Whole Genome Sequencing of Oryza brachyantha Reveals Mechanisms Underlying Oryza Genome Evolution

We report the 261-Mb de novo assembled genome sequence of Oryza brachyantha, a wild relative of staple food crop Oryza sativa (rice). The compact genome of O. brachyantha resulted from the low activity of LTR retrotransposons and massive internal deletions of ancient LTR elements. We modeled 32,038 protein-coding genes in O. brachyantha genome, of which only 69% are located in collinear positions in comparison to the rice genome. Analyzing breakpoints of non-collinear genes suggests that double-strand break repair through non-homologous end joining (NHEJ) plays an important role in gene movement and erosion of collinearity in the Oryza genomes. Transition of euchromatin to heterochromatin occurred in the rice genome is accompanied by segmental and tandem duplications, further expanded by transposable element insertions. The high-quality reference genome sequence of O. brachyantha provides an important resource for functional and evolutionary studies in the genus Oryza.