Abstract

Exploiting novel gene sources from wild relatives has proven to be an efficient approach to advance crop genetic breeding efforts. Oryza granulata, with the GG genome type, occupies the basal position of the Oryza phylogeny and has the second largest genome (~882 Mb). As an upland wild rice species, it possesses renowned traits that distinguish it from other Oryza species, such as tolerance to shade and drought, immunity to bacterial blight and resistance to the brown planthopper. Here, we generated a 736.66-Mb genome assembly of O. granulata with 40,131 predicted protein-coding genes. With Hi-C data, for the first time, we anchored ~98.2% of the genome assembly to the twelve pseudo-chromosomes. This chromosome-length genome assembly of O. granulata will provide novel insights into rice genome evolution, enhance our efforts to search for new genes for future rice breeding programmes and facilitate the conservation of germplasm of this endangered wild rice species.

Measurement(s)

DNA • RNA • transcriptome • genome coverage • sequence_assembly • sequence feature annotation

Technology Type(s)

DNA sequencing • RNA sequencing • flow cytometry method • computational modeling technique • sequence assembly process • sequence annotation

Sample Characteristic - Organism

Oryza granulata

Machine-accessible metadata file describing the reported data: 10.6084/m9.figshare.12063198

Details

Title
The draft genome sequence of an upland wild rice species, Oryza granulata
Author
Shi, Cong 1 ; Li, Wei 2 ; Zhang Qun-Jie 2 ; Zhang, Yun 3 ; Tong, Yan 3 ; Li, Kui 2 ; Yun-Long, Liu 3 ; Li-Zhi, Gao 4   VIAFID ORCID Logo 

1  Chinese Academy of Sciences, Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwestern China, Kunming Institute of Botany, Kunming, China (GRID:grid.9227.e) (ISNI:0000000119573309); University of Chinese Academy of Sciences, Beijing, China (GRID:grid.410726.6) (ISNI:0000 0004 1797 8419) 
2  South China Agricultural University, Institution of Genomics and Bioinformatics, Guangzhou, China (GRID:grid.20561.30) (ISNI:0000 0000 9546 5767) 
3  Chinese Academy of Sciences, Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwestern China, Kunming Institute of Botany, Kunming, China (GRID:grid.9227.e) (ISNI:0000000119573309) 
4  Chinese Academy of Sciences, Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwestern China, Kunming Institute of Botany, Kunming, China (GRID:grid.9227.e) (ISNI:0000000119573309); South China Agricultural University, Institution of Genomics and Bioinformatics, Guangzhou, China (GRID:grid.20561.30) (ISNI:0000 0000 9546 5767) 
Publication year
2020
Publication date
2020
Publisher
Nature Publishing Group
e-ISSN
20524463
Source type
Scholarly Journal
Language of publication
English
DOI
https://doi.org/10.1038/s41597-020-0470-2
ProQuest document ID
2396287925
Copyright
© The Author(s) 2020. This work is published under http://creativecommons.org/licenses/by/4.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.