Telomere-to-telomere assemblies of Glycine soja and Glycine max uncover novel genomic features of soybean

Achieving complete, gap-free genome assemblies remains a central challenge in genomics, particularly for repeat-rich plant genomes. Although several telomere-to-telomere (T2T) assemblies have been reported for soybean, highly repetitive genomic regions and the mitochondrial genome remain insufficiently resolved. Here, we assembled gap-free T2T nuclear genomes together with complete mitochondrial and chloroplast genomes for the wild soybean (Glycine soja) SoyW02 and the cultivated soybean (Glycine max) Zhonghuang 13. These assemblies substantially improved the resolution of repetitive genomic regions and enabled biological insights that were previously inaccessible. Comparative analyses uncovered a conserved subtelomeric exchange hub and refined the landscape of soybean satellite repeats, including pericentromere-enriched and chromosome-specific satellites. We further developed a de novo pipeline for identifying tandem duplication gene clusters, enabling systematic analyses of transcriptional and protein sequence divergence, and experimentally demonstrating expression and functional diversification between two duplicated oxidosqualene cyclases. Together, these assemblies establish a foundation for investigating the evolution and functional organization of repetitive genomic regions and will facilitate future soybean functional genomics and molecular breeding.