김준 (한국생명공학연구원, 현 충남대학교) | 한빛사논문 > 한빛사

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김준Jun Kim

한국생명공학연구원, 현 충남대학교

Nucleic Acids Res., Jan 07 2025, 53 (1) gkae1294 | https://doi.org/10.1093/nar/gkae1294 Highly accurate Korean draft genomes reveal structural variation highlighting human telomere evolution

Jun Kim ^1,2,†, Jong Lyul Park^2,5,†, Jin Ok Yang ^3,4,†, Sangok Kim^3,5,†, Soobok Joe^3,†, Gunwoo Park³, Taeyeon Hwang³, Mun-Jeong Cho⁵, Seungjae Lee⁶, Jong-Eun Lee⁶, Ji-Hwan Park^3,7,*, Min-Kyung Yeo^8,* and Seon-Young Kim^3,5,*

¹Department of Convergent Bioscience and Informatics, College of Bioscience and Biotechnology, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, Republic of Korea
²Personalized Genomic Medicine Research Center, Korea Research Institute of Bioscience & Biotechnology, 125, Gwahak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
³Korea Bioinformation Center, Korea Research Institute of Bioscience & Biotechnology, 125, Gwahak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
⁴Department of Bio and Brain Engineering, Korea Advanced Institute of Science & Technology (KAIST), 291, Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
⁵Department of Bioscience, University of Science and Technology (UST), 217, Gajeong-ro, Yuseong-gu, Daejeon 34113, Republic of Korea
⁶DNALink, Inc, 31, Magokjungang 8-ro 3-gil, Gangseo-gu, Seoul 07793, Republic of Korea
⁷Department of Biological Science, Ajou University, 206, World cup-ro, Yeongtong-gu, Suwon 16499, Republic of Korea
⁸Department of Pathology, Chungnam National University School of Medicine, 282, Munhwa-ro, Jung-gu, Daejeon 35015, Republic of Korea

^*To whom correspondence should be addressed. : Ji-Hwan Park
Correspondence may also be addressed to Min-Kyung Yeo.
Correspondence may also be addressed to Seon-Young Kim.
^†The first five authors should be regarded as Joint First Authors.

Abstract

Given the presence of highly repetitive genomic regions such as subtelomeric regions, understanding human genomic evolution remains challenging. Recently, long-read sequencing technology has facilitated the identification of complex genetic variants, including structural variants (SVs), at the single-nucleotide level. Here, we resolved SVs and their underlying DNA damage-repair mechanisms in subtelomeric regions, which are among the most uncharted genomic regions. We generated ∼20 × high-fidelity long-read sequencing data from three Korean individuals and their partially phased high-quality de novo genome assemblies (contig N50: 6.3-58.2 Mb). We identified 131 138 deletion and 121 461 insertion SVs, 41.6% of which were prevalent in the East Asian population. The commonality of the SVs identified among the Korean population was examined by short-read sequencing data from 103 Korean individuals, providing the first comprehensive SV set representing the population based on the long-read assemblies. Manual investigation of 19 large subtelomeric SVs (≥5 kb) and their associated repair signatures revealed the potential repair mechanisms leading to the formation of these SVs. Our study provides mechanistic insight into human telomere evolution and can facilitate our understanding of human SV formation.

논문정보

형식Research article
게재일2025년 01월 (BRIC 등록일 2025-01-09)
연구진국내 연구진
분야 생명과학 > 유전학

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