Evolution and diversity of the wild rice Oryza officinalis complex, across continents genome types, and ploidy levels.

Matt Shenton; Masaaki Kobayashi; Shin Terashima; Hajime Ohyanagi; Dario Copetti; Tania Hernández-Hernández; Jianwei Zhang; Nobuko Ohmido; Masahiro Fujita; Atsushi Toyoda; Hiroshi Ikawa; Asao Fujiyama; Hiroyasu Furuumi; Toshie Miyabayashi; Takahiko Kubo; David Kudrna; Rod Wing; Kentaro Yano; Ken-Ichi Nonomura; Yutaka Sato; Nori Kurata

doi:10.1093/gbe/evaa037

Evolution and diversity of the wild rice Oryza officinalis complex, across continents genome types, and ploidy levels.

Matt Shenton, Masaaki Kobayashi, Shin Terashima, Hajime Ohyanagi, Dario Copetti, Tania Hernández-Hernández, Jianwei Zhang, Nobuko Ohmido, Masahiro Fujita, Atsushi Toyoda, Hiroshi Ikawa, Asao Fujiyama, Hiroyasu Furuumi, Toshie Miyabayashi, Takahiko Kubo, David Kudrna, Rod Wing, Kentaro Yano, Ken-Ichi Nonomura, Yutaka SatoNori Kurata

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

22 Scopus citations

Abstract

The Oryza officinalis complex is the largest species group in Oryza, with more than nine species from four continents, and is a tertiary gene pool that can be exploited in breeding programs for the improvement of cultivated rice. Most diploid and tetraploid members of this group have a C genome. Using a new reference C genome for the diploid species Oryza officinalis, and draft genomes for two other C genome diploid species O. eichingeri and O. rhizomatis, we examine the influence of transposable elements on genome structure and provide a detailed phylogeny and evolutionary history of the Oryza C genomes. The O. officinalis genome is 1.6 times larger than the A genome of cultivated O. sativa, mostly due to proliferation of Gypsy type long-terminal repeat (LTR) transposable elements, but overall syntenic relationships are maintained with other Oryza genomes (A, B and F). Draft genome assemblies of the two other C genome diploid species, O. eichingeri and O. rhizomatis, and short-read resequencing of a series of other C genome species and accessions reveal that after the divergence of the C genome progenitor, there was still a substantial degree of variation within the C genome species through proliferation and loss of both DNA and LTR transposable elements. We provide a detailed phylogeny and evolutionary history of the Oryza C genomes, and a genomic resource for the exploitation of the Oryza tertiary gene pool.

Original language	English (US)
Pages (from-to)	413-428
Number of pages	16
Journal	Genome biology and evolution
Volume	12
Issue number	4
DOIs	https://doi.org/10.1093/gbe/evaa037
State	Published - Mar 4 2020

Bibliographical note

KAUST Repository Item: Exported on 2020-10-01
Acknowledgements: This work was supported by the NBRP Genome Information Upgrading Program (NBRP MEXT, Japan) for NK; the National Bioresource Project (NBRP AMED, Japan) for YS; and the Systems Functional Genetics Project of the Transdisciplinary Research Integration Center, ROIS, Japan for NK.

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10.1093/gbe/evaa037

https://repository.kaust.edu.sa/bitstream/10754/661931/1/evaa037.pdf

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Shenton, M., Kobayashi, M., Terashima, S., Ohyanagi, H., Copetti, D., Hernández-Hernández, T., Zhang, J., Ohmido, N., Fujita, M., Toyoda, A., Ikawa, H., Fujiyama, A., Furuumi, H., Miyabayashi, T., Kubo, T., Kudrna, D., Wing, R., Yano, K., Nonomura, K.-I., ... Kurata, N. (2020). Evolution and diversity of the wild rice Oryza officinalis complex, across continents genome types, and ploidy levels. Genome biology and evolution, 12(4), 413-428. https://doi.org/10.1093/gbe/evaa037

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title = "Evolution and diversity of the wild rice Oryza officinalis complex, across continents genome types, and ploidy levels.",

abstract = "The Oryza officinalis complex is the largest species group in Oryza, with more than nine species from four continents, and is a tertiary gene pool that can be exploited in breeding programs for the improvement of cultivated rice. Most diploid and tetraploid members of this group have a C genome. Using a new reference C genome for the diploid species Oryza officinalis, and draft genomes for two other C genome diploid species O. eichingeri and O. rhizomatis, we examine the influence of transposable elements on genome structure and provide a detailed phylogeny and evolutionary history of the Oryza C genomes. The O. officinalis genome is 1.6 times larger than the A genome of cultivated O. sativa, mostly due to proliferation of Gypsy type long-terminal repeat (LTR) transposable elements, but overall syntenic relationships are maintained with other Oryza genomes (A, B and F). Draft genome assemblies of the two other C genome diploid species, O. eichingeri and O. rhizomatis, and short-read resequencing of a series of other C genome species and accessions reveal that after the divergence of the C genome progenitor, there was still a substantial degree of variation within the C genome species through proliferation and loss of both DNA and LTR transposable elements. We provide a detailed phylogeny and evolutionary history of the Oryza C genomes, and a genomic resource for the exploitation of the Oryza tertiary gene pool.",

author = "Matt Shenton and Masaaki Kobayashi and Shin Terashima and Hajime Ohyanagi and Dario Copetti and Tania Hern{\'a}ndez-Hern{\'a}ndez and Jianwei Zhang and Nobuko Ohmido and Masahiro Fujita and Atsushi Toyoda and Hiroshi Ikawa and Asao Fujiyama and Hiroyasu Furuumi and Toshie Miyabayashi and Takahiko Kubo and David Kudrna and Rod Wing and Kentaro Yano and Ken-Ichi Nonomura and Yutaka Sato and Nori Kurata",

