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Accurate, Scalable Structural Variant Genotyping in Complex Genomes at Population Scales

文献类型： 外文期刊

作者： Hu, Ming 1 ; Wan, Penglong 1 ; Chen, Chengjie 2 ; Tang, Shuyuan 1 ; Chen, Jiahao 1 ; Wang, Liang 1 ; Chakraborty, Mahul 3 ; Zhou, Yongfeng 2 ; Chen, Jinfeng 4 ; Gaut, Brandon S. 5 ; Emerson, J. J. 5 ; Liao, Yi 1 ;

作者机构： 1.South China Agr Univ, Coll Hort, Key Lab Biol & Genet Improvement Hort Crops South, Minist Agr & Rural Affairs, Guangzhou 510642, Peoples R China

2.Chinese Acad Trop Agr Sci, Lab Crop Gene Resources & Germplasm Enhancement So, Trop Crops Genet Resources Inst,Key Lab Trop Crops, State Key Lab Trop Crop Breeding,Minist Agr & Rura, Hainan 571101, Peoples R China

3.Texas A&M Univ, Dept Biol, College Stn, TX 77843 USA

4.Chinese Acad Sci, Inst Zool, State Key Lab Integrated Management Pest Insects &, Beijing 100101, Peoples R China

5.Univ Calif Irvine, Dept Ecol & Evolutionary Biol, Irvine, CA 92697 USA

关键词： structural variation; population genotyping; pangenome; comparing methods; plant genome

期刊名称：MOLECULAR BIOLOGY AND EVOLUTION （ 影响因子：5.3； 五年影响因子：11.9 ）

ISSN： 0737-4038

年卷期： 2025 年 42 卷 8 期

页码：

收录情况： SCI

摘要： Comparisons of complete genome assemblies offer a direct procedure for characterizing all genetic differences among them. However, existing tools are often limited to specific aligners or optimized for specific organisms, narrowing their applicability, particularly for large and repetitive plant genomes. Here, we introduce Structural Variants Genotyping of Assemblies on Population scales (SVGAP), a pipeline for structural variant (SV) discovery, genotyping, and annotation from high-quality genome assemblies at the population level. Through extensive benchmarks using simulated SV datasets at individual, population, and phylogenetic contexts, we demonstrate that SVGAP performs favorably relative to existing tools in SV discovery. Additionally, SVGAP is one of the few tools to address the challenge of genotyping SVs within large assembled genome samples, and it generates fully genotyped VCF files. Applying SVGAP to 26 maize genomes revealed hidden genomic diversity in centromeres, driven by abundant insertions of centromere-specific LTR-retrotransposons. The output of SVGAP is well-suited for pangenome construction and facilitates the interpretation of previously unexplored genomic regions.

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