The Oryza australiensis genome reveals potential as a source of genes for rice improvement

The wild relatives of cultivated rice (Oryza sativa L.) represent largely untapped sources of novel genetic material for crop improvement. Here, we present a chromosome-level, haplotype-resolved genome for O. australiensis, an Australian wild rice relative, assembled de novo using PacBio HiFi long reads (80 × coverage). The final assembly had a 99.3% BUSCO completeness score and a total length of 909 Mb. The assembly was highly contiguous (contig N50 of 72.6 Mb) despite its extremely high repeat element content, which was estimated to comprise 76% of the genome. There were 26,529 transcripts and 23,929 potential genes annotated from the assembly, of which 1,431 were species-specific to O. australiensis and not found in cultivated rice. Annotation of these revealed enrichment for functions associated with DNA integration, as well as those linked to abiotic and biotic response signalling. Structural analyses highlighted considerable synteny between O. australiensis and cultivated rice, despite a long period of evolutionary divergence between the two species. Despite the presence of little structural variation between the haplotypes, there was considerable variation observed between the current assembly and a previously published O. australiensis genome, suggesting local divergence that may be associated with adaptation of populations to heterogenous environments.