Chromosome-level scaffolding of haplotype-resolved assemblies using Hi-C data without reference genomes

文献类型： 外文期刊

第一作者： Zeng, Xiaofei

作者： Zeng, Xiaofei;Du, Yuhui;Li, Yu;Zhou, Zhiqing;Chen, Sijie;Zhao, Huijie;Chen, Guoan;Zeng, Xiaofei;Zhang, Xingtan;Wang, Yibin;Yi, Zili;Yang, Sai;Yi, Zili;Yang, Sai

作者机构：

期刊名称：NATURE PLANTS （ 影响因子：15.8； 五年影响因子：17.1 ）

ISSN： 2055-026X

年卷期： 2024 年 10 卷 8 期

页码：

收录情况： SCI

摘要： Scaffolding is crucial for constructing most chromosome-level genomes. The high-throughput chromatin conformation capture (Hi-C) technology has become the primary scaffolding strategy due to its convenience and cost-effectiveness. As sequencing technologies and assembly algorithms advance, constructing haplotype-resolved genomes is increasingly preferred because haplotypes can provide additional genetic information on allelic and non-allelic variations. ALLHiC is a widely used allele-aware scaffolding tool designed for this purpose. However, its dependence on chromosome-level reference genomes and a higher chromosome misassignment rate still impede the unravelling of haplotype-resolved genomes. Here we present HapHiC, a reference-independent allele-aware scaffolding tool with superior performance on chromosome assignment as well as contig ordering and orientation. In addition, we provide new insights into the challenges in allele-aware scaffolding by conducting comprehensive analyses on various adverse factors. Finally, with the help of HapHiC, we constructed the haplotype-resolved allotriploid genome for Miscanthus x giganteus, an important lignocellulosic bioenergy crop. This study uncovers key challenges in allele-aware genome scaffolding with Hi-C data. A reference-independent Hi-C scaffolder showing superior performance was developed to construct the haplotype-resolved genome of triploid Miscanthus x giganteus.

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