast).

change to:

female germ-line cyst formation (sensu Insecta) ; GO:0030727 Formation of a cluster of germ-line cells, in the female gonad, derived from a single founder cell (cystoblast), as in Insecta.

I'll do this on the 18th July if no one objects.

Thanks, Jen

Original comment by: jenclark

gocentral commented 21 years ago

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No need to change the definition of 30727; if you want consistent wordings for the 'sensu Insecta' terms, you could plunk 'insect' into some of the others instead of tacking 'as seen in insects' on the end. There are other existing terms that already use the construction with 'insect' (or whatever) worked into the middle.

m

Original comment by: mah11

gocentral commented 21 years ago

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Did this:

Generic terms to be added:

gametogenesis ; GO:0007276 --<germ-cell development ; GO:0007281 ----<germ-line stem cell division ; GO:new GO:0048131 ------%female germ-line stem cell division ; GO:new GO:0048132 ------%male germ-line stem cell division ; GO:new GO:0048133 ----<germ-line cyst formation ; GO:new GO:0048134 ------%female germ-line cyst formation ; GO:new GO:0048135 --------%female germ-line cyst formation (sensu Insecta) ; GO:0030727 --------<cystoblast cell division (sensu Insecta) ; GO:0007282 ------%male germ-line cyst formation ; GO:new GO:0048136 --------<spermatogonial cell division ; GO:0007284 --------<primary spermatocyte growth ; GO:0007285 --------<spermatocyte cell division ; GO:new GO:0048137 --<germ-line cyst encapsulation ; GO:new GO:0048138 ----%female germ-line cyst encapsulation ; GO:new GO:0048139 ------%female germ-line cyst encapsulation (sensu Insecta) ; GO:0030708 ----%male germ-line cyst encapsulation ; GO:new GO:0048140

--%spermatogenesis ; GO:0007283 ----<male germ-line stem cell division ; GO:new ----<male germ-line cyst formation ; GO:new ----<male germ-line cyst encapsulation ; GO:new

--%oogenesis ; GO:0007292 ----<female germ-line stem cell division ; GO:new ----<female germ-line cyst formation ; GO:new ----<female germ-line cyst encapsulation ; GO:new ----%oogenesis (sensu Insecta) ; GO:0009993 ------%female germ-line stem cell division (sensu Insecta) ; GO:new GO:0048141 ------<female germ-line cyst formation (sensu Insecta) ; GO:0030727 --------<cystoblast cell division (sensu Insecta) ; GO:new GO:0048142 ------<female cyst encapsulation (sensu Insecta) ; GO:0030708

germ-line stem cell renewal ; GO:0042078 --<germ-line stem cell division ; GO:new

Additional parents:

----<female germ-line stem cell division ; GO:new ------%female germ-line stem cell division (sensu Insecta) ; GO:new

------<female germ-line cyst formation ; GO:new ---------%female germ-line cyst formation (sensu Insecta) ; GO:0030727

--------<cystoblast cell division ; GO:new -----------%cystoblast cell division (sensu Insecta) ; GO:0007282

------<female germ-line cyst encapsulation ; GO:new ---------%female germ-line cyst encapsulation (sensu Insecta) ; GO:0030708 (name changed from 'female cyst encapsulation (sensu Insecta) ; GO:0030708')

----<germ-line cyst formation ; GO:new ------%female germ-line cyst formation (sensu Insecta) ; GO:0030727

Remove: cystoblast cell division ; GO:0007282 and spermatogonial cell division as children of germ-line stem cell renewal ; GO:0042078.

new: cystoblast cell division (sensu Insecta) ; GO:0048142