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.

东乡野生稻（Dongxiang wild rice, DXWR, Oryza rufipogon Griff.）是栽培稻的直系野生祖先种，拥有水稻育种领域极具价值的基因资源。然而，东乡野生稻的分布范围正快速缩减，且截至目前尚未有其参考基因组发表。本研究依托牛津纳米孔测序技术（Oxford Nanopore Technology, ONT）与高通量染色体构象捕获技术（High-through chromosome conformation capture, Hi-C），构建了东乡野生稻的染色体级参考基因组。总计获得58.41 Gb清洁数据，经从头组装得到231个重叠群（contig），总长度为413.46 Mb，重叠群N50长度达5.18 Mb。借助Hi-C数据，这些重叠群被聚类并锚定至12条伪染色体，覆盖约97.39%的组装序列，最终骨架序列（scaffold）N50长度为33.47 Mb。此外，基因组序列中54.10%被鉴定为重复序列。在预测得到的35942个蛋白质编码序列中，33862个（占比94.21%）获得了功能注释。与其他稻属物种相比，东乡野生稻中与抗病、抗寒相关的基因发生了大规模扩张，这可能是东乡野生稻具备更强抗病与抗寒能力的重要原因之一。进化分析表明，东乡野生稻与栽培稻（O. sativa）、普通野生稻（O. rufipogon）约在86万年前由共同祖先分化而来。东乡野生稻与栽培稻之间共线性程度较高，但仍存在若干显著结构变异，包括11号染色体上的特异性倒位，该变异可能与东乡野生稻的物种分化密切相关。本研究组装获得的高质量东乡野生稻染色体级参考基因组，将成为未来水稻分子育种与遗传学研究的宝贵资源。