AbstractScaffolding 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.

摘要脚手架对于构建大多数染色体水平的基因组至关重要。高通量染色质构象捕获（Hi-C）技术由于其方便性和成本效益而成为主要的支架策略。随着测序技术和组装算法的进步，构建单倍型解析的基因组越来越受欢迎，因为单倍型可以提供有关等位基因和非等位基因变异的其他遗传信息。

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.

ALLHiC是为此目的设计的一种广泛使用的等位基因感知脚手架工具。然而，它对染色体水平参考基因组的依赖性和较高的染色体错配率仍然阻碍了单倍型解析基因组的解开。在这里，我们介绍了HapHiC，这是一种独立于参考的等位基因感知支架工具，在染色体分配以及重叠群排序和定向方面具有优异的性能。

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 × giganteus, an important lignocellulosic bioenergy crop..

此外，我们通过对各种不利因素进行全面分析，为等位基因感知支架的挑战提供了新的见解。最后，在HapHiC的帮助下，我们为重要的木质纤维素生物能源作物芒草构建了单倍型解析的异源三倍体基因组。。

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Fig. 1: Overview of the HapHiC pipeline.Fig. 2: Comprehensive performance analysis of Hi-C-based scaffolding tools in chromosome assignment under various adverse conditions.Fig. 3: Evaluation of Hi-C-based scaffolding tools’ performance in contig ordering and orientation across assemblies with varying contig N50 values.Fig.

图1:HapHiC管道概述。图2：在各种不利条件下，基于Hi-C的脚手架工具在染色体分配中的综合性能分析。图3：基于Hi-C的脚手架工具在具有不同重叠群N50值的组件中的重叠群排序和定向性能的评估。图。

4: Comparative analysis of execution time and memory usage for Hi-C-based scaffolding tools.Fig. 5: Comparative analysis and examples of HapHiC in scaffolding published autotetraploid genomes.Fig. 6: Comparative genomic analysis of M. × giganteus and other Miscanthus species..

4： 基于Hi-C的脚手架工具的执行时间和内存使用的比较分析。图5：脚手架公布的同源四倍体基因组中HapHiC的比较分析和例子。图6:M.×giganteus和其他芒属物种的比较基因组分析。。

Data availability

数据可用性

All raw sequencing data and the final chromosome-level haplotype-resolved genome of M. × giganteus have been deposited in the National Genomics Data Center (NGDC, https://ngdc.cncb.ac.cn) under BioProject PRJCA021366. The genome assembly of M. sativa XinJiangDaYe used as the ground truth for validating HapHiC is available via Figshare at https://doi.org/10.6084/m9.figshare.26037289.v1 (ref.

所有原始测序数据和最终的染色体水平单倍型解析基因组均已保存在国家基因组学数据中心（NGDC，https://ngdc.cncb.ac.cn)在生物项目PRJCA021366下。作为验证HapHiC的基本事实的苜蓿新疆大叶的基因组组装可通过Figshare获得https://doi.org/10.6084/m9.figshare.26037289.v1（参考。

54). The potato C88 genome assembled in this work is available via Figshare at https://doi.org/10.6084/m9.figshare.26063938.v1 (ref. 55). All published raw sequencing data and genome assemblies of real cases used for HapHiC validation are listed in Supplementary Data 4, including potato C88 (Hi-C reads on NGDC: CRR381057; assembly at http://solomics.agis.org.cn/potato/ftp/tetraploid/C88.v1.fa.gz), S.

54）。这项工作中组装的马铃薯C88基因组可通过Figshare获得https://doi.org/10.6084/m9.figshare.26063938.v1（参考文献55）。补充数据4列出了所有已发布的用于单倍体验证的真实病例的原始测序数据和基因组装配，包括马铃薯C88（NGDC上的Hi-C读数：CRR381057；装配在http://solomics.agis.org.cn/potato/ftp/tetraploid/C88.v1.fa.gz)，S。

spontaneum Np-X (Hi-C reads on the National Center for Biotechnology Information (NCBI): SRR22405988, SRR22405989; assembly on NCBI: GCA_022457205.1), S. spontaneum AP85-411 (Hi-C reads on NGDC: CRR055769, CRR055770, CRR055771, CRR055772; assembly at https://www.life.illinois.edu/ming/downloads/Spontaneum_genome/Sspon.HiC_chr_asm.fasta), M.

