配子分箱以实现单倍型解析基因组组装。

Gamete Binning to Achieve Haplotype-Resolved Genome Assembly.

机构信息

Faculty of Biology, LMU Munich, Planegg-Martinsried, Germany.

Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany.

出版信息

Methods Mol Biol. 2023;2590:201-218. doi: 10.1007/978-1-0716-2819-5_13.

DOI:10.1007/978-1-0716-2819-5_13

PMID:36335501

Abstract

Haplotype-resolved genome assemblies remain a challenge in practice. Here, we provide a step-by-step guide on gamete binning, a method to generate haplotype-resolved genome assemblies for diploid species. The protocol starts by phasing heterozygous variants to individual haplotypes of specific chromosomes using the genome information of individual haploid gametes of the focal individual. Using phased variants, the whole-genome sequencing reads from the diploid genome can be genotyped and assigned into groups, which represent the individual haplotypes of each of the chromosomes. Finally, haplotype-specific chromosomes can be assembled independently using standard assembly tools. First applications of gamete binning revealed a haplotyping accuracy over 99%, which outperformed sequence-only or Hi-C-based haplotype-resolved genome assemblies.Availability: github.com/schneebergerlab/GameteBinning_prac .

摘要

单体型 resolved 基因组组装在实践中仍然是一个挑战。在这里，我们提供了一个关于配子 binning 的分步指南，这是一种用于产生二倍体物种单体型 resolved 基因组组装的方法。该方案首先使用焦点个体的单个单倍体配子的基因组信息，将杂合变体相位到特定染色体的个体单倍型上。使用相异变体，可以对来自二倍体基因组的全基因组测序读取进行基因分型并分配到代表每个染色体的个体单倍型的组中。最后，可以使用标准的组装工具独立地组装每个单体型的染色体。配子 binning 的首次应用显示出超过 99%的单体型准确性，优于仅基于序列或基于 Hi-C 的单体型 resolved 基因组组装。