Supporting data for "Telomere-to-telomere African wild rice (Oryza longistaminata) reference genome reveals segmental and structural variation"

Rice (<i>Oryza sativa</i>) is one of the most important staple food crops worldwide, and its wild relatives serve as an important gene pool in its breeding. Compared with cultivated rice species, African wild rice (<i>Oryza longistaminata</i>) has several advantageous traits, such as resistance to increased biomass production, clonal propagation via rhizomes, and biotic stresses. However, previous <i>O. longistaminata</i><em> </em>genome assemblies have been hampered by gaps and incompleteness, restricting detailed investigations into their genomes. To streamline breeding endeavors and facilitate functional genomics studies, we generated a 331 Mb telomere-to-telomere (T2T) genome assembly for this species, covering all telomeres and centromeres across the 12 chromosomes. This newly assembled genome has markedly improved over previous versions. Comparative analysis revealed a high degree of synteny with previously published genomes. A large number of structural variations were identified between <i>O. longistaminata</i> and <i>O. sativa</i><em>.</em> A total of 2,466 segmentally duplicated genes were identified and enriched in cellular amino acid metabolic processes. We detected a slight expansion of some subfamilies of resistance genes and transcription factors. This newly assembled T2T genome of <i>O. longistaminata</i> provides a valuable resource for the exploration and exploitation of beneficial alleles present in wild relative species of cultivated rice.