文献类型： 外文期刊
作者： Cui, Xue 1 ; Liu, Yuxin 1 ; Sun, Miao 2 ; Zhao, Qiyue 1 ; Huang, Yicheng 3 ; Zhang, Jianwei 3 ; Yao, Qiulin 5 ; Yin, Hang 2 ; Zhang, Huixin 6 ; Mo, Fulei 6 ; Zhong, Hongbin 7 ; Liu, Yang 1 ; Chen, Xiuling 1 ; Zhang, Yao 6 ; Liu, Jiayin 1 ; Qiu, Youwen 6 ; Feng, Mingfang 6 ; Chen, Xu 1 ; Ghanizadeh, Hossein 1 ; Zhou, Yao 2 ; Wang, Aoxue 1 ;
作者机构： 1.Northeast Agr Univ, Coll Hort & Landscape Architecture, Harbin 150030, Peoples R China
2.Chinese Acad Sci, Inst Bot, State Key Lab Forage Breeding By Design & Utilizat, Key Lab Plant Mol Physiol, Beijing 100093, Peoples R China
3.Huazhong Agr Univ, Natl Key Lab Crop Genet Improvement, Wuhan 430070, Peoples R China
4.Chinese Acad Agr Sci, Minist Agr & Rural Affairs, Shenzhen Key Lab Agr Synthet Biol, Shenzhen Branch,Guangdong Lab Lingnan Modern Agr,, Shenzhen 518124, Peoples R China
5.Wuhan Jianbing Technol Co Ltd, Wuhan, Peoples R China
6.Northeast Agr Univ, Coll Life Sci, Harbin 150030, Peoples R China
7.Shenzhen CEM Biomed Technol Ltd, Shenzhen, Peoples R China
8.Natl Ctr Technol Innovat Comprehens Utilizat Salin, Academician Workstn Agr High Tech Ind Area Yellow, Dongying 257300, Peoples R China
期刊名称：HORTICULTURE RESEARCH （ 影响因子：8.5； 五年影响因子：9.1 ）
ISSN： 2662-6810
年卷期： 2025 年 12 卷 7 期
页码：
收录情况： SCI
摘要： 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 bona fide SVs with precise breakpoints, including substitutions (223), which should be taken as a fundamental SV type, alongside insertions (780), deletions (619), and inversions (13), all showing preferences for SV occurrence within AT-repeat regions of regulatory loci. This precise resolution of complex SVs will foster genome analysis and crop improvement.
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