数字农科院2.0

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

文献类型: 外文期刊

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

作者机构:

关键词: (1-1-2)Gap filling;Genome assembly;Reference-guided genome assembly;Segmental duplications;Tandem repeats

期刊名称: Genome Biology

ISSN: 1474-760X

年卷期: 2025 年 26 卷 1 期

页码:

收录情况: SCIE(2025版)

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.

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