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

Abstract

Rice (Oryza sativa) 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 (Oryza longistaminata) has several advantageous traits, such as resistance to increased biomass production, clonal propagation via rhizomes, and biotic stresses. However, previous O. longistaminata 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 using a hybrid approach combining PacBio HiFi, Hi-C, and CycloneSEQ ultra-long reads, 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 O. longistaminata, O. glaberrima, and O. sativa. A total of 2,466 segmentally duplicated genes were enriched in cellular amino acid metabolic processes. We detected slight expansion of some subfamilies of resistance genes and transcription factors. This newly assembled T2T genome of O. longistaminata provides a valuable resource for the exploration and exploitation of beneficial alleles present in wild relative species of cultivated rice.