Abstract
Rice (Oryza sativa L.) is a vital staple food globally, but its genetic diversity has decreased due to extensive breeding. However, research on genome evolution and diversity of wild rice species, particularly those with BB, CC, BBCC, CCDD, EE, FF, and GG genome types, is limited, impeding their potential in rice breeding1,2. This study presents chromosome-scale genomes of thirteen representatives wild rice species from the Oryza genus. By integrating these genomes with four previously published ones, a total of 101,723 gene families were identified across the genus, including 9,834 (9.67%) core gene families. Additionally, 63,881 new gene families absent in cultivated rice species were discovered. Comparative genomic analysis among Oryza genomes reveals potential mechanisms underlying genome size variation, centromere evolution, and gene number and expression influenced by transposable elements. Extensive structural rearrangements, large scale sub-genomes exchanges, and widespread allelic variations and regulatory sequence variations were discovered in wild rice. We noticed an inversion that are pervasive occurred in Oryza rufipogon and Oryza sativa japonica, which is tightly linked to a locus that might contributed to the expansion of geographical range. Interestingly, a notable expansion but less diversity in disease resistance genes in cultivated genomes was observed, likely due to the random loss of some R genes and extensive amplification of others for specific diseases during domestication and artificial selection. This comprehensive study not only provide previously hidden legacy accessible to genetic studies and breeding but also deepens our understanding of rice evolution and biology.