新加坡国立大学Wing-Kin Sung研究小组通过优化单倍体纳米孔组装构建端粒到端粒的二倍体基因组。相关论文于2024年3月8日在线发表在《自然—方法学》杂志上。

研究人员表示，众所周知，由牛津纳米孔技术公司（ONT）长读数生成的基因组草图错误率较高。虽然现有的基因组优化器可以提高其质量，但错误率（包括错配、嵌合以及父系和母系单倍型之间的切换错误）可能很高。

为解决这一问题，研究人员开发了两种基因组优化器：hypo-short和hypo-hybrid。hypo-short利用Illumina短读数来打磨基于ONT的组装草案，从而得到低错误率和低切换错误的高质量组装。在此基础上，hypo-hybrid结合了ONT长读数，进一步完善了二倍体组装。在hypo-hybrid的基础上，研究人员创建了一个名为hypo-assembler的二倍体基因组组装管线。hypo-assembler利用ONT长读数、Illumina短读数和可选的Hi-C读数，自动生成高精度、连续和近乎完整的二倍体组装。

值得注意的是，这个解决方案甚至可以通过额外的人工步骤生成端粒到端粒的二倍体基因组。作为概念性验证，研究人员成功地组装了HG00733的全阶段端粒到端粒二倍体基因组，质量值超过了50。

附：英文原文

Title: Constructing telomere-to-telomere diploid genome by polishing haploid nanopore-based assembly

Author: Darian, Joshua Casey, Kundu, Ritu, Rajaby, Ramesh, Sung, Wing-Kin

Issue&Volume: 2024-03-08

Abstract: Draft genomes generated from Oxford Nanopore Technologies (ONT) long reads are known to have a higher error rate. Although existing genome polishers can enhance their quality, the error rate (including mismatches, indels and switching errors between paternal and maternal haplotypes) can be significant. Here, we develop two polishers, hypo-short and hypo-hybrid to address this issue. Hypo-short utilizes Illumina short reads to polish an ONT-based draft assembly, resulting in a high-quality assembly with low error rates and switching errors. Expanding on this, hypo-hybrid incorporates ONT long reads to further refine the assembly into a diploid representation. Leveraging on hypo-hybrid, we have created a diploid genome assembly pipeline called hypo-assembler. Hypo-assembler automates the generation of highly accurate, contiguous and nearly complete diploid assemblies using ONT long reads, Illumina short reads and optionally Hi-C reads. Notably, our solution even allows for the production of telomere-to-telomere diploid genomes with additional manual steps. As a proof of concept, we successfully assembled a fully phased telomere-to-telomere diploid genome of HG00733, achieving a quality value exceeding 50.

DOI: 10.1038/s41592-023-02141-1

Source: https://www.nature.com/articles/s41592-023-02141-1