Ming Hu, Penglong Wan, Chengjie Chen, Shuyuan Tang, Jiahao Chen, Liang Wang, Mahul Chakraborty, Yongfeng Zhou, Jinfeng Chen, Brandon S Gaut, J J Emerson, Yi Liao
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引用次数: 0
Abstract
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.
期刊介绍:
Molecular Biology and Evolution
Journal Overview:
Publishes research at the interface of molecular (including genomics) and evolutionary biology
Considers manuscripts containing patterns, processes, and predictions at all levels of organization: population, taxonomic, functional, and phenotypic
Interested in fundamental discoveries, new and improved methods, resources, technologies, and theories advancing evolutionary research
Publishes balanced reviews of recent developments in genome evolution and forward-looking perspectives suggesting future directions in molecular evolution applications.