Pan-genomes from large natural populations can capture genetic diversity and reveal genomic complexity. Using de novo long-read assembly, we generated a graph-based super pan-genome of rice consisting of a 251-accession panel comprising both cultivated and wild species of Asian and African rice. Our pan-genome reveals extensive structural variations (SVs) and gene presence/absence variations. Additionally, our pan-genome enables the accurate identification of nucleotide-binding leucine-rich repeat genes and characterization of their inter- and intraspecific diversity. Moreover, we uncovered grain weight-associated SVs which specify traits by affecting the expression of their nearby genes. We characterized genetic variants associated with submergence tolerance, seed shattering and plant architecture and found independent selection for a common set of genes that drove adaptation and domestication in Asian and African rice. This super pan-genome facilitates pinpointing of lineage-specific haplotypes for trait-associated genes and provides insights into the evolutionary events that have shaped the genomic architecture of various rice species.

来自大型自然群体的泛基因组可以捕获遗传多样性并揭示基因组复杂性。使用从头长读组装，我们生成了基于图的水稻超级泛基因组，其中包含 251 个种质组，其中包括亚洲和非洲的栽培种和野生种水稻。我们的泛基因组揭示了广泛的结构变异（SV）和基因存在/缺失变异。此外，我们的泛基因组能够准确识别核苷酸结合的富含亮氨酸的重复基因，并表征其种间和种内多样性。此外，我们还发现了与粒重相关的 SV，它们通过影响附近基因的表达来指定性状。我们表征了与耐淹性、种子落粒和植物结构相关的遗传变异，并发现了一组共同​​基因的独立选择，这些基因推动了亚洲和非洲水稻的适应和驯化。这种超级泛基因组有助于精确定位性状相关基因的谱系特异性单倍型，并提供对塑造各种水稻品种基因组结构的进化事件的见解。