Create glyma.Sugawara_Umehara_2019

[ellatownsend90]

first attempt on this article

[ScottKalberer]

A few quick comments before we get too far here. When you have a citation with three or more authors [such as Sugawara, Umehara et al, 2019] the format would be "LastName, LastName et al., YEAR". So there is a period at the end of "al", as in "et al.", because "et al." - which just means "and others" in Latin - is a shortened form of "et alii" for a group of men or a mixed group of men and women, or "et aliae" if the non-named authors all were women. So shortening the phrase to "et al." saves space and the need to figure out Latin grammatical gender rules. Some style manuals have you drop all the periods and italics on these sorts of latin abbreviations, which would recognize that we use them as English words and in fact do not understand Latin, but as far as I know that isn't as common in plant sciences.

[ScottKalberer]

Also, when we list the gene symbols there isn't a name directly after the "gene_symbols:" top-level key like you have in this file as "gene_symbols: RJ2". Each gene_symbol would be listed after a dash and space in an array of key-value pairs like in the example below, even if there is in fact only one gene_symbol. Furthermore, normally the gene symbol gets a genus-species prefix in front even if the paper didn't use such a format, in this case "Gm" for Glycine max. Let me know if this formatting isn't clear yet.

gene_symbols:
  - GmRJ2

[StevenCannon-USDA]

I agree with Scott's comments.

For the gene_model_full_id: the assembly 1 gene ID is acceptable, but I'd like to standardize on assembly 4 when such a gene is available. That gene here is glyma.Wm82.gnm4.ann1.Glyma.16G212300
See the gene tree (new first, then old/current):
http://dev.lis.ncgr.org:50082/?family=Legume.fam3.21630
https://funnotate.legumeinfo.org/?family=L_01CW53&gene_name=glyma.Wm82.gnm4.ann1.Glyma.16G212300

For confidence: let's use 5. They tested using a complementation test and by examining responses in 79 soybean accessions. They established that a single base change is responsible for the observed compatibility/incompatibility phenotype.

Comments: the convention is that a upper-cased gene symbol refers to the dominant allele and lower-cased symbol refers to the recessive allele, so the comment about the dominant/recessive symbols doesn't add information. Instead, let's use:

  - Cultivated soybean carrying the Rj2 allele restricts nodulation with specific Bradyrhizobium strains via host immunity, mediated by rhizobial type III secretory protein NopP and the host resistance protein Rj2. 
  - The Rj2 gene appears to have been maintained during the process of soybean domestication to adapt to high rhizobial diversity.

The synopsis needs to be more accurate, precise, and informative. How about:

  - The Rj2 protein mediates compatibility with rhizobial strains.