Gapless assembly of complete human and plant chromosomes using only nanopore sequencing.

Autor:	Koren S; Genome Informatics Section, Center for Genomics and Data Science Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA; sergey.koren@nih.gov adam.phillippy@nih.gov., Bao Z; Department of Molecular Biology, Max Planck Institute for Biology Tübingen, 72076 Tübingen, Baden-Württemberg, Germany.; Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China., Guarracino A; Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, Tennessee 38163, USA., Ou S; Department of Molecular Genetics, Ohio State University, Columbus, Ohio 43210, USA., Goodwin S; Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA., Jenike KM; Department of Computer Science, Johns Hopkins University, Baltimore, Maryland 21218, USA., Lucas J; Genomics Institute, University of California Santa Cruz, Santa Cruz, California 95060, USA., McNulty B; Genomics Institute, University of California Santa Cruz, Santa Cruz, California 95060, USA., Park J; Genomics Institute, University of California Santa Cruz, Santa Cruz, California 95060, USA., Rautiainen M; Genome Informatics Section, Center for Genomics and Data Science Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA., Rhie A; Genome Informatics Section, Center for Genomics and Data Science Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA., Roelofs D; KeyGene, 6708 PW Wageningen, Netherlands., Schneiders H; KeyGene, 6708 PW Wageningen, Netherlands., Vrijenhoek I; KeyGene, 6708 PW Wageningen, Netherlands., Nijbroek K; KeyGene, 6708 PW Wageningen, Netherlands., Nordesjo O; Oxford Nanopore Technologies, Oxford OX4 4DQ, United Kingdom., Nurk S; Oxford Nanopore Technologies, Oxford OX4 4DQ, United Kingdom., Vella M; Oxford Nanopore Technologies, Oxford OX4 4DQ, United Kingdom., Lawrence KR; Oxford Nanopore Technologies, Oxford OX4 4DQ, United Kingdom., Ware D; Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA.; USDA ARS NEA Plant, Soil and Nutrition Laboratory Research Unit, Ithaca, New York 14853, USA., Schatz MC; Department of Computer Science, Johns Hopkins University, Baltimore, Maryland 21218, USA., Garrison E; Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, Tennessee 38163, USA., Huang S; Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China.; State Key Laboratory of Tropical Crop Breeding, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan 571101, China., McCombie WR; Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA., Miga KH; Genomics Institute, University of California Santa Cruz, Santa Cruz, California 95060, USA., Wittenberg AHJ; KeyGene, 6708 PW Wageningen, Netherlands., Phillippy AM; Genome Informatics Section, Center for Genomics and Data Science Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA; sergey.koren@nih.gov adam.phillippy@nih.gov.
Jazyk:	angličtina
Zdroj:	Genome research [Genome Res] 2024 Nov 06. Date of Electronic Publication: 2024 Nov 06.
DOI:	10.1101/gr.279334.124
Abstrakt:	The combination of ultra-long (UL) Oxford Nanopore Technologies (ONT) sequencing reads with long, accurate Pacific Bioscience (PacBio) High Fidelity (HiFi) reads has enabled the completion of a human genome and spurred similar efforts to complete the genomes of many other species. However, this approach for complete, "telomere-to-telomere" genome assembly relies on multiple sequencing platforms, limiting its accessibility. ONT "Duplex" sequencing reads, where both strands of the DNA are read to improve quality, promise high per-base accuracy. To evaluate this new data type, we generated ONT Duplex data for three widely studied genomes: human HG002, Solanum lycopersicum Heinz 1706 (tomato), and Zea mays B73 (maize). For the diploid, heterozygous HG002 genome, we also used "Pore-C" chromatin contact mapping to completely phase the haplotypes. We found the accuracy of Duplex data to be similar to HiFi sequencing, but with read lengths tens of kilobases longer, and the Pore-C data to be compatible with existing diploid assembly algorithms. This combination of read length and accuracy enables the construction of a high-quality initial assembly, which can then be further resolved using the UL reads, and finally phased into chromosome-scale haplotypes with Pore-C. The resulting assemblies have a base accuracy exceeding 99.999% (Q50) and near-perfect continuity, with most chromosomes assembled as single contigs. We conclude that ONT sequencing is a viable alternative to HiFi sequencing for de novo genome assembly, and provides a multirun single-instrument solution for the reconstruction of complete genomes. (© 2024 Koren et al.; Published by Cold Spring Harbor Laboratory Press.)
Databáze:	MEDLINE
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