文献类型： 外文期刊

作者： Koren, Sergey ¹ ; Bao, Zhigui ² ; Guarracino, Andrea ⁴ ; Ou, Shujun ⁵ ; Goodwin, Sara ⁶ ; Jenike, Katharine M. ⁷ ; Lucas, Julian ⁸ ; Mcnulty, Brandy ⁸ ; Park, Jimin ⁸ ; Rautiainen, Mikko ¹ ; Rhie, Arang ¹ ; Roelofs, Dick ⁹ ; Schneiders, Harrie ⁹ ; Vrijenhoek, Ilse ⁹ ; Nijbroek, Koen ⁹ ; Nordesjo, Olle ¹⁰ ; Nurk, Sergey ¹⁰ ; Vella, Mike ¹⁰ ; Lawrence, Katherine R. ¹⁰ ; Ware, Doreen ⁶ ; Schatz, Michael C. ⁷ ; Garrison, Erik ⁴ ; Huang, Sanwen ³ ; Mccombie, William Richard ⁶ ; Miga, Karen H. ⁸ ; Wittenberg, Alexander H. J. ⁹ ; Phillippy, Adam M. ¹ ;

作者机构： 1.Natl Human Genome Res Inst, Genome Informat Sect, Ctr Genom & Data Sci Res, NIH, Bethesda, MD 20892 USA

2.Max Planck Inst Biol Tubingen, Dept Mol Biol, D-72076 Tubingen, Germany

3.Chinese Acad Agr Sci, Agr Genom Inst Shenzhen, Guangdong Lab Lingnan Modern Agr, Shenzhen Branch,Genome Anal Lab,Minist Agr & Rural, Shenzhen 518120, Peoples R China

4.Univ Tennessee, Hlth Sci Ctr, Dept Genet Genom & Informat, Memphis, TN 38163 USA

5.Ohio State Univ, Dept Mol Genet, Columbus, OH 43210 USA

6.Cold Spring Harbor Lab, Cold Spring Harbor, NY 11724 USA

7.Johns Hopkins Univ, Dept Comp Sci, Baltimore, MD 21218 USA

8.Univ Calif Santa Cruz, Santa Cruz, CA 95060 USA

9.KeyGene, NL-6708 PW Wageningen, Netherlands

10.Oxford Nanopore Technol, Oxford OX4 4DQ, England

11.USDA ARS, NEA Plant Soil & Nutr Lab, Res Unit, Ithaca, NY 14853 USA

12.Chinese Acad Trop Agr Sci, State Key Lab Trop Crop Breeding, Haikou 571101, Hainan, Peoples R China

期刊名称：GENOME RESEARCH （ 影响因子：5.5； 五年影响因子：7.3 ）

ISSN： 1088-9051

年卷期： 2024 年 34 卷 11 期

页码：

收录情况： SCI

摘要： 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.