自发性Np-X（Hi-C阅读国家生物技术信息中心（NCBI）：SRR22405988，SRR22405989；在NCBI上组装：GCA\U 022457205.1），自发性链球菌AP85-411（在NGDC上的Hi-C读数：CRR055769，CRR055770，CRR055771，CRR055772；在https://www.life.illinois.edu/ming/downloads/Spontaneum_genome/Sspon.HiC_chr_asm.fasta)，M。

sativa XinJiangDaYe (Hi-C reads on NCBI: SRR9026577, SRR9026578; assembly at https://doi.org/10.6084/m9.figshare.12327602.v3 (ref. 56)), M. sativa Zhongmu-4 (Hi-C reads on NGDC: CRR330262, CRR330263, CRR330264, CRR330265, CRR330266; assembly at https://figshare.com/s/fb4ba8e0b871007a9e6c (ref. 57)), C.

苜蓿新疆大叶（Hi-C读入NCBI:SRR9026577，SRR9026578；组装于https://doi.org/10.6084/m9.figshare.12327602.v3（参考文献56）），M.sativa Zhongmu-4（Hi-C在NGDC上读取：CRR330262，CRR330263，CRR330264，CRR330265，CRR330266；组装于https://figshare.com/s/fb4ba8e0b871007a9e6c（参考文献57）），C。

sinensis Tieguanyin (Hi-C reads on NCBI: SRR12744827; assembly on NGDC: GWHASIX00000000), human HG002 (Hi-C reads: HG002.HiC_1* at https://s3-us-west-2.amazonaws.com/human-pangenomics/index.html?prefix=NHGRI_UCSC_panel/HG002/hpp_HG002_NA24385_son_v1/hic/, HG002.HiC_* at https://s3-us-west-2.amazonaws.com/human-pangenomics/index.html?prefix=NHGRI_UCSC_pa.

中华铁观音（Hi-C在NCBI上读取：SRR12744827；在NGDC上组装：GWHASIX00000000），人HG002（Hi-C读取：HG002。HiC\u 1*athttps://s3-us-west-2.amazonaws.com/human-pangenomics/index.html?prefix=NHGRI_UCSC_panel/HG002/hpp_HG002_NA24385_son_v1/hic/，HG002。HiC\u*athttps://s3-us-west-2.amazonaws.com/human-pangenomics/index.html?prefix=NHGRI_UCSC_pa.

Code availability

代码可用性

HapHiC and all custom scripts for dataset simulation are available via GitHub at https://github.com/zengxiaofei/HapHiC. The source code of modified ALLHiC are available via GitHub at https://github.com/zengxiaofei/allhic.

HapHiC和所有用于数据集模拟的自定义脚本都可以通过GitHub获得https://github.com/zengxiaofei/HapHiC.修改后的ALLHiC的源代码可通过GitHub获得https://github.com/zengxiaofei/allhic.

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。figshare公司https://doi.org/10.6084/m9.figshare.13013795.v1（2020年）。Miao，J。Mlu\u HiC\u cds.fasta.gz。figshare公司https://doi.org/10.6084/m9.figshare.12992984.v2（2020年）。下载参考文献致谢这项工作得到了国家自然科学基金（32100459）和中国博士后科学基金（2020M672695）对X的资助。

Zeng. Additional funding was provided by the Shenzhen Municipal Science and Technology Innovation Commission Foundation (JCYJ20220530114415036, JCYJ20210324104800001) and the National Natural Science Foundation of China (32070625) to G.C. and by the National Natural Science Foundation of China (32222019) to X.

曾。深圳市科学技术创新委员会基金（JCYJ20253011415036，JCYJ20210324104800001）和国家自然科学基金（32070625）向G.C.和国家自然科学基金（3222019）向X提供了额外的资金。

Zhang. The Center for Computational Science and Engineering at Southern University of Science and Technology also provided support for this work. We thank D. Zhang and D. Ru from Lanzhou University, Z. Bao from the Max Planck Institute for Biology Tübingen and S. Zhu from Huazhong Agricultural University for their valuable suggestions and contributions to HapHiC.Author informationAuthors and AffiliationsDepartment of Human Cell Biology and Genetics, Joint Laboratory of Guangdong-Hong Kong Universities.

张。南方科技大学计算科学与工程中心也为这项工作提供了支持。我们感谢兰州大学的D.Zhang和D.Ru，蒂宾根马克斯·普朗克生物研究所的Z.Bao和华中农业大学的S.Zhu为HapHiC提供了宝贵的建议和贡献。作者信息作者和附属机构粤港大学联合实验室人类细胞生物学与遗传学系。

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PubMed Google ScholarContributionsX. Zeng designed the algorithms, implemented HapHiC, analysed the genome of M. × giganteus and wrote the manuscript. Z.Y. and S.Y. managed and provided the plant materials of M. × giganteus. X. Zeng, Y.D., Y.L., Z.Z., S.C. and H.Z. benchmarked HapHiC and other scaffolding tools.

PubMed谷歌学术贡献x。曾设计了算法，实现了HapHiC，分析了M.×giganteus的基因组并撰写了手稿。Z、 Y.和S.Y.管理并提供了M.×giganteus的植物材料。十、 Zeng，Y.D.，Y.L.，Z.Z.，S.C.和H.Z.以HapHiC和其他脚手架工具为基准。

G.C., X. Zhang and Y.W. provided suggestions for the algorithms. G.C. and X. Zhang revised the manuscript.Corresponding authorsCorrespondence to.

G、 C.，X.Zhang和Y.W.为算法提供了建议。G、 C.和X.Zhang修改了手稿。通讯作者通讯。

Xiaofei Zeng or Guoan Chen.Ethics declarations

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Competing interests

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The authors declare no competing interests.

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Peer review

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Nature Plants thanks Haoyu Cheng and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

Nature Plants感谢Haoyu Cheng和另一位匿名审稿人为这项工作的同行评审做出的贡献。

Additional informationPublisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.Extended dataExtended Data Fig. 1 Workflow for simulating datasets with various adverse factors.Rounded rectangles represent chromosome-level genomes in FASTA format, while rectangles denote simulated assemblies and/or Hi-C data.

Additional informationPublisher的注释Springer Nature在已发布的地图和机构隶属关系中的管辖权主张方面保持中立。。圆形矩形表示FASTA格式的染色体水平基因组，而矩形表示模拟组件和/或Hi-C数据。

The Hi-C reads for the assemblies in red rectangles originate from real sequencing data, whereas the Hi-C reads for the assemblies in blue rectangles were simulated using sim3C. Arrows depict the simulation processes.Extended Data Fig. 2 Assembly correction method in HapHiC.The brown line chart represents the Hi-C spanning coverage along contig CM039579.1_ctg399_+.

红色矩形中组件的Hi-C读数来自实际测序数据，而蓝色矩形中组件的Hi-C读数是使用sim3C模拟的。箭头描绘了模拟过程。扩展数据图2 HapHiC中的装配校正方法。。

The dashed blue line illustrates the coverage threshold, which is set at one-fifth of the median coverage by default. Regions of high and low coverage are denoted by red and blue rectangles, respectively. The green triangle indicates the breakpoint as determined by HapHiC.Extended Data Fig. 3 Rank-sum algorithm for identifying chimeric and collapsed contigs in HapHiC.a, A network graph illustrates contigs connected via Hi-C links.

蓝色虚线表示覆盖率阈值，默认情况下该阈值设置为中值覆盖率的五分之一。高覆盖率和低覆盖率的区域分别用红色和蓝色矩形表示。绿色三角形表示由HapHiC确定的断点。。

Red and blue circles (vertices) represent contigs from different haplotypes. Bicolor and purple circles symbolize chimeric and collapsed contigs, respectively. Edges connecting these circles indicate Hi-C links between contigs, with the number of Hi-C links displayed adjacent to the edges. b, The ranking of each contig relative to others based on the number of Hi-C links.

红色和蓝色圆圈（顶点）代表来自不同单倍型的重叠群。双色和紫色圆圈分别代表嵌合和塌陷的重叠群。连接这些圆圈的边缘表示重叠群之间的Hi-C链接，在边缘附近显示Hi-C链接的数量。b、 根据Hi-C链接的数量，每个重叠群相对于其他重叠群的排名。

Gray numbers indicate the absence of direct connections between contigs. c, The calculation of rank-sum values. Different colors are used to trace the origin of the ranks.Extended Data Fig. 4 Comparison of inter-allele Hi-C links betwe.

灰色数字表示重叠群之间没有直接联系。c、 。不同的颜色被用来追踪等级的起源。扩展数据图4等位基因间Hi-C链接的比较。

Nat. Plants (2024). https://doi.org/10.1038/s41477-024-01755-3Download citationReceived: 13 December 2023Accepted: 01 July 2024Published: 05 August 2024DOI: https://doi.org/10.1038/s41477-024-01755-3Share this articleAnyone you share the following link with will be able to read this content:Get shareable linkSorry, a shareable link is not currently available for this article.Copy to clipboard.

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