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Abstract
The wild relatives of rice have adapted to different ecological environments and constitute a useful reservoir of agronomic traits for genetic improvement. Here we present the ~777 Mb de novo assembled genome sequence of Oryza granulata. Recent bursts of long-terminal repeat retrotransposons, especially RIRE2, led to a rapid twofold increase in genome size after O. granulata speciation. Universal centromeric tandem repeats are absent within its centromeres, while gypsy-type LTRs constitute the main centromere-specific repetitive elements. A total of 40,116 protein-coding genes were predicted in O. granulata, which is close to that of Oryza sativa. Both the copy number and function of genes involved in photosynthesis and energy production have undergone positive selection during the evolution of O. granulata, which might have facilitated its adaptation to the low light habitats. Together, our findings reveal the rapid genome expansion, distinctive centromere organization, and adaptive evolution of O. granulata.
Highlights
The wild relatives of rice have adapted to different ecological environments and constitute a useful reservoir of agronomic traits for genetic improvement
We annotated 40,116 genes in O. granulata, which is comparable to that of O. sativa[13]. Both the copy number and function of genes involved in photosynthesis and energy production have undergone positive selection, which would facilitate the adaptation of O. granulata to its low light habitats
By homology searching with sequences of RIRE2, ATLANTYS, and Copia long-terminal repeats (LTRs), we found that all the three LTRs are present in Oryza brachyantha and O. sativa (Mb) 40
Summary
The wild relatives of rice have adapted to different ecological environments and constitute a useful reservoir of agronomic traits for genetic improvement. A total of 40,116 protein-coding genes were predicted in O. granulata, which is close to that of Oryza sativa Both the copy number and function of genes involved in photosynthesis and energy production have undergone positive selection during the evolution of O. granulata, which might have facilitated its adaptation to the low light habitats. Comparative analysis of orthologous regions or whole-genomic sequences within closely related species, especially within the same genus, may shed more light on the mechanism of genome evolution. Its genome is dramatically expanded, with a genome size twice that of O. sativa, and contains a different set of repeat sequences relative to other Oryza species[14,15]. Comparative analyses of O. granulata with other sequenced Oryza genomes provide a unique opportunity to explore genomic size variation and adaptive evolution in this genus. Both the copy number and function of genes involved in photosynthesis and energy production have undergone positive selection, which would facilitate the adaptation of O. granulata to its low light habitats
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