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; Eric Schranz; Rod A. Wing

doi:10.1038/s41588-025-02183-5

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-SorensonMarie Christine Carpentier, Olivier Panaud, Kenneth L. McNally, Jianwei Zhang, Andrea Zuccolo^*, Eric Schranz^*, Rod A. Wing^*

^*Corresponding author for this work

Research output: Contribution to journal › Article › Academic › peer-review

1 Citation (Scopus)

Abstract

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.

Original language	English
Article number	113
Pages (from-to)	1287-1297
Journal	Nature Genetics
Volume	57
Issue number	5
Early online date	28 Apr 2025
DOIs	https://doi.org/10.1038/s41588-025-02183-5
Publication status	Published - 2025

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Fornasiero, A., Feng, T., Al-Bader, N., Alsantely, A., Mussurova, S., Hoang, N. V., Misra, G., Zhou, Y., Fabbian, L., Mohammed, N., Rivera Serna, L., Thimma, M., Llaca, V., Parakkal, P., Kudrna, D., Copetti, D., Rajasekar, S., Lee, S., Talag, J., ... Wing, R. A. (2025). Oryza genome evolution through a tetraploid lens. Nature Genetics, 57(5), 1287-1297. Article 113. https://doi.org/10.1038/s41588-025-02183-5

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title = "Oryza genome evolution through a tetraploid lens",

abstract = "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.",

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

year = "2025",

doi = "10.1038/s41588-025-02183-5",

language = "English",

volume = "57",

pages = "1287--1297",

journal = "Nature Genetics",

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Fornasiero, A, Feng, T, Al-Bader, N, Alsantely, A, Mussurova, S, Hoang, NV, Misra, G, Zhou, Y, Fabbian, L, Mohammed, N, Rivera Serna, L, Thimma, M, Llaca, V, Parakkal, P, Kudrna, D, Copetti, D, Rajasekar, S, Lee, S, Talag, J, Sobel-Sorenson, C, Carpentier, MC, Panaud, O, McNally, KL, Zhang, J, Zuccolo, A, Schranz, E & Wing, RA 2025, 'Oryza genome evolution through a tetraploid lens', Nature Genetics, vol. 57, no. 5, 113, pp. 1287-1297. https://doi.org/10.1038/s41588-025-02183-5

TY - JOUR

T1 - Oryza genome evolution through a tetraploid lens

AU - Fornasiero, Alice

AU - Feng, Tao

AU - Al-Bader, Noor

AU - Alsantely, Aseel

AU - Mussurova, Saule

AU - Hoang, Nam V.

AU - Misra, Gopal

AU - Zhou, Yong

AU - Fabbian, Leonardo

AU - Mohammed, Nahed

AU - Rivera Serna, Luis

AU - Thimma, Manjula

AU - Llaca, Victor

AU - Parakkal, Praveena

AU - Kudrna, David

AU - Copetti, Dario

AU - Rajasekar, Shanmugam

AU - Lee, Seunghee

AU - Talag, Jayson

AU - Sobel-Sorenson, Chandler

AU - Carpentier, Marie Christine

AU - Panaud, Olivier

AU - McNally, Kenneth L.

AU - Zhang, Jianwei

AU - Zuccolo, Andrea

AU - Schranz, Eric

AU - Wing, Rod A.

PY - 2025

Y1 - 2025

N2 - 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.

AB - 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.

U2 - 10.1038/s41588-025-02183-5

DO - 10.1038/s41588-025-02183-5

M3 - Article

AN - SCOPUS:105003763297

SN - 1061-4036

VL - 57

SP - 1287

EP - 1297

JO - Nature Genetics

JF - Nature Genetics

IS - 5

M1 - 113

ER -

Oryza genome evolution through a tetraploid lens

Abstract

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