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March 28, 2007 - female gametophyte development and related terms

Tanya Berardini, Donghui Li, Jennifer Clark

Done

We have done a great deal on 'female gametophyte development' and its child terms in today's meeting. Specifically:

female gametophyte development

Replaced the term name 'female gametophyte development' with 'embryo sac development'. Included 'female gametophyte development' as a synonym of 'embryo sac development'.

Created a separate term 'megagametogenesis' (GO:0009561).
Regrouped the child terms of 'embryo sac development' into 'megagametogeneis' and 'megasporogenesis'.

'megagametogenesis' was previously used as a synonym to 'female gametophyte development' (or embryo sac development). We have adopted the definitions by Howell (1998, Molecular Genetics of Plant Development, Cambridge University Press, ISBN 0-521-58784-0) and divided 'embryo sac development' into 'megasporogenesis' (refering to the formation of megaspores from megasporocyte) and 'megagametogenesis' (from megaspores to embryo sac).

antipodal cell differentiation (GO:0009557)

Unchanged. Now a child of 'megagametogenesis'.

cellularization of megagametophyte (GO:0009558)

Definition revised. Now a child of 'megagametogenesis'.

female gametophyte central cell differentiation (GO:0009559)

Renamed: embryo sac central cell differentiation to be consistent with 'embryo sac development' and other related terms. New definition. Now a child of 'megagametogenesis'.

female gametophyte egg cell differentiation (GO:0009560)

Renamed to 'embryo sac egg cell differentiation'. New definition. Now a child of 'megagametogenesis'.

female gametophyte morphogenesis (GO:0048314)

Renamed to 'embryo sac morphogenesis'. Defintion revised. Now a child of 'megagametogenesis'.

megagametophyte nuclear division (GO:0009561)

Now becomes a synonym of 'megagametogensis' (GO:0009561).

megagametophyte nuclear migration (GO:0009562)

Renamed to 'embryo sac nuclear migration'. Defition revised. Now a child of 'megagametogenesis'. Created two new child terms:

nuclear migration to embryo sac poles (GO:0023002) 
nuclear migration to the embryo sac center (GO:0023003)
polar nucleus fusion

See Action Item 1.

synergid differentiation (GO:0009563)

Now a child of 'megagametogenesis'; otherwise untouched.

egg apparatus differentiation, ovule primordium differentiation, ovule primordium dvelopment

In the original SourceForge item, Jen has requested the above and other related regulation terms. We have decided not to create these terms.

megasporocyte differentiation

This term was requested in the SF item. We did not create this term because the formation of megaspores from megasporocyte ('megasporocyte differentiation') is a meiosis, not a differentiation process.

Action Items

Action Item 1: Tanya Term 'polar nucleus fusion' (GO:0010197). Need to examine the nature of the 'nucleus fusion' prior to the endosperm fertilization. Also need to look at existing annotations associated with this term. Need to figure out the relationship between this term and 'embryo sac central cell differentiation'?

Consulted PMID:9758709. Quoting directly from the paper:

"Megagametogenesis in wild-type Arabidopsis has been described (Misra, 1962; Poliakova, 1964; Webb and Gunning, 1990; Mansfield et al., 1991; Murgia et al., 1993; Webb and Gunning, 1994; Schneitz et al., 1995; Christensen et al., 1997) and has been divided into seven morphologically distinct stages that are depicted in Fig. 2A (Christensen et al., 1997). First, the surviving megaspore (stage FG1) undergoes mitosis to produce a two-nucleate cell (stage FG2). Shortly thereafter, the two nuclei separate to the chalazal and micropylar poles and a vacuole forms in the center (stage FG3). The developing female gametophyte then undergoes second (stage FG4) and third rounds of mitosis. This results in an eightnucleate cell with four nuclei at each of two poles separated by a large central vacuole (beginning of stage FG5). Next, one nucleus from each pole (the polar nuclei) migrates toward the female gametophyte’s center and the embryo sac becomes cellularized. The polar nuclei eventually fuse and the female gametophyte consists of seven cells and seven nuclei (stage FG6; Figs. 1A and 1B). As a final developmental step, the three antipodal cells undergo cell death. Thus, the mature Arabidopsis female gametophyte (stage FG7) consists of one haploid egg cell, two haploid synergid cells, and one diploid central cell (Figs. 1C and 2B)."

Donghui: I have come across a paper which describes the female gametophyte development in Arabidopsis. Information from this 2007 PLoS paper is consitent with that in the above paper. Prior to fertilization, the two polar neuclei fuse to form one large central cell nucleus (hence 7-nucleate) and the antipodal cells degenerate.


TO DO:

1. I think we should extend the definition of 'embryo sac development' to include polar nucleus fusion and antipodal cell degeneration.

2. I think that 'polar nucleus fusion' should be a part of 'embryo sac central cell differentiation.'

3. I think that we should extend the definition of 'embryo sac central cell differentiation' to include the fusion of the polar nuclei and end with the mononucleate diploid central cell.

4. Need to create a term: antipodal cell degeneration. In lis-1 mutant described in this paper, the two polar nuclei are un-fused and the antipodal cells do not degenerate. Thus lis-1 will be annotated to these two terms: polar nucleus fusion and antipodal cell degeneration.

The suggested parent terms for 'antipodal cell degeneration' are part_of embryo sac development; is_a programmed cell death (compare: GO:0010198 synergid death).

http://biology.plosjournals.org/perlserv/?request=get-document&doi=10.1371%2Fjournal.pbio.0050047

Action Item 2: Donghui

Term 'megasporogenesis' currently is a child of 'anatomical structure development'. However, the outcome of this process is the formation of an multicellular organism 'embryo sac'. Note that 'megasporogenesis' is a child of 'embryo sac development' which in turn is a child of 'multicellular organism development'. We could leave the parentage of this term as it is. (Donghui)

Checked with David about parentage of 'megagametogenesis'. Right now, it's is_a 'anatomical structure development'. After discussion, we decided it should just be is_a 'developmental process'. It doesn't fit the def of either 'anatomical structure development' or 'multicellular organismal development' so it needs to go up one level. (Tanya - DONE, Rev. 5.256).

April 4, 2007 - male gametophyte development and related terms

Tanya Berardini, Donghui Li, Jennifer Clark

Action Items

Action Item 1: Donghui

We have updated the defintion of 'pollen development'. Microgametogenesis, which was previously an exact synonym of 'pollen development' is now a new term. The current version of 'pollen development' includes 'microsporogenesis' and 'microgametogenesis'. Need to re-visit annotations associated with 'pollen development' [this term used to be 'male gametophyte development'; there are 21 annotations associated with this term at TAIR database] and re-assign these annotations to 'pollen development' or 'microgametogenesis' accordingly (pollen development is a broader term than microgametogenesis).

Action Item 2

Figure out the parentage of male gametophyte development terms. Next meeting.