Genome sequence of wild soybean (Glycine soja): Genome-wide analysis of crop domestication

Soybean (Glycine max), a commercially important crop, has recently been included among the completely sequenced genomes of four crop species1. Here we report the first full genome sequence of G. soja var. IT182932 which is the wild relative of G. max. G. soja is the first wild plant species2 that is fully sequenced to date. It is also the first genome that has been compared with a reference that is not from the same species. Two massively parallel sequencing (MPS) technologies were used. First, Illumina-GA sequencers produced 27.92 Gb short DNA reads. The reads were then aligned to the domesticated G. max reference genome (909.1 Mb, 96.97% coverage), achieving 26.13-fold average mapping depth. Secondly, a GS-FLX sequencer was used to generate longer DNA reads that confirmed 99.99 of SNPs, 95.07% of indel callings, and 35% of large deletion events. The G. soja genome showed a ~4% difference from the G. max genome represented by 2.1 million single nucleotide polymorphisms or variations (SNPs) and a significant amount of small insertions/deletions (indels), as well as 33 Mb large deletions and 6 Mb inversions. Considering the 33 Mb large deletions and Mb novel contigs assembled additionally to the mapped 909.1 Mb, the G. soja genome was nearly completely sequenced. This genome-wide comparison of the domesticated and wild species of a crop allowed us to systematically catalogue the whole repertoire of genetic variants. Therefore, our results can open a new chapter for understanding plant domestication processes and will eventually provide a framework toward crop-tailored improvement strategies.