Genome assembly of the popular Korean soybean cultivar Hwangkeum

Cited 2 time in scopus
Metadata Downloads
Title
Genome assembly of the popular Korean soybean cultivar Hwangkeum
Author(s)
Myung-Shin Kim; T Lee; J Baek; Ji Hong Kim; C Kim; Soon-Chun Jeong
Bibliographic Citation
G3-Genes Genomes Genetics, vol. 11, no. 10, pp. jkab272-jkab272
Publication Year
2021
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.
Keyword
Glycine maxGenetic mapGenome assemblySoybeanStructural variation
ISSN
2160-1836
Publisher
Genetics Society America
DOI
http://dx.doi.org/10.1093/g3journal/jkab272
Type
Article
Appears in Collections:
Division of Bio Technology Innovation > Bio-Evaluation Center > 1. Journal Articles
Ochang Branch Institute > 1. Journal Articles
Files in This Item:
  • There are no files associated with this item.


Items in OpenAccess@KRIBB are protected by copyright, with all rights reserved, unless otherwise indicated.