Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza
Abstract
The genus Oryza is a model system for the study of molecular evolution over time scales ranging from a few thousand to 15 million years. Using 13 reference genomes spanning the Oryza species tree, we show that despite few large-scale chromosomal rearrangements rapid species diversification is mirrored by lineage-specific emergence and turnover of many novel elements, including transposons, and potential new coding and noncoding genes. Our study resolves controversial areas of the Oryza phylogeny, showing a complex history of introgression among different chromosomes in the young 'AA' subclade containing the two domesticated species. This study highlights the prevalence of functionally coupled disease resistance genes and identifies many new haplotypes of potential use for future crop protection. Finally, this study marks a milestone in modern rice research with the release of a complete long-read assembly of IR 8 'Miracle Rice', which relieved famine and drove the Green Revolution in Asia 50 years ago.
- Authors:
-
more »
- Cold Spring Harbor Lab., NY (United States)
- Univ. of Arizona, Tucson, AZ (United States); Phyzen, Inc., Seoul (South Korea)
- Univ. of Arizona, Tucson, AZ (United States); International Rice Research Inst., Los Baños (Philippines)
- Univ. of Arizona, Tucson, AZ (United States)
- Univ. of Chicago, IL (United States)
- Cold Spring Harbor Lab., NY (United States); Univ. of Arizona, Tucson, AZ (United States)
- Univ. of Georgia, Athens, GA (United States)
- Wayne State Univ., Detroit, MI (United States)
- Chinese Academy of Sciences (CAS), Beijing (China)
- Univ. of Arizona, Tucson, AZ (United States); Friedrich Miescher Lab. of the Max Planck Society, Tübingen (Germany)
- Univ. of Arizona, Tucson, AZ (United States); Univ. of Hohenheim, Stuttgart (Germany)
- Max Planck Inst. for Developmental Biology, Tübingen (Germany)
- Univ. of Arizona, Tucson, AZ (United States); Rice Experiment Station, Biggs, CA (United States)
- Univ. of Arizona, Tucson, AZ (United States); Sant'Anna School of Advanced Studies, Pisa (Italy)
- Univ. of Arizona, Tucson, AZ (United States); DuPont-Pioneer, Johnston, IA (United States)
- Univ. of Arizona, Tucson, AZ (United States); BIOS-Parque Los Yarumos, Manizales (Colombia)
- Academia Sinica, Taipei (Taiwan); National Taiwan Univ., Taipei (Taiwan)
- Academia Sinica, Taipei (Taiwan); Ghent Univ. (Belgium)
- Academia Sinica, Taipei (Taiwan)
- Academia Sinica, Taipei (Taiwan); Forestry and Forest Products Research Inst., Tsukuba (Japan)
- Chinese Academy of Sciences (CAS), Shanghai (China)
- Univ. of Perpignan-Domitian (France)
- Federal Univ. of Pelotas (Brazil)
- Univ. of Maryland, College Park, MD (United States)
- International Rice Research Inst., Los Baños (Philippines)
- HudsonAlpha Inst. for Biotechnology, Huntsville, AL (United States)
- Univ. of Zurich (Switzerland)
- Univ. of Queensland, Brisbane (Australia)
- National Inst. of Genetics, Mishima (Japan)
- Cold Spring Harbor Lab., NY (United States); US Dept. of Agriculture-Agricultural Research Service (USDA-ARS), Ithaca, NY (United States)
- Publication Date:
- Research Org.:
- Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States). National Energy Research Scientific Computing Center (NERSC)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER); National Science Foundation (NSF)
- OSTI Identifier:
- 1543774
- Alternate Identifier(s):
- OSTI ID: 1616059
- Grant/Contract Number:
- AC02-05CH11231
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Nature Genetics
- Additional Journal Information:
- Journal Volume: 50; Journal Issue: 2; Journal ID: ISSN 1061-4036
- Publisher:
- Nature Publishing Group
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES
Citation Formats
Stein, Joshua C., Yu, Yeisoo, Copetti, Dario, Zwickl, Derrick J., Zhang, Li, Zhang, Chengjun, Chougule, Kapeel, Gao, Dongying, Iwata, Aiko, Goicoechea, Jose Luis, Wei, Sharon, Wang, Jun, Liao, Yi, Wang, Muhua, Jacquemin, Julie, Becker, Claude, Kudrna, Dave, Zhang, Jianwei, Londono, Carlos E. M., Song, Xiang, Lee, Seunghee, Sanchez, Paul, Zuccolo, Andrea, Ammiraju, Jetty S. S., Talag, Jayson, Danowitz, Ann, Rivera, Luis F., Gschwend, Andrea R., Noutsos, Christos, Wu, Cheng-chieh, Kao, Shu-min, Zeng, Jhih-wun, Wei, Fu-jin, Zhao, Qiang, Feng, Qi, El Baidouri, Moaine, Carpentier, Marie-Christine, Lasserre, Eric, Cooke, Richard, Rosa Farias, Daniel da, da Maia, Luciano Carlos, dos Santos, Railson S., Nyberg, Kevin G., McNally, Kenneth L., Mauleon, Ramil, Alexandrov, Nickolai, Schmutz, Jeremy, Flowers, Dave, Fan, Chuanzhu, Weigel, Detlef, Jena, Kshirod K., Wicker, Thomas, Chen, Mingsheng, Han, Bin, Henry, Robert, Hsing, Yue-ie C., Kurata, Nori, de Oliveira, Antonio Costa, Panaud, Olivier, Jackson, Scott A., Machado, Carlos A., Sanderson, Michael J., Long, Manyuan, Ware, Doreen, and Wing, Rod A. Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza. United States: N. p., 2018.
