Papaya (Carica papaya L.) is a nutritionally and medicinally important tropical fruit crop, yet its genetic improvement has been limited by insufficient genomic resources. In this study, we constructed chromosome-level genomes for three key varieties (Zhufeng, T3, and T5) and integrated them with three existing assemblies to build a comprehensive pangenome, including graph-based, linear, and syntelog-based representations. The syntelog-based pangenome revealed 24 453 syntelog groups (SGs). Leveraging resequencing data from 222 accessions aligned to the graph-based pangenome, we identified 26 173 structural variations (SVs), including a functionally relevant 94-bp deletion in the RETARDED ROOT GROWTH (RRG) gene in the T3 genome. This deletion affects the expression of the RRG, resulting in a reduction in its expression level in T3. Further phenotypic analysis showed that RRG can influence papaya root length by promoting the proliferation of root meristem cells and inhibiting cell elongation. Additionally, the linear pangenome uncovered 5273 translocations and 1440 inversions, significantly expanding the known SV repertoire in papaya. This study provides a critical genomic resource for deciphering domestication-related traits and accelerating marker-assisted breeding, ultimately advancing the genetic improvement of papaya.

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