Oryza genome evolution through a tetraploid lens

Oryza is remarkable genus - with two domesticated (i.e. Asian and African rice) and 25 diploid and tetraploid wild species, 11 extant genome types, and a ∼3.4-fold genome size variation - that possesses a virtually untapped reservoir of genes that can be used for crop improvement. Here we unveil and interrogate 11 new chromosome-level assemblies of nine tetraploid and two diploid wild Oryza species in the context of ∼15 million years of evolution of the genus. We show that the core Oryza (sub)genome across all genome types is only ∼200 Mb and largely syntenic, while the remaining nuclear fractions, spanning ∼80-600 Mb, are intermingled, extremely plastic and rapidly evolving. For the halophyte O. coarctata , we show that - despite the detection of gene fractionation in the subgenomes - homoeologous genes are expressed at higher levels in one subgenome over the other in a mosaic form, thereby showing subgenome equivalence. The integration of these 11 new ultra-high quality reference genomes with our previously published genome data sets provide a nearly complete picture of the consequences of natural and artificial selection across the evolutionary history of Oryza . This in turn opens the door to unlock their genetic potential for future crop improvement and neodomestication. ### Competing Interest Statement The authors have declared no competing interest.