Web. doi:10.1038/s41588-018-0040-0.
Stein, Joshua C., Yu, Yeisoo, Copetti, Dario, Zwickl, Derrick J., Zhang, Li, Zhang, Chengjun, Chougule, Kapeel, Gao, Dongying, Iwata, Aiko, Goicoechea, Jose Luis, Wei, Sharon, Wang, Jun, Liao, Yi, Wang, Muhua, Jacquemin, Julie, Becker, Claude, Kudrna, Dave, Zhang, Jianwei, Londono, Carlos E. M., Song, Xiang, Lee, Seunghee, Sanchez, Paul, Zuccolo, Andrea, Ammiraju, Jetty S. S., Talag, Jayson, Danowitz, Ann, Rivera, Luis F., Gschwend, Andrea R., Noutsos, Christos, Wu, Cheng-chieh, Kao, Shu-min, Zeng, Jhih-wun, Wei, Fu-jin, Zhao, Qiang, Feng, Qi, El Baidouri, Moaine, Carpentier, Marie-Christine, Lasserre, Eric, Cooke, Richard, Rosa Farias, Daniel da, da Maia, Luciano Carlos, dos Santos, Railson S., Nyberg, Kevin G., McNally, Kenneth L., Mauleon, Ramil, Alexandrov, Nickolai, Schmutz, Jeremy, Flowers, Dave, Fan, Chuanzhu, Weigel, Detlef, Jena, Kshirod K., Wicker, Thomas, Chen, Mingsheng, Han, Bin, Henry, Robert, Hsing, Yue-ie C., Kurata, Nori, de Oliveira, Antonio Costa, Panaud, Olivier, Jackson, Scott A., Machado, Carlos A., Sanderson, Michael J., Long, Manyuan, Ware, Doreen, & Wing, Rod A. Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza. United States. https://doi.org/10.1038/s41588-018-0040-0
Stein, Joshua C., Yu, Yeisoo, Copetti, Dario, Zwickl, Derrick J., Zhang, Li, Zhang, Chengjun, Chougule, Kapeel, Gao, Dongying, Iwata, Aiko, Goicoechea, Jose Luis, Wei, Sharon, Wang, Jun, Liao, Yi, Wang, Muhua, Jacquemin, Julie, Becker, Claude, Kudrna, Dave, Zhang, Jianwei, Londono, Carlos E. M., Song, Xiang, Lee, Seunghee, Sanchez, Paul, Zuccolo, Andrea, Ammiraju, Jetty S. S., Talag, Jayson, Danowitz, Ann, Rivera, Luis F., Gschwend, Andrea R., Noutsos, Christos, Wu, Cheng-chieh, Kao, Shu-min, Zeng, Jhih-wun, Wei, Fu-jin, Zhao, Qiang, Feng, Qi, El Baidouri, Moaine, Carpentier, Marie-Christine, Lasserre, Eric, Cooke, Richard, Rosa Farias, Daniel da, da Maia, Luciano Carlos, dos Santos, Railson S., Nyberg, Kevin G., McNally, Kenneth L., Mauleon, Ramil, Alexandrov, Nickolai, Schmutz, Jeremy, Flowers, Dave, Fan, Chuanzhu, Weigel, Detlef, Jena, Kshirod K., Wicker, Thomas, Chen, Mingsheng, Han, Bin, Henry, Robert, Hsing, Yue-ie C., Kurata, Nori, de Oliveira, Antonio Costa, Panaud, Olivier, Jackson, Scott A., Machado, Carlos A., Sanderson, Michael J., Long, Manyuan, Ware, Doreen, and Wing, Rod A. Mon .
"Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza". United States. https://doi.org/10.1038/s41588-018-0040-0. https://www.osti.gov/servlets/purl/1543774.
@article{osti_1543774,
title = {Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza},
author = {Stein, Joshua C. and Yu, Yeisoo and Copetti, Dario and Zwickl, Derrick J. and Zhang, Li and Zhang, Chengjun and Chougule, Kapeel and Gao, Dongying and Iwata, Aiko and Goicoechea, Jose Luis and Wei, Sharon and Wang, Jun and Liao, Yi and Wang, Muhua and Jacquemin, Julie and Becker, Claude and Kudrna, Dave and Zhang, Jianwei and Londono, Carlos E. M. and Song, Xiang and Lee, Seunghee and Sanchez, Paul and Zuccolo, Andrea and Ammiraju, Jetty S. S. and Talag, Jayson and Danowitz, Ann and Rivera, