This page describes new (early 2018) high-quality genome assemblies for soybean (Glycine max) and wild soybean (Glycine soja). These should provide useful complements to the primary reference assembly for Glycine max cv. Williams 82 (Wm82.a2).

The new G. max assembly is for cultivar "Lee," which has been used a parent in many southern U.S. breeding projects.

The G. soja assembly is for accession PI 483463. This line was chosen for its high genotypic dissimilarity with respect to cultivated soybean. It originates from Shanxi Province, in north-central China.

This sequencing project was supported by the United Soybean Board. Project members are Henry Nguyen (project PI), Babu Valliyodan, Gunvant Patil, Steven Cannon, Hon Ming Lam, Dave Edwards, Philipp Bayer, Jacqueline Campbell, Ting-Fung Chan, Qijian Song.

Please note that for both assemblies usage restrictions apply until the first formal description is published by the PI group. The Usage Policy can be viewed directly or in the repositories described below.

Glycine max cv. Lee:

  Genome assembly: https://data.soybase.org/Glycine/max/genomes/Lee.gnm1.BXNC

  Genome browser: https://legacy.soybase.org/gb2/gbrowse/glyma.Lee.gnm1/

Glycine soja PI 483463:

  Genome assembly: https://data.soybase.org/Glycine/soja/genomes/PI483463.gnm1.YJWS

  Genome browser: https://legacy.soybase.org/gb2/gbrowse/glyso.PI483463.gnm1/

Additional details about the assemblies (and for comparison the Wm82.a2 reference genome assembly):
• G. max cv. Williams 82 assembly 2 (Wm82.a2) genome stats:
  •   Assembly size: 949,183,385
  •   Sequence anchored in pseudomolecules: 978,495,272
  •   Proportion of assembly as Ns: 2.36%
• G. soja PI 483463 (PI483463.a1) genome stats:
  •   Assembly size: 962,330,378
  •   Sequence anchored in pseudomolecules: 985,259,765
  •   Proportion of assembly as Ns: 3.44% Ns
• G. max cv. Lee (Lee.a1) genome stats:
  •   Assembly size: 1,015,016,903
  •   Sequence anchored in pseudomolecules: 990,714,026
  •   Proportion of assembly as Ns: 4.24%

The G. soja accession PI 483463 assembly incorporates Illumina sequence from NRGene. Pseudomolecule anchoring of scaffolds was accomplished using two dense genetic maps as well as synteny comparisons with the Glycine max reference assembly for cultivar Williams 82 (JGI Glyma.Wm82.a2) and Glycine max cultivar Lee.

The G. max cv. Lee assembly incorporates PacBio long reads, optical mapping from BioNano, and Illumina sequences from NRGene. Pseudomolecule anchoring of scaffolds was accomplished using two dense genetic maps as well as synteny comparisons with the Glycine max reference assembly for cultivar Williams 82 (JGI Glyma.Wm82.a2) and Glycine soja PI PI483463.