T2T Assembly of Oryza australiensis Reveals Centromere Repositioning Mechanisms and Identifies the EE Genome as Direct Donor of the Extinct DD Lineage

Oryza australiensis (EE genome), as the sole representative of the EE genome in the genus Oryza, holds significant research value due to its extreme environmental adaptability, unique grain pigmentation and starch properties, and making it a critical resource for deciphering polyploid evolution and mining stress-resistance genes for crop breeding. Here, a telomere-to-telomere (T2T) assembly of O. australiensis has been generated, yielding a 901 Mb chromosome-scale genome with 12 complete chromosomes (BUSCO:99.2%; LAI:22.67). This enabled comprehensive annotation of centromeres, telomeres, and 36,753 genes, revealing non-canonical telomeric repeats and three distinct centromere repositioning mechanisms in Oryza: inversion-driven shifts, segmental duplication-mediated neocentromeres, and transposon burst-induced neocentromere formation to the EE genome. Crucially, transposon dynamics revealed synchronized amplification of Angela LTR retrotransposons in EE genome and the DD subgenome of allotetraploid O. alta (CCDD) prior to 1.7 million years ago (Mya). Phylogenetic and synteny analyses of conserved Angela LTR integrase domains, alongside a unique 275-bp repeat marker exclusive to EE and DD, demonstrate that the pre-1.7 Mya EE lineage served as the direct donor of the extinct DD genome. This resolves a major controversy in Oryza evolution and establishes transposon-centric approaches for reconstructing paleogenomic histories.