Haplotype-resolved Chinese male genome assembly based on high-fidelity sequencing

Yang, Xiaofei; Zhao, Xixi; Qu, Su; Jia, Peng; Wang, Bo; Gao, Shenghan; Xu, Tun; Zhang, Wenxin; Huang, Jie; Ye, Kai

doi:10.1016/j.fmre.2022.02.005

Cited by 16 publications

(15 citation statements)

References 44 publications

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“…Research then shifted toward northern individuals: the first northern Han Chinese individual genome, NH1.0, appeared in 2019 (Du et al . 2019), and the most recent Han Chinese haplotype-resolved genome, HJ-H1 and HJ-H2, was released in early 2022 (Yang et al . 2022).…”

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

“…In addition to these four Han Chinese genomes, two other individual genomes, each representing an ethnic group closely related to Han, have been assembled: ZF1 (a Tibetan individual) (Yang et al 2022) and TJ1.p0/TJ1.p1 (a Tujia individual) (Lou et al 2022). However, all of these genomes still contain gaps and none were fully annotated.…”

Section: Introductionmentioning

confidence: 99%

“…Subsequently, another southern Han Chinese individual genome, HX1, was de novo assembled using single-molecule real-time (SMRT) long reads (Shi et al 2016). Research then shifted toward northern individuals: the first northern Han Chinese individual genome, NH1.0, appeared in 2019 (Du et al 2019), and the most recent Han Chinese haplotype-resolved genome, HJ-H1 and HJ-H2, was released in early 2022 (Yang et al 2022). In addition to these four Han Chinese genomes, two other individual genomes, each representing an ethnic group closely related to Han, have been assembled: ZF1 (a Tibetan individual) (Yang et al 2022) and TJ1.p0/TJ1.p1 (a Tujia individual) (Lou et al 2022).…”

Section: Introductionmentioning

confidence: 99%

“…2 Statistics calculated directly from the CHM13 assembly, v2.0. 3 Statistics taken from Table1and results of Yang et al(Yang et al 2022). 4 Statistics calculated directly from the YH2.0 assembly, downloaded from NCBI at https://www.ncbi.nlm.nih.gov/assembly/GCA_000004845.2/.…”

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confidence: 99%

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The first gapless, reference-quality, fully annotated genome from a Southern Han Chinese individual

Chao

Zimin

Pertea

et al. 2022

Preprint

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We used long-read DNA sequencing to assemble the genome of a Southern Han Chinese male. We organized the sequence into chromosomes and filled in gaps using the recently completed CHM13 genome as a guide, yielding a gap-free genome, Han1, containing 3,099,707,698 bases. Using the CHM13 annotation as a reference, we mapped all genes onto the Han1 genome and identified additional gene copies, generating a total of 60,708 genes, of which 20,003 are protein coding. A comprehensive comparison between the genes revealed that 235 protein-coding genes were substantially different between the individuals, with frameshifts or truncations affecting the protein-coding sequence. Most of these were heterozygous variants in which one gene copy was unaffected. This represents the first gene-level comparison between two finished, annotated individual human genomes.

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Section: Introductionmentioning

confidence: 99%