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Genome Assembly of the Popular Korean Soybean Cultivar Hwangkeum

View ORCID ProfileMyung-Shin Kim, Taeyoung Lee, Jeonghun Baek, Ji Hong Kim, Changhoon Kim, View ORCID ProfileSoon-Chun Jeong
doi: https://doi.org/10.1101/2021.04.19.440529
Myung-Shin Kim
*Bio-Evaluation Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju, Chungbuk 28116, Republic of Korea
†Plant Immunity Research Center, Interdisciplinary Program in Agricultural Genomics, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea
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Taeyoung Lee
‡Bioinformatics Institute, Macrogen Inc., Seoul 08511, Republic of Korea
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Jeonghun Baek
‡Bioinformatics Institute, Macrogen Inc., Seoul 08511, Republic of Korea
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Ji Hong Kim
*Bio-Evaluation Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju, Chungbuk 28116, Republic of Korea
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Changhoon Kim
‡Bioinformatics Institute, Macrogen Inc., Seoul 08511, Republic of Korea
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  • For correspondence: scjeong@kribb.re.kr kimchan@macrogen.com
Soon-Chun Jeong
*Bio-Evaluation Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju, Chungbuk 28116, Republic of Korea
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  • ORCID record for Soon-Chun Jeong
  • For correspondence: scjeong@kribb.re.kr kimchan@macrogen.com
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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 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 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 groups, we found that soybean contains four clearly separated groups 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.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted April 20, 2021.
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Genome Assembly of the Popular Korean Soybean Cultivar Hwangkeum
Myung-Shin Kim, Taeyoung Lee, Jeonghun Baek, Ji Hong Kim, Changhoon Kim, Soon-Chun Jeong
bioRxiv 2021.04.19.440529; doi: https://doi.org/10.1101/2021.04.19.440529
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Genome Assembly of the Popular Korean Soybean Cultivar Hwangkeum
Myung-Shin Kim, Taeyoung Lee, Jeonghun Baek, Ji Hong Kim, Changhoon Kim, Soon-Chun Jeong
bioRxiv 2021.04.19.440529; doi: https://doi.org/10.1101/2021.04.19.440529

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