Research on Soybean assemblies

[weix-cshl]

Bruno found a recent paper (Aug 2019) reporting the release of three soybean genomes, and we want to explore the opportunity to bring them in

https://onlinelibrary.wiley.com/doi/abs/10.1111/tpj.14500

[weix-cshl]

I skim through the paper, the three assemblies are

1. An improved assembly of the northern U.S. accession Williams 82; this is the same species as the soybean in Ensembl plant. However they didn’t provide assembly accession, only a study number 'PRJNA48389’, which I failed to locate in ENA.
2. Assembly for the southern U.S. accession Lee (PI 548656), assembly accession ‘GCA_002905335.1'
3. Assembly for G. soja accession PI 483463. wild relative of the other two domesticated soybeans. assembly accession ‘GCA_002907465.1’

None of them have gene annotations in ENA.

Ensembl plants and Gramene already host one soybean genome accession ‘GCA_000004515.4’, which is the northern U.S. accession Williams 82. Unless there is strong call from the community, I do not see the reason to host additional soybean lines. It falls into the scope of a panGenome site. As for the improved assembly of Williams 82, it seems the improved assembly is not in ENA yet. We could potentially update the Epl/Gramene soybean assembly to this version once it becomes available in ENA.