| 项目编号 | PRJCA024131 | ||||||||||||||||
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| 项目标题 | A pangenome reference of wild and cultivated rice | ||||||||||||||||
| 涉及领域 | Pan genome | ||||||||||||||||
| 数据类型 |
Whole genome sequencing
Transcriptome or Gene expression Variation Genome sequencing and assembly Raw sequence reads Genome sequencing Assembly Genome annotation |
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| 物种名称 |
Oryza sativa
Oryza longistaminata Oryza meridionalis Oryza rufipogon |
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| 描述信息 | The wild rice Oryza rufipogon, progenitor of Asian cultivated rice O. sativa, is an important resource for rice breeding. Here we presented a wild-cultivated rice pangenome based on 145 chromosome-level assemblies, comprising 129 genetically diverse O. rufipogon accessions and 16 diverse O. sativa varieties. This pangenome contains 3.87 Gb novel sequences absent in the japonica Nipponbare reference genome. We captured alternate assemblies that included heterozygous information missing in the primary assemblies, and identified a total of 69,531 pan-genes with 28,907 core-genes and 13,728 wild rice-specific genes. We observed a higher abundance and a significantly greater diversity of resistance gene analogs in wild rice compared to that in cultivars. Our analysis indicated that two cultivated subpopulations, intro-indica and basmati were generated through gene flows among cultivars in South Asia. We also provided strong evidence to support the initial domestication of all Asian cultivated rice occurred only once. Furthermore, we captured 855,122 SNPs and 13,853 PAVs differentiated between indica and japonica, which mainly be traced back to the divergence of their respective ancestors and a larger genetic bottleneck in japonica. This study provides reference resource for enhancing rice improvements and enriches our understanding of the origin and domestication process of rice. | ||||||||||||||||
| 样品范围 | Multiisolate | ||||||||||||||||
| 发布日期 | 2025-02-18 | ||||||||||||||||
| 项目资金来源 |
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| 本项目在其他数据库系统中的项目序列号 |
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| 提交者 | Yan Zhao (yzhao@ncgr.ac.cn) | ||||||||||||||||
| 提交单位 | State Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China | ||||||||||||||||
| 提交日期 | 2024-03-07 |