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

Kuan-Hao Chao; Aleksey V Zimin; Mihaela Pertea; Steven L Salzberg

doi:10.1093/g3journal/jkac321

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

G3 (Bethesda). 2023 Mar 9;13(3):jkac321. doi: 10.1093/g3journal/jkac321.

Authors

Kuan-Hao Chao^{1

2}, Aleksey V Zimin^{2

3}, Mihaela Pertea^{2

3}, Steven L Salzberg^{1

2

3

4}

Affiliations

¹ Department of Computer Science, Johns Hopkins University, Baltimore, MD 21218, USA.
² Center for Computational Biology, Johns Hopkins University, Baltimore, MD 21218, USA.
³ Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA.
⁴ Department of Biostatistics, Johns Hopkins University, Baltimore, MD 21211, USA.

Abstract

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 T2T-CHM13 genome as a guide, yielding a gap-free genome, Han1, containing 3,099,707,698 bases. Using the T2T-CHM13 annotation as a reference, we mapped all genes onto the Han1 genome and identified additional gene copies, generating a total of 60,708 putative 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.

Keywords: DNA sequencing; annotation; genome assembly; reference genome; variant calling.

Publication types

Research Support, U.S. Gov't, Non-P.H.S.
Research Support, N.I.H., Extramural

MeSH terms

East Asian People* / genetics
Genome, Human*
Humans
Male
Molecular Sequence Annotation
Sequence Analysis, DNA

Abstract

Publication types

MeSH terms

Grants and funding