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.
UR - http://hdl.handle.net/10754/661931
UR - https://academic.oup.com/gbe/advance-article/doi/10.1093/gbe/evaa037/5775507
UR - http://www.scopus.com/inward/record.url?scp=85084167044&partnerID=8YFLogxK
U2 - 10.1093/gbe/evaa037
DO - 10.1093/gbe/evaa037
M3 - Article
C2 - 32125373
VL - 12
SP - 413
EP - 428
JO - Genome biology and evolution
JF - Genome biology and evolution
SN - 1759-6653
IS - 4
ER -