ArticleScience China. Life sciences2021
A chromosome-level genome assembly of the wild rice Oryza rufipogon facilitates tracing the origins of Asian cultivated rice.
Article in Science China. Life sciences, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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17 citing papers in PubMed.
- Genus-Wide Pan-Genome Analysis ofPlants (Basel, Switzerland) · 2025Article
- The genomes of the most diverse AA genome rice species provide a resource for rice improvement and studies of rice evolution and domestication.BMC genomics · 2025Article
- Genome evolution and diversity of wild and cultivated rice species.Nature communications · 2024Article
- A pan-TE map highlights transposable elements underlying domestication and agronomic traits in Asian rice.National science review · 2024Article
- Haplotype-resolved gapless genome and chromosome segment substitution lines facilitate gene identification in wild rice.Nature communications · 2024Article
- Detection of locally adapted genomic regions in wild rice (Oryza rufipogon) using environmental association analysis.G3 (Bethesda, Md.) · 2023Article
- A syntelog-based pan-genome provides insights into rice domestication and de-domestication.Genome biology · 2023Article
- Insights into the Transcriptomics of Crop Wild Relatives to Unravel the Salinity Stress Adaptive Mechanisms.International journal of molecular sciences · 2023Review
- Monsoon boosted radiation of the endemic East Asian carps.Science China. Life sciences · 2023Article
- A super pan-genomic landscape of rice.Cell research · 2022Article
- GGDB: A Grameneae genome alignment database of homologous genes hierarchically related to evolutionary events.Plant physiology · 2022Article
- High-quality genome assembly of Huazhan and Tianfeng, the parents of an elite rice hybrid Tian-you-hua-zhan.Science China. Life sciences · 2022Article
- Genome Size Variation and Evolution Driven by Transposable Elements in the GenusFrontiers in plant science · 2022Article
- Article
- The genome of the rice variety LTH provides insight into its universal susceptibility mechanism to worldwide rice blast fungal strains.Computational and structural biotechnology journal · 2022Article
- Rice functional genomics: decades' efforts and roads ahead.Science China. Life sciences · 2022Review
- Genome-Wide Analysis ofFrontiers in plant science · 2021Article
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10 authors.
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Abstract
Oryza rufipogon Griff. is a wild progenitor of the Asian cultivated rice Oryza sativa. To better understand the genomic diversity of the wild rice, high-quality reference genomes of O. rufipogon populations are needed, which also facilitate utilization of the wild genetic resources in rice breeding. In this study, we generated a chromosome-level genome assembly of O. rufipogon using a combination of short-read sequencing, single-molecule sequencing, BioNano and Hi-C platforms. The genome sequence (399.8 Mb) was assembled into 46 scaffolds on the 12 chromosomes, with contig N50 and scaffold N50 of 13.2 Mb and 20.3 Mb, respectively. The genome contains 36,520 protein-coding genes, and 49.37% of the genome consists of repetitive elements. The genome has strong synteny with those of the O. sativa subspecies indica and japonica, but containing some large structural variations. Evolutionary analysis unveiled the polyphyletic origins of O. sativa, in which the japonica and indica genome formations involved different divergent O. rufipogon (including O. nivara) lineages, accompanied by introgression of genomic regions between japonica and indica. This high-quality reference genome provides insight on the genome evolution of the wild rice and the origins of the O. sativa subspecies, and valuable information for basic research and rice breeding.
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