김용민 (한국생명공학연구원) | 한빛사논문 > 한빛사

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조회639

김용민Yong-Min Kim

한국생명공학연구원

CV File 313 kb

Sci. Data, Oct 18 2023, 10 (1) | https://doi.org/10.1038/s41597-023-02631-z Two long read-based genome assembly and annotation of polyploidy woody plants, Hibiscus syriacus L. using PacBio and Nanopore platforms

Hyunjin Koo^1,6, Gir-Won Lee^2,6, Seo-Rin Ko^1,3, SangjinGo^1,3, Suk-Yoon Kwon^1,3, YongMin Kim^1,4,5 & Ah-Young Shin^1,4

¹Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea.

²SML Genetree Co. Ltd., Seoul, 05855, Republic of Korea.

³Biosystems and Bioengineering Program, University of Science and Technology, Daejeon, 34113, Korea.

⁴Department of Bioinformatics, KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon, 34141, Republic of Korea.

⁵Digital Biotech Innovation Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea.

⁶These authors contributed equally: Hyunjin Koo, Gir-Won Lee.

Corresponding authors : Correspondence to Yong-Min Kim or Ah-Young Shin.

Abstract

Improvements in long read DNA sequencing and related techniques facilitated the generation of complex eukaryotic genomes. Despite these advances, the quality of constructed plant reference genomes remains relatively poor due to the large size of genomes, high content of repetitive sequences, and wide variety of ploidy. Here, we developed the de novo sequencing and assembly of high polyploid plant genome, Hibiscus syriacus, a flowering plant species of the Malvaceae family, using the Oxford Nanopore Technologies and Pacific Biosciences Sequel sequencing platforms. We investigated an efficient combination of high-quality and high-molecular-weight DNA isolation procedure and suitable assembler to achieve optimal results using long read sequencing data. We found that abundant ultra-long reads allow for large and complex polyploid plant genome assemblies with great recovery of repetitive sequences and error correction even at relatively low depth Nanopore sequencing data and polishing compared to previous studies. Collectively, our combination provides cost effective methods to improve genome continuity and quality compared to the previously reported reference genome by accessing highly repetitive regions. The application of this combination may enable genetic research and breeding of polyploid crops, thus leading to improvements in crop production.

논문정보

형식Research article
게재일2023년 10월 (BRIC 등록일 2023-10-19)
연구진국내 연구진
분야 생명과학 > 유전학

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