Abstract
After two decades of improvements, the current human reference genome (GRCh38) is the most accurate and complete vertebrate genome ever produced. However, no single chromosome has been finished end to end, and hundreds of unresolved gaps persist1,2. Here we present a human genome assembly that surpasses the continuity of GRCh382, along with a gapless, telomere-to-telomere assembly of a human chromosome. This was enabled by high-coverage, ultra-long-read nanopore sequencing of the complete hydatidiform mole CHM13 genome, combined with complementary technologies for quality improvement and validation. Focusing our efforts on the human X chromosome3, we reconstructed the centromeric satellite DNA array (approximately 3.1 Mb) and closed the 29 remaining gaps in the current reference, including new sequences from the human pseudoautosomal regions and from cancer-testis ampliconic gene families (CT-X and GAGE). These sequences will be integrated into future human reference genome releases. In addition, the complete chromosome X, combined with the ultra-long nanopore data, allowed us to map methylation patterns across complex tandem repeats and satellite arrays. Our results demonstrate that finishing the entire human genome is now within reach, and the data presented here will facilitate ongoing efforts to complete the other human chromosomes.
Highlights
The fundamental challenge of reconstructing a genome from many comparatively short sequencing reads—a process known as genome assembly—is distinguishing the repeated sequences from one another[13]
We present a human genome assembly that surpasses the continuity of GRCh382, along with a gapless, telomere-to-telomere assembly of a human chromosome. This was enabled by high-coverage, ultra-long-read nanopore sequencing of the complete hydatidiform mole CHM13 genome, combined with complementary technologies for quality improvement and validation
At present, unresolved areas of the human genome are defined by multi-megabase satellite arrays in the pericentromeric regions and the ribosomal DNA arrays on acrocentric short arms, as well as regions enriched in segmental duplications that are greater than hundreds of kilobases in length and that exhibit sequence identity of more than 98% between paralogues
Summary
We present a human genome assembly that surpasses the continuity of GRCh382, along with a gapless, telomere-to-telomere assembly of a human chromosome This was enabled by high-coverage, ultra-long-read nanopore sequencing of the complete hydatidiform mole CHM13 genome, combined with complementary technologies for quality improvement and validation. We hypothesized that high-coverage ultra-long-read nanopore sequencing would enable the first complete assembly of human chromosomes. Canu selected the longest 30×-coverage ultra-long and 7×-coverage PacBio reads for correction and assembly This initial assembly totalled 2.90 Gb, with half of the genome contained in continuous sequences (contigs) of length 75 Mb or greater (NG50), which exceeds the continuity of the GRCh38 reference genome (75 versus 56 Mb for NG50).
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