Genome assembly of the popular Korean soybean cultivar Hwangkeum

Massive resequencing efforts has been undertaken to catalogue allelic variants in major crop species including soybean, but scope of the information for genetic variation often depends on short sequence reads mapped to the extant reference genome. An additional de novo assembled genome sequence provides a unique opportunity for exploring of a dispensable genome fraction in the pangenome of a species. Here, we report de novo assembly and annotation of Hwangkeum, a popular soybean cultivar in Korea. The assembly was constructed using PromethION nanopore sequencing data and two 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. Although the comparison of the Hwangkeum assembly with the soybean reference genome sequence revealed hundreds of large natural structural variants, there was no natural megabase-scale chromosomal rearrangement.