Kuderna Lukas F K, Solís-Moruno Manuel, Batlle-Masó Laura, Julià Eva, Lizano Esther, Anglada Roger, Ramírez Erika, Bote Alex, Tormo Marc, Marquès-Bonet Tomàs, Fornas Òscar, Casals Ferran
Institut de Biologia Evolutiva, CSIC-Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona (PRBB)", Barcelona, Spain.
Genomics Core Facility, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona (PRBB), Barcelona, Spain.
Front Genet. 2020 Jan 9;10:1315. doi: 10.3389/fgene.2019.01315. eCollection 2019.
Sorting of individual chromosomes by Flow Cytometry (flow-sorting) is an enrichment method to potentially simplify genome assembly by isolating chromosomes from the context of the genome. We have recently developed a workflow to sequence native, unamplified DNA and applied it to the smallest human chromosome, the Y chromosome. Here, we modify improve upon that workflow to increase DNA recovery from chromosome sorting as well as sequencing yield. We apply it to sequence and assemble the largest human chromosome - chromosome 1 - of a Chinese individual using a single Oxford Nanopore MinION flow cell. We generate a selective and highly continuous assembly whose continuity reaches into the order of magnitude of the human reference GRCh38. We then use this assembly to call candidate structural variants against the reference and find 685 putative novel SV candidates. We propose this workflow as a potential solution to assemble structurally complex chromosomes, or the study of very large plant or animal genomes that might challenge traditional assembly strategies.
通过流式细胞术对单个染色体进行分选（流式分选）是一种富集方法，可通过从基因组背景中分离染色体来潜在地简化基因组组装。我们最近开发了一种对天然未扩增DNA进行测序的工作流程，并将其应用于最小的人类染色体——Y染色体。在此，我们改进了该工作流程，以提高染色体分选的DNA回收率以及测序产量。我们应用它对一名中国个体的最大人类染色体——1号染色体进行测序和组装，使用单个牛津纳米孔MinION流动槽。我们生成了一个选择性且高度连续的组装体，其连续性达到了人类参考基因组GRCh38的数量级。然后，我们使用这个组装体与参考基因组比对来调用候选结构变异，发现了685个推定的新型SV候选物。我们提出这个工作流程作为组装结构复杂染色体或研究可能挑战传统组装策略的非常大的植物或动物基因组的潜在解决方案。
