Genome phasing is a recently developed assembly method that separates heterozygous eukaryotic genomic regions and builds haplotype-resolved assemblies. Because differences between haplotypes are ignored in most published de novo genomes, assemblies are available as consensus genomes consisting of haplotype mixtures, thus increasing the need for genome phasing. Here, we review the operating principles and characteristics of several freely available and widely used phasing tools (TrioCanu, FALCON-Phase, and ALLHiC). An examination of downstream analyses using haplotype-resolved genome assemblies in plants indicated significant differences among haplotypes regarding chromosomal rearrangements, sequence insertions, and expression of specific alleles that contribute to the acquisition of the biological characteristics of plant species. Finally, we suggest directions to solve addressing limitations of current genome-phasing methods. This review provides insights into the current progress, limitations, and future directions of de novo genome phasing, which will enable researchers to easily access and utilize genome-phasing in studies involving highly heterozygous complex plant genomes.

中文翻译：

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从头定相解析复杂植物基因组中的单倍型序列

基因组定相是最近开发的一种组装方法，可分离杂合真核基因组区域并构建单倍型解析的组装。因为在大多数从头发表的文章中忽略了单倍型之间的差异在基因组中，组装可作为由单倍型混合物组成的共有基因组获得，因此增加了对基因组定相的需求。在这里，我们回顾了几种免费提供且广泛使用的定相工具（TrioCanu、FALCON-Phase 和 ALLHiC）的工作原理和特点。使用植物中单倍型解析的基因组组装对下游分析的检查表明，单倍型之间在染色体重排、序列插入和有助于获得植物物种生物学特征的特定等位基因的表达方面存在显着差异。最后，我们提出了解决当前基因组定相方法局限性的方向。本综述提供了对de novo的当前进展、局限性和未来方向的见解基因组定相，这将使研究人员能够在涉及高度杂合的复杂植物基因组的研究中轻松访问和利用基因组定相。