Evolution and diversity of the wild rice Oryza officinalis Complex, across continents, genome types, and ploidy levels
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. Usi...
| Autores principales: | , , , , , , , , , , , , , , , , , , , , |
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| Formato: | Journal Article |
| Lenguaje: | Inglés |
| Publicado: |
Oxford University Press
2020
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| Materias: | |
| Acceso en línea: | https://hdl.handle.net/10568/164535 |
| _version_ | 1855542132888043520 |
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| author | Shenton, Matt Kobayashi, Masaaki Terashima, Shin Ohyanagi, Hajime Copetti, Dario Hernández-Hernández, Tania Zhang, Jianwei Ohmido, Nobuko Fujita, Masahiro Toyoda, Atsushi Ikawa, Hiroshi Fujiyama, Asao Furuumi, Hiroyasu Miyabayashi, Toshie Kubo, Takahiko Kudrna, David Wing, Rod Yano, Kentaro Nonomura, Ken-ichi Sato, Yutaka Kurata, Nori |
| author_browse | Copetti, Dario Fujita, Masahiro Fujiyama, Asao Furuumi, Hiroyasu Hernández-Hernández, Tania Ikawa, Hiroshi Kobayashi, Masaaki Kubo, Takahiko Kudrna, David Kurata, Nori Miyabayashi, Toshie Nonomura, Ken-ichi Ohmido, Nobuko Ohyanagi, Hajime Sato, Yutaka Shenton, Matt Terashima, Shin Toyoda, Atsushi Wing, Rod Yano, Kentaro Zhang, Jianwei |
| author_facet | Shenton, Matt Kobayashi, Masaaki Terashima, Shin Ohyanagi, Hajime Copetti, Dario Hernández-Hernández, Tania Zhang, Jianwei Ohmido, Nobuko Fujita, Masahiro Toyoda, Atsushi Ikawa, Hiroshi Fujiyama, Asao Furuumi, Hiroyasu Miyabayashi, Toshie Kubo, Takahiko Kudrna, David Wing, Rod Yano, Kentaro Nonomura, Ken-ichi Sato, Yutaka Kurata, Nori |
| author_sort | Shenton, Matt |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | 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. |
| format | Journal Article |
| id | CGSpace164535 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2020 |
| publishDateRange | 2020 |
| publishDateSort | 2020 |
| publisher | Oxford University Press |
| publisherStr | Oxford University Press |
| record_format | dspace |
| spelling | CGSpace1645352026-01-06T12:03:49Z Evolution and diversity of the wild rice Oryza officinalis Complex, across continents, genome types, and ploidy levels Shenton, Matt Kobayashi, Masaaki Terashima, Shin Ohyanagi, Hajime Copetti, Dario Hernández-Hernández, Tania Zhang, Jianwei Ohmido, Nobuko Fujita, Masahiro Toyoda, Atsushi Ikawa, Hiroshi Fujiyama, Asao Furuumi, Hiroyasu Miyabayashi, Toshie Kubo, Takahiko Kudrna, David Wing, Rod Yano, Kentaro Nonomura, Ken-ichi Sato, Yutaka Kurata, Nori ecology evolution behavior and systematics genetics 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. 2020-03-03 2024-12-19T12:54:00Z 2024-12-19T12:54:00Z Journal Article https://hdl.handle.net/10568/164535 en Open Access Oxford University Press Kurata, Nori. 2020. Evolution and diversity of the wild rice Oryza officinalis Complex, across continents, genome types, and ploidy levels. Genome Bioloy and Evolution, Volume 12, no. 4; pages 413-428. |
| spellingShingle | ecology evolution behavior and systematics genetics Shenton, Matt Kobayashi, Masaaki Terashima, Shin Ohyanagi, Hajime Copetti, Dario Hernández-Hernández, Tania Zhang, Jianwei Ohmido, Nobuko Fujita, Masahiro Toyoda, Atsushi Ikawa, Hiroshi Fujiyama, Asao Furuumi, Hiroyasu Miyabayashi, Toshie Kubo, Takahiko Kudrna, David Wing, Rod Yano, Kentaro Nonomura, Ken-ichi Sato, Yutaka Kurata, Nori Evolution and diversity of the wild rice Oryza officinalis Complex, across continents, genome types, and ploidy levels |
| title | Evolution and diversity of the wild rice Oryza officinalis Complex, across continents, genome types, and ploidy levels |
| title_full | Evolution and diversity of the wild rice Oryza officinalis Complex, across continents, genome types, and ploidy levels |
| title_fullStr | Evolution and diversity of the wild rice Oryza officinalis Complex, across continents, genome types, and ploidy levels |
| title_full_unstemmed | Evolution and diversity of the wild rice Oryza officinalis Complex, across continents, genome types, and ploidy levels |
| title_short | Evolution and diversity of the wild rice Oryza officinalis Complex, across continents, genome types, and ploidy levels |
| title_sort | evolution and diversity of the wild rice oryza officinalis complex across continents genome types and ploidy levels |
| topic | ecology evolution behavior and systematics genetics |
| url | https://hdl.handle.net/10568/164535 |
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