A draft genome assembly and comparative transcriptomics of the African wild rice species Oryza longistaminata

Background: Oryza longistaminata, an African wild AA genome (2n=24) relative of Asian cultivated rice (Oryza sativa L.), is characterized by a number of valuable traits that could be used for improvement of cultivars. Here we report the draft genome assembly of O. longistaminata and transcriptomes of four pairs of relative traits’ tissues. Results: Although high heterozygosity from obligate outcrossing obstructed our ability to generate a high-quality reference genome, we were able to produce a relatively good draft genome assembly that can be used to annotate 34,090 protein-coding genes. The total length of the assembled draft genome is 373 Mb with a scaffold N50 size of 82.52 kb. The average sequence divergence between O. longistaminata and O. sativa is 5.23% in aligned regions. Consistent with the fact that O. longistaminata is highly resistant to many plant pathogens, our genome annotation revealed more disease resistant genes than in cultivated rice. Detailed analysis of four pairs of transcriptomes permitted the identification of some rhizome- and self-incompatibility-related genes. Conclusions: These large quantities of data not only provides a valuable resource of many genes for cultivated rice improvement, but also offers new insights into the evolution of the genus Oryza and genic basis of rhizome and self-incompatibility.