A high-quality chromosome-level wild rice genome of <i>Oryza coarctata</i>.

<i>Oryza coarctata</i> (2n=4X=48, KKLL) is an allotetraploid, undomesticated relative of rice and the only species in the genus <i>Oryza</i> with tolerance to high salinity and submergence. Therefore, it contains important stress and tolerance genes/factors for rice. The initial draft genome published was limited by data and technical restrictions, leading to an incomplete and highly fragmented assembly. This study reports a new, highly contiguous chromosome-level genome assembly and annotation of <i>O. coarctata</i>. PacBio high-quality HiFi reads generated 460 contigs with a total length of 573.4 Mb and an N50 of 23.1 Mb, which were assembled into scaffolds with Hi-C data, anchoring 96.99% of the assembly onto 24 chromosomes. The genome assembly comprises 45,571 genes, and repetitive content contributes 25.5% of the genome. This study provides the novel identification of the KK and LL genome types of the genus <i>Oryza</i>, leading to valuable insights into rice genome evolution. The chromosome-level genome assembly of <i>O. coarctata </i>is a valuable resource for rice research and molecular breeding.紧穗野生稻（Oryza coarctata，染色体组型2n=4X=48，基因组组型KKLL）是异源四倍体水稻的未驯化近缘物种，亦是稻属（Oryza）中唯一兼具高盐耐受与耐淹特性的物种，因此该物种携带有水稻抗逆育种所需的关键功能基因与调控因子。此前发布的该物种初始基因组草图受限于数据规模与技术瓶颈，存在组装不完整、片段化程度极高的缺陷。本研究报道了紧穗野生稻一套全新的、高度连续的染色体水平基因组组装与注释结果：研究利用PacBio平台获取的高质量HiFi测序读段，共组装得到460个重叠群（contig），总长度达573.4 Mb，重叠群N50值为23.1 Mb；随后借助Hi-C（染色质构象捕获技术）数据将上述重叠群锚定至支架序列（scaffold），最终使96.99%的组装序列被锚定到24条染色体上。本次组装的基因组共注释得到45571个编码基因，重复序列占基因组总长度的25.5%。本研究首次明确鉴定了稻属KK与LL基因组组型，为水稻基因组演化研究提供了极具价值的理论参考。紧穗野生稻的染色体水平基因组组装将成为水稻基础研究与分子育种的宝贵资源。