Evidence map›Paper›PMID 40721805›Full record

ArticleGenome biology2025

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

Huaming Wen, Jinbao Yang, Xianjia Zhao, Xingbin Wang, Jiawei Lei, Yanchun Li, Wenjie Du, Dongxi Li, Yun Xu, Stefano Lonardi and 1 more

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In one paragraph

Article in Genome biology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.

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0cells of the map it votes in
5citing papers in PubMed
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1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

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3 · Its place in the literature

Who cites it

5 citing papers in PubMed.

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4 · The record

Corrections and comments

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5 · Who and what money

Authors and funding

11 authors.

Huaming Wen *School of Computer Science and Technology, University of Science and Technology of China, Hefei, 230027, China.
Jinbao Yang *State Key Laboratory of Genome and Multi-Omics Technologies, Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China.
Xianjia ZhaoState Key Laboratory of Genome and Multi-Omics Technologies, Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China.
Xingbin WangState Key Laboratory of Genome and Multi-Omics Technologies, Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China.
Jiawei LeiState Key Laboratory of Genome and Multi-Omics Technologies, Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China.
Yanchun LiState Key Laboratory of Genome and Multi-Omics Technologies, Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China.
Wenjie DuState Key Laboratory of Genome and Multi-Omics Technologies, Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China.
Dongxi LiCollege of Computer Science and Technology, Taiyuan University of Technology, Taiyuan, 030024, China.
Yun XuSchool of Computer Science and Technology, University of Science and Technology of China, Hefei, 230027, China.
Stefano LonardiDepartment of Computer Science and Engineering, University of California, Riverside, CA, 92521, USA. stelo@cs.ucr.edu.
Weihua PanState Key Laboratory of Genome and Multi-Omics Technologies, Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China. panweihua@caas.cn.

Funding

National Natural Science Foundation of China 32100501the Agricultural Science and Technology Innovation Program ZDRW202503The Agricultural Science and Technology Innovation Program CAAS-CSIAF-202301the Youth Innovation Program of the Chinese Academy of Agricultural Sciences Y2025QC36
6 · The paper itself

Abstract

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.

Indexed as

AlgorithmsSequence Analysis, DNATandem Repeat SequencesCentromereHumansSoftwareSolanum lycopersicumTelomereGap fillingGenome assemblyReference-guided genome assemblySegmental duplicationsTandem repeats

Identifiers

PMID40721805
PMCPMC12305924

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