A chromosome-level genome assembly of the wild rice Oryza rufipogon facilitates tracing the origins of Asian cultivated rice
| Autor: | Weizhi Liu, Chengzhi Liang, Huilong Du, Tie Li, Zhansheng Lin, Jianian Tang, Yao-Guang Liu, Tan Xiyu, Xianrong Xie, Huiwu Tang |
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| Rok vydání: | 2020 |
| Předmět: |
Crops
Agricultural 0301 basic medicine Genome evolution Asia Genes Plant Synteny Genome Chromosomes Plant General Biochemistry Genetics and Molecular Biology DNA sequencing Evolution Molecular 03 medical and health sciences 0302 clinical medicine Species Specificity Phylogeny General Environmental Science Whole genome sequencing Genetics Polymorphism Genetic Oryza sativa biology Chromosome Mapping food and beverages Oryza Sequence Analysis DNA biology.organism_classification Oryza rufipogon Plant Breeding 030104 developmental biology 030220 oncology & carcinogenesis General Agricultural and Biological Sciences Genome Plant Reference genome |
| Zdroj: | Science China Life Sciences. 64:282-293 |
| ISSN: | 1869-1889 1674-7305 |
| DOI: | 10.1007/s11427-020-1738-x |
| Popis: | 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. |
| Databáze: | OpenAIRE |
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