Genome assembly of the popular Korean soybean cultivar Hwangkeum

Abstract

Massive resequencing efforts have been undertaken to catalog allelic variants in major crop species including soybean, but the scope of the information for genetic variation often depends on short sequence reads mapped to the extant reference genome. Additional de novo assembled genome sequences provide a unique opportunity to explore a dispensable genome fraction in the pan-genome of a species. Here, we report the 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 was then error-corrected using Illumina short-reads and PacBio SMRT reads. The 933.12 Mb assembly was annotated as containing 79,870 transcripts for 58,550 genes using RNA-Seq data and the public soybean annotation set. Comparison of the Hwangkeum assembly with the Williams 82 soybean reference genome sequence (Wm82.a2.v1) revealed 1.8 million single-nucleotide polymorphisms, 0.5 million indels, and 25 thousand putative structural variants. However, there was no natural megabase-scale chromosomal rearrangement. Incidentally, by adding two novel subfamilies, we found that soybean contains four clearly separated subfamilies of centromeric satellite repeats. Analyses of satellite repeats and gene content suggested that the Hwangkeum assembly is a high-quality assembly. This was further supported by comparison of the marker arrangement of anthocyanin biosynthesis genes and of gene arrangement at the Rsv3 locus. Therefore, the results indicate that the de novo assembly of Hwangkeum is a valuable additional reference genome resource for characterizing traits for the improvement of this important crop species.

SoybeanGDB: A comprehensive genomic and bioinformatic platform for soybean genetics and genomics

“…A comprehensive collection of 39 high-quality de novo genome assemblies of soybean, previously reported in various studies, has been integrated into SoybeanGDB ( Table S1 ) [4] , [11] , [17] , [18] , [19] , [20] , [21] , [22] . Out of these, the genomes of 28 soybean accessions consisting of three wild soybeans, nine landraces and 16 improved cultivars, were downloaded from the Genome Warehouse ( https://ngdc.cncb.ac.cn/gwh/ ) [23] .…”

“…Following this, a pan-genome analysis was conducted based on the genome sequence of Zhonghuang 13 and high-quality de novo assemblies of 26 other representative soybeans [4] . Furthermore, the high-quality genomes of Glycine max Lee, Glycine max Hwangkeum, Glycine soja PI483463, Glycine soja W05 and six perennial Glycine species have enriched the genomic resources available for soybean research [18] , [19] , [20] , [21] . Moreover, the re-sequencing data of diverse soybean accessions, which is another valuable resource for mining candidate variations or genes, is consistently increasing [4] , [7] .…”

“…Moreover, the re-sequencing data of diverse soybean accessions, which is another valuable resource for mining candidate variations or genes, is consistently increasing [4] , [7] . Despite the enormous amount of newly sequenced data reported in recent years, including high-quality genome assemblies of soybean and genomic variations among thousands of soybean accessions [4] , [7] , [18] , [19] , [20] , [21] , it has not been fully integrated into any database such as SoyBase, SoyKB or WildsoyDB [11] , [12] , [13] , [14] . To address this issue, we have developed an integrative genomic database, SoybeanGDB.…”

Genome assembly of the JD17 soybean provides a new reference genome for comparative genomics

“…The application of Iso-Seq protocol has enhanced genome annotation ( Jiang et al 2017 ; Jiao et al 2017 ; Li et al 2018 ; Magrini et al 2018 ). Benefiting from improved technologies, more and more reference genomes of various soybean materials have been sequenced and reported, including the Chinese cultivar ZH13 ( Shen et al 2019 ), 3 reference genomes ( G. max WM82v4, G. max Lee, and Glycine soja PI 483463) ( Valliyodan et al 2019 ), the wild strain W05 genome ( Xie et al 2019 ), the pan-genome constructed from 26 different soybean species ( Liu et al 2020 ), and the recently published Korean Hwangkeum genome ( Kim et al 2021 ) and 8 soybean genomes ( Chu et al 2021 ).…”

Applied genomics toward targeted improvement of soybean

“…The first assembly (Wm82.a1.v1) predicted ~46k gene models, described a genome rich in repetitive elements, and confirmed previous reports of multiple whole genome duplication events by illuminating regions of synteny between disparate chromosomes. More recently, several additional wild and cultivated soybean accessions have been sequenced and assembled de novo to develop a collection of reference genomes which, together, represent the broader genetic diversity of soybean (Lam et al, 2010, Li et al, 2014, Shen et al, 2018, Valliyodan et al, 2019, Kim et al, 2021. In 2020, Liu et al, published the first graph-based genome of soybean, composed of 26 de novo assembled wild and cultivated soybean accessions, as a means to capture a greater degree of genetic diversity in a single, mosaic-like reference genome, and to complement the existing cv 'Lee' and G. soja reference genomes (Liu et al, 2020b).…”