The Phytozome Annotation Group has released an updated assembly for the Williams 82 Genomic Sequence.

The genome sequence and gene models have been substantially improved in the latest release, and are now the defaults used at SoyBase. However, one consequence of this is that the new gene models are sometimes substantially different from the cognates in previous annotations. To differentiate the various genome assemblies and annotations a new nomenclature has been adopted and the genes annotated to the new genome assembly have been named using this style.

In short, the new nomenclature makes these changes:

A dot (i.e. period character) now separates the GenusSpecies prefix from the rest of the name.
The number of digits after the 'g' is now 6 and steps between genes are now 100.
Assembly and annotation info are now included in ID names.

For example, for Williams 82 assembly version 2 annotation version 1
Locus:     Glyma.01g000100
Locus ID:     Glyma.01g000100.Wm82.a2.v1

Transcript:     Glyma.01g000100.1
Transcript ID:     Glyma.01g000100.1.Wm82.a2.v1

Although the names have changed to reflect the new nomenclature, 48606 of the 56044 Wm82.a2.v1 gene models can be unambiguously matched to those in the previous Glyma1.1 annotation. This page provides a tool that accepts a list of gene names and returns a table of correspondences as provided by JGI.

To use this tool, paste a list of gene model names into the text box or upload the list and click the Submit button. The gene model list can contain either names from Wm82.a1, Wm82.a2 or a mix of the two. A file will be prepared ready for download to your computer.

Alternately you may download the full correspondence files.

Download complete Glyma1.1<> Wm82.v2.a1 correspondence list

Download complete Wm82.a4.v1 correspondence list