Evidence map›Paper›PMID 40406505›Full record

ArticleHorticulture research2025

The nature of complex structural variations in tomatoes.

Xue Cui, Yuxin Liu, Miao Sun, Qiyue Zhao, Yicheng Huang, Jianwei Zhang, Qiulin Yao, Hang Yin, Huixin Zhang, Fulei Mo and 11 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Horticulture research, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers, 1 of them a synthesis that pooled it.

0numbers the graph read from it
0cells of the map it votes in
5citing papers in PubMed, 1 pooled it
–field-weighted citation impact
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

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

5 citing papers in PubMed, 1 synthesis or guideline pooled it.

  1. Research evolution of flat peach (Frontiers in plant science · 2025
    Pooled it
  2. Multi-variant GWAS and genomic prediction dissect the genetic architecture underlying tomato fruit weight.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026
    Article
  3. Structural Variation and Its Roles in Plant Genomes.Plants (Basel, Switzerland) · 2026
    Review
  4. Article
  5. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

21 authors.

Xue CuiCollege of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China.
Yuxin LiuCollege of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China.
Miao SunState Key Laboratory of Forage Breeding-by-Design and Utilization, Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.
Qiyue ZhaoCollege of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China.
Yicheng HuangNational Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China.
Jianwei ZhangNational Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China.
Qiulin YaoWuhan Jianbing Technology Co., Ltd., Wuhan, China.
Hang YinState Key Laboratory of Forage Breeding-by-Design and Utilization, Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.
Huixin ZhangCollege of Life Sciences, Northeast Agricultural University, Harbin 150030, China.
Fulei MoCollege of Life Sciences, Northeast Agricultural University, Harbin 150030, China.
Hongbin ZhongShenzhen CEM Biomedical Technology Ltd., Shenzhen, China.
Yang LiuCollege of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China.
Xiuling ChenCollege of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China.
Yao ZhangCollege of Life Sciences, Northeast Agricultural University, Harbin 150030, China.
Jiayin LiuCollege of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China.
Youwen QiuCollege of Life Sciences, Northeast Agricultural University, Harbin 150030, China.
Mingfang FengCollege of Life Sciences, Northeast Agricultural University, Harbin 150030, China.
Xu ChenCollege of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China.
Hossein GhanizadehCollege of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China.
Yao ZhouState Key Laboratory of Forage Breeding-by-Design and Utilization, Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.
Aoxue WangCollege of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Structural variations (SVs) in repetitive sequences could only be detected within a broad region due to imprecise breakpoints, leading to classification errors and inaccurate trait analysis. Through manual inspection at 4532 variant regions identified by integrating 14 detection pipelines between two tomato genomes, we generated an SV benchmark at base-pair resolution. Evaluation of all pipelines yielded F1-scores below 53.77% with this benchmark, underscoring the urgent need for advanced detection algorithms in plant genomics. Analyzing the alignment features of the repetitive sequences in each region, we summarized four patterns of SV breakpoints and revealed that deviations in breakpoint identification were primarily due to copy misalignment. According to the similarities among copies, we identified 1635

Identifiers

PMID40406505
PMCPMC12096311

What OpenQuestion holds

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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.