Oryza genome evolution through a tetraploid lens

Alice Fornasiero, Tao Feng, Noor Al-Bader, Aseel Alsantely, Saule Mussurova, Nam V. Hoang, Gopal Misra, Yong Zhou, Leonardo Fabbian, Nahed Mohammed, Luis Rivera Serna, Manjula Thimma, Victor Llaca, Praveena Parakkal, David Kudrna, Dario Copetti, Shanmugam Rajasekar, Seunghee Lee, Jayson Talag, Chandler Sobel-Sorenson, Marie-Christine Carpentier, Olivier Panaud, Kenneth L. McNally, Jianwei Zhang, Andrea Zuccolo, M. Eric Schranz2 & Rod A. Wing

Nature Genetics; Volume 57 | May 2025 | 1287–129

Oryza is a remarkable genus comprising 27 species and 11 genome types, with ~3.4-fold genome size variation, that possesses a virtually untapped reservoir of genes that can be used for crop improvement and neodomestication. Here we present 11 chromosome-level assemblies (nine tetraploid, two diploid) in the context of ~15 million years of evolution and show that the core Oryza (sub)genome is only ~200 Mb and largely syntenic, whereas the remaining nuclear fractions (~80–600 Mb) are intermingled, plastic and rapidly evolving. For the halophyte Oryza coarctata, we found that despite detection of gene fractionation in the subgenomes, homoeologous genes were expressed at higher levels in one subgenome over the other in a mosaic form, demonstrating subgenome equivalence. The integration of these 11 new reference genomes with previously published genome datasets provides a nearly complete view of the consequences of evolution for genome diversification across the genus.

See https://www.nature.com/articles/s41588-025-02183-5

Fig. 1 | Overview of the syntenic landscape and large-scale structural rearrangements of 12 Oryza species (21 (sub)genomes) with the outgroup L. perrieri. Riparian plot showing macro-syntenic regions and large-scale structural rearrangements (large duplications and translocations) across the chromosomes of 12 Oryza species (21 (sub)genomes) and outgroup species L. perrieri. Genome types are shown according to the phylogenetic order in the genus, from the top (O. sativa (AA)) to the bottom (O. meyeriana (GG)). Each chromosome is colored as follows: Chr1, orange; Chr2, beige; Chr3, celeste; Chr4, steel blue; Chr5, navy blue; Chr6, deep purple; Chr7, plum; Chr8, magenta; Chr9, raspberry; Chr10, ruby; Chr11, coral; Chr12, salmon. Chromosomes are scaled by assembly length.