Abstract
The wild species of the genus
Oryza
contain a largely untapped reservoir of agronomically important genes for rice improvement. Here we report the 261-Mb
de novo
assembled genome sequence of
Oryza brachyantha
. Low activity of long-terminal repeat retrotransposons and massive internal deletions of ancient long-terminal repeat elements lead to the compact genome of
Oryza brachyantha
. We model 32,038 protein-coding genes in the
Oryza brachyantha
genome, of which only 70% are located in collinear positions in comparison with the rice genome. Analysing breakpoints of non-collinear genes suggests that double-strand break repair through non-homologous end joining has an important role in gene movement and erosion of collinearity in the
Oryza
genomes. Transition of euchromatin to heterochromatin in the rice genome is accompanied by segmental and tandem duplications, further expanded by transposable element insertions. The high-quality reference genome sequence of
Oryza brachyantha
provides an important resource for functional and evolutionary studies in the genus
Oryza
.
The wild rice species can be used as germplasm resources for this crop’s genetic improvement. Here Chen and colleagues report the
de novo
sequencing of the
O. brachyantha
genome, and identify the origin of genome size variation, the role of gene movement and its implications on heterochromatin evolution in the rice genome.