note = "KAUST Repository Item: Exported on 2020-10-01 Acknowledgements: This work was supported by the NBRP Genome Information Upgrading Program (NBRP MEXT, Japan) for NK; the National Bioresource Project (NBRP AMED, Japan) for YS; and the Systems Functional Genetics Project of the Transdisciplinary Research Integration Center, ROIS, Japan for NK.",

year = "2020",

month = mar,

day = "4",

doi = "10.1093/gbe/evaa037",

language = "English (US)",

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Shenton, M, Kobayashi, M, Terashima, S, Ohyanagi, H, Copetti, D, Hernández-Hernández, T, Zhang, J, Ohmido, N, Fujita, M, Toyoda, A, Ikawa, H, Fujiyama, A, Furuumi, H, Miyabayashi, T, Kubo, T, Kudrna, D, Wing, R, Yano, K, Nonomura, K-I, Sato, Y & Kurata, N 2020, 'Evolution and diversity of the wild rice Oryza officinalis complex, across continents genome types, and ploidy levels.', Genome biology and evolution, vol. 12, no. 4, pp. 413-428. https://doi.org/10.1093/gbe/evaa037

TY - JOUR

T1 - Evolution and diversity of the wild rice Oryza officinalis complex, across continents genome types, and ploidy levels.

AU - Shenton, Matt

AU - Kobayashi, Masaaki

AU - Terashima, Shin

AU - Ohyanagi, Hajime

AU - Copetti, Dario

AU - Hernández-Hernández, Tania

AU - Zhang, Jianwei

AU - Ohmido, Nobuko

AU - Fujita, Masahiro

AU - Toyoda, Atsushi

AU - Ikawa, Hiroshi

AU - Fujiyama, Asao

AU - Furuumi, Hiroyasu

AU - Miyabayashi, Toshie

AU - Kubo, Takahiko

AU - Kudrna, David

AU - Wing, Rod

AU - Yano, Kentaro

AU - Nonomura, Ken-Ichi

AU - Sato, Yutaka

AU - Kurata, Nori

N1 - KAUST Repository Item: Exported on 2020-10-01 Acknowledgements: This work was supported by the NBRP Genome Information Upgrading Program (NBRP MEXT, Japan) for NK; the National Bioresource Project (NBRP AMED, Japan) for YS; and the Systems Functional Genetics Project of the Transdisciplinary Research Integration Center, ROIS, Japan for NK.

PY - 2020/3/4

Y1 - 2020/3/4

N2 - The Oryza officinalis complex is the largest species group in Oryza, with more than nine species from four continents, and is a tertiary gene pool that can be exploited in breeding programs for the improvement of cultivated rice. Most diploid and tetraploid members of this group have a C genome. Using a new reference C genome for the diploid species Oryza officinalis, and draft genomes for two other C genome diploid species O. eichingeri and O. rhizomatis, we examine the influence of transposable elements on genome structure and provide a detailed phylogeny and evolutionary history of the Oryza C genomes. The O. officinalis genome is 1.6 times larger than the A genome of cultivated O. sativa, mostly due to proliferation of Gypsy type long-terminal repeat (LTR) transposable elements, but overall syntenic relationships are maintained with other Oryza genomes (A, B and F). Draft genome assemblies of the two other C genome diploid species, O. eichingeri and O. rhizomatis, and short-read resequencing of a series of other C genome species and accessions reveal that after the divergence of the C genome progenitor, there was still a substantial degree of variation within the C genome species through proliferation and loss of both DNA and LTR transposable elements. We provide a detailed phylogeny and evolutionary history of the Oryza C genomes, and a genomic resource for the exploitation of the Oryza tertiary gene pool.

AB - The Oryza officinalis complex is the largest species group in Oryza, with more than nine species from four continents, and is a tertiary gene pool that can be exploited in breeding programs for the improvement of cultivated rice. Most diploid and tetraploid members of this group have a C genome. Using a new reference C genome for the diploid species Oryza officinalis, and draft genomes for two other C genome diploid species O. eichingeri and O. rhizomatis, we examine the influence of transposable elements on genome structure and provide a detailed phylogeny and evolutionary history of the Oryza C genomes. The O. officinalis genome is 1.6 times larger than the A genome of cultivated O. sativa, mostly due to proliferation of Gypsy type long-terminal repeat (LTR) transposable elements, but overall syntenic relationships are maintained with other Oryza genomes (A, B and F). Draft genome assemblies of the two other C genome diploid species, O. eichingeri and O. rhizomatis, and short-read resequencing of a series of other C genome species and accessions reveal that after the divergence of the C genome progenitor, there was still a substantial degree of variation within the C genome species through proliferation and loss of both DNA and LTR transposable elements. We provide a detailed phylogeny and evolutionary history of the Oryza C genomes, and a genomic resource for the exploitation of the Oryza tertiary gene pool.

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UR - https://academic.oup.com/gbe/advance-article/doi/10.1093/gbe/evaa037/5775507

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DO - 10.1093/gbe/evaa037

M3 - Article

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SN - 1759-6653

VL - 12

SP - 413

EP - 428

JO - Genome biology and evolution

JF - Genome biology and evolution

IS - 4

ER -

Evolution and diversity of the wild rice Oryza officinalis complex, across continents genome types, and ploidy levels.

Abstract

Bibliographical note

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Oryza officinalis complex gene and repeat annotations

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Evolution and diversity of the wild rice Oryza officinalis complex, across continents genome types, and ploidy levels.

Abstract

Bibliographical note

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Oryza officinalis complex gene and repeat annotations

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