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

Oryza coarctata (2n=4X=48, KKLL) is an allotetraploid, undomesticated relative of rice and the only species in the genus Oryza 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 O. coarctata. 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 Oryza, leading to valuable insights into rice genome evolution. The chromosome-level genome assembly of O. coarctata is a valuable resource for rice research and molecular breeding.紧穗野生稻（Oryza coarctata，体细胞染色体数2n=4X=48，染色体组型KKLL）是异源四倍体水稻的未驯化近缘种，亦是稻属（Oryza）中唯一兼具高盐胁迫与淹水耐受能力的物种。因此，该物种携带水稻重要的抗逆相关基因与调控因子。此前已发表的该物种初始基因组草图受限于数据与技术瓶颈，导致组装结果不完整且片段化程度极高。本研究报道了紧穗野生稻全新的、高度连续的染色体级基因组组装与注释结果。本研究利用PacBio平台产出的高质量HiFi测序读段，组装得到460条重叠群（contig），总长度达573.4 Mb，N50值为23.1 Mb；随后借助Hi-C（高通量染色体构象捕获）数据将上述重叠群锚定为支架序列（scaffold），使96.99%的组装序列被锚定至24条染色体上。该基因组组装结果共包含45571个编码基因，重复序列占基因组总长的25.5%。本研究首次明确鉴定了稻属KK与LL染色体组型，为解析水稻基因组演化提供了宝贵的研究见解。紧穗野生稻的染色体级基因组组装结果，将为水稻研究与分子育种提供极具价值的遗传资源。