Wild species of crops serve as a valuable germplasm resource for breeding of modern cultivars. Rice (Oryza sativa L.) is a vital global staple food. However, research on genome evolution and diversity of wild rice species remains limited. Here, we present nearly complete genomes of 13 representative wild rice species. By integrating with four previously published genomes for pangenome analysis, a total of 101,723 gene families are identified across the genus, including 9834 (9.67%) core gene families. Additionally, 63,881 gene families absent in cultivated rice species but present in wild rice species are discovered. Extensive structural rearrangements, sub-genomes exchanges, widespread allelic variations, and regulatory sequence variations are observed in wild rice species. Interestingly, expanded but less diverse disease resistance genes in the genomes of cultivated rice, likely due to the loss of some resistance genes and the fixing and amplification of genes encoding resistance genes to specific diseases during domestication and artificial selection. This study not only reveals natural variations valuable for gene-level studies and breeding selection but also enhances our understanding on rice evolution and domestication.

野生作物物种是培育现代栽培品种的宝贵种质资源。大米 （Oryza sativa L.） 是全球重要的主食。然而，关于野生稻物种基因组进化和多样性的研究仍然有限。在这里，我们展示了 13 种代表性野生稻种的几乎完整的基因组。通过与先前发表的四个基因组整合进行泛基因组分析，整个属共鉴定出 101,723 个基因家族，包括 9834 个 （9.67%） 核心基因家族。此外，还发现了 63,881 个基因家族，这些基因家族在栽培稻物种中不存在，但在野生稻物种中存在。在野生稻物种中观察到广泛的结构重排、亚基因组交换、广泛的等位基因变异和调节序列变异。有趣的是，栽培稻基因组中扩增但多样性较低的抗病基因，这可能是由于一些抗性基因的丢失以及在驯化和人工选择过程中编码对特定疾病的抗性基因的固定和扩增。这项研究不仅揭示了对基因水平研究和育种选择有价值的自然变异，还增强了我们对水稻进化和驯化的理解。