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<p>The highly repetitive content of eukaryotic genomes, including long tandem repeats, segmental duplications, and centromeres, makes haplotype-resolved genome assembly hard. Repeat sequences introduce gaps or mis-joins in the assemblies. We introduce TRFill, a novel algorithm that can close the gaps in a draft chromosome-level assembly using exclusively PacBio HiFi and Hi-C data. Experimental results on human centromeres and tomato subtelomeres show that TRFill can improve the completeness and correctness of about two-thirds of the tandem repeats. We also show that the improved completeness of subtelomeric tandem repeats in the tomato pangenome enables a population-level analysis of these complex repeats.</p>

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TRFill: synergistic use of HiFi and Hi-C sequencing enables accurate assembly of tandem repeats for population-level analysis

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2025年7月28日

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  • Huaming Wen,
  • Jinbao Yang,
  • Xianjia Zhao,
  • Xingbin Wang,
  • Jiawei Lei,
  • Yanchun Li,
  • Wenjie Du,
  • Dongxi Li,
  • Yun Xu,
  • Stefano Lonardi,
  • Weihua Pan

摘要

The highly repetitive content of eukaryotic genomes, including long tandem repeats, segmental duplications, and centromeres, makes haplotype-resolved genome assembly hard. Repeat sequences introduce gaps or mis-joins in the assemblies. We introduce TRFill, a novel algorithm that can close the gaps in a draft chromosome-level assembly using exclusively PacBio HiFi and Hi-C data. Experimental results on human centromeres and tomato subtelomeres show that TRFill can improve the completeness and correctness of about two-thirds of the tandem repeats. We also show that the improved completeness of subtelomeric tandem repeats in the tomato pangenome enables a population-level analysis of these complex repeats.