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warelab / gramene-ensembl

Gramene's Ensembl plugins, extensions, configuration.
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Research on Soybean assemblies #3

Open weix-cshl opened 5 years ago

weix-cshl commented 5 years ago

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 commented 5 years ago

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.
    1. Assembly for the southern U.S. accession Lee (PI 548656), assembly accession ‘GCA_002905335.1'
    2. 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.