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

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.

Nanopore Cas9‐targeted sequencing enables accurate and simultaneous identification of transgene integration sites, their structure and epigenetic status in recombinant Chinese hamster ovary cells

“…Here we present an alternative fast and accurate method to identify and characterize transgene ISs, the precise vector structure, and its integrity with simultaneous DNA methylation profiling in recombinant CHO cell lines by applying nanopore Cas9-targeted sequencing (nCats). Nanopore sequencing is a long-read sequencing technology that offers the possibility to sequence long, continuous, and native DNA molecules achieving read lengths above 2 Mb (Payne et al, 2019), which allows to span repetitive regions and structural variants facilitating a comprehensive assembly of genomic regions (Chao et al, 2023;Nurk et al, 2022;Zimin et al, 2022). Additionally, native DNA sequencing by nanopore allows the identification of DNA modifications (e.g., CpG methylation), which overcomes existing issues of bisulfite sequencing (BS-seq) (Figure 1a).…”

The complete diploid reference genome of RPE-1 identifies human phased epigenetic landscapes

“…These, and others that have since been added [4][5][6] , represent an important step toward a more equitable and fair representation of human genomic diversity 3,7 . Comparative analyses of the currently available complete assemblies have revealed an unexpected level of sequence variation 3,8 . Complete understanding of the divergence between individuals 3 and population-level variants [9][10][11] , including their functional significance, is ongoing.…”

“…Comparative analyses of the currently available complete assemblies have revealed an unexpected level of sequence variation 3,8 . Complete understanding of the divergence between individuals 3 and population-level variants [9][10][11] , including their functional significance, is ongoing. In addition to allelic variation within the population, differences within an individual genome pertaining to the parental alleles can be reliably explored and characterized as more completely phased diploid genomes become available 2,12 .…”

“…In spite of these significant steps 1,22,[36][37][38][39] , reliable assembly of complete centromeres for all chromosomes remains a challenge 40 . Centromeres were in fact omitted from comparative analyses in the recent human Pangenome draft 3 . Recent genetic and epigenetic characterization of complete centromeres leveraged near-homozygous ad hoc cell lines 1,22,27 , that do not allow for the assessment of inter-haplotype polymorphism within the same diploid individual.…”

“…These include the near-homozygous CHM13 1 and genomes from individuals of diverse ancestry 2,3 . These and others that have since been added 4–6 represent an important step toward a more equitable representation of human genomic diversity 3,7 . Comparative analyses of the currently available assemblies have revealed an unexpected level of sequence variation 3,8 , including inter-individuals divergence 3 and population-level variants 9–11 .…”