A chromosome-level genome assembly of the wild rice Oryza rufipogon facilitates tracing the origins of Asian cultivated rice

• Published in: Science China. Life sciences Vol. 64; no. 2; pp. 282 - 293
• Main Authors: Xie, Xianrong, Du, Huilong, Tang, Huiwu, Tang, Jianian, Tan, Xiyu, Liu, Weizhi, Li, Tie, Lin, Zhansheng, Liang, Chengzhi, Liu, Yao-Guang
• Format: Journal Article
• Language: English
• Published: Beijing Science China Press 01-02-2021; Springer Nature B.V
• Subjects: Biomedical and Life Sciences; Divergence; Genetic resources; Genomes; Life Sciences; Nucleotide sequence; Oryza rufipogon; Plant breeding; Research Paper; Rice; Synteny; genome; genome sequencing; evolution; rice; Oryza rufipogon
• ISSN: 1674-7305; 1869-1889
• DOI: 10.1007/s11427-020-1738-x

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.