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.
Highlights
Background & SummaryAs one of the most important crops in the world, rice is the most water-consuming cereal
Braun) Heer was identified according to a spikelet fossil, which was found in an excavation site of Miocene age in Germany and appears to resemble the spikelet of extant O. granulata based on its morphology[3,4]
Our results showed that a total of 89,977 transcripts could be successfully aligned to the genome assembly with a mapping rate of 65.5%
Summary
As one of the most important crops in the world, rice is the most water-consuming cereal. Compared to that for other wild species closely related to cultivated rice, little effort has been made to perform genetic studies and germplasm exploitation in O. granulata due to the lack of a high-quality genome assembly. Great progress has been made in comparative genomics of cultivated rice and its wild relatives[1,12,13,14,15,16,17], with much of this work performed at the chromosome scale. Sequencing an additional genome of O. granulata from a genetically different population compared with the previously sequenced accession collected in India[11] is needed. The availability of a chromosome-scale genome of O. granulata will lay the foundation for further evolutionary studies as well as the improvement of desired agronomic traits relevant to rice breeding programmes. The obtained genome assembly will provide novel insights into the genomic diversity and genome evolution of the genus Oryza and enhance the exploration of precious wild rice germplasm resources
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