A megabase-scale supergene in the wild progenitor of soybean

Glycine soja (Sieb. & Zucc.) is the wild progenitor of soybean (Glycine max [L.] Merr.) and is an important source of novel agronomic genes and alleles. Although hundreds of resequencing genomes of soybean accessions revealed higher genetic diversity in G. soja than in G. max under a species level, very little is known about the degree of genomic collinearity between G. soja and G. max. Here, we report de novo assembly and annotation of G. soja accession Yongin-0. The assembly was constructed using PromethION nanopore sequencing data and three genetic maps and then was error-corrected using Illumina short reads and PacBio Sequel sequencing data. Annotation was performed using RNA-Seq data and public soybean annotation set. The comparison of the Yongin-0 assembly with the soybean reference genome sequence revealed one natural megabase-scale inversion.