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

Area of Science:

• Genomics
• Human Genetics
• Bioinformatics

Background:

• High-quality, gap-free human genome assemblies are crucial for understanding genetic variation.
• Previous genome assemblies have contained gaps and inaccuracies, limiting comprehensive gene-level analysis.

Purpose of the Study:

• To generate a complete, gap-free genome assembly for a Southern Han Chinese individual.
• To perform the first gene-level comparison between two finished, annotated human genomes.

Main Methods:

• Long-read DNA sequencing was employed to assemble the genome.
• The T2T-CHM13 genome was used as a reference to fill gaps and organize sequences into chromosomes.
• Gene annotation and comparison were performed using established bioinformatics pipelines.

Main Results:

• A gap-free genome, Han1, comprising 3,099,707,698 bases was successfully assembled.
• A total of 60,708 putative genes, including 20,003 protein-coding genes, were identified.
• A comprehensive gene comparison revealed 235 protein-coding genes with substantial differences, including frameshifts and truncations, mostly as heterozygous variants.

Conclusions:

• The study presents the first gene-level comparison between two finished, annotated individual human genomes.
• Significant protein-coding gene differences were identified, highlighting the importance of high-quality genome assemblies for genetic variation studies.
• This work provides a valuable resource for human population genetics and personalized medicine research.