A Chromosome-Level Reference Genome Assembly and Evolution of Dongxiang Wild Rice

Dongxiang wild rice (DXWR, Oryza rufipogon Griff.) is the immediate ancestral progenitor of cultivated rice, possessing important gene resources for rice breeding. However, the distribution of DXWR is decreasing rapidly, and no reference genome has been published to date. In this study, we constructed a chromosome-level reference genome of DXWR by Oxford Nanopore Technology (ONT) and High-through chromosome conformation capture (Hi-C). A total of 58.41 Gb clean data were de novo assembled into 231 contigs with the total length of 413.46 Mb and N50 length of 5.18 Mb. These contigs were clustered and ordered onto 12 pseudo-chromosomes covering about 97.39% assembly with Hi-C data, with a scaffold N50 length of 33.47Mb. Moreover, 54.10% of the genome sequences were identified as repeat sequences. 33,862 (94.21%) genes were functionally annotated from a total of predicted 35,942 protein-coding sequences. Compared with other Oryza species, the genes related to disease and cold resistance in DXWR had undergone a large-scale expansion, which may be one of the reasons for the stronger disease resistance and cold resistance of DXWR. Evolution analysis showed that DXWR and O. sativa, O. rufipogon diverged from a common ancestor approximately 0.86 million years ago. The collinearity between DXWR and cultivated rice was high, but there were still some significant structural variations, including a specific inversion on chromosome 11, which may be related to the differentiation of DXWR. The high-quality chromosome-level reference genome of DXWR assembled in this study will become a valuable resource for rice molecular breeding and genetic research in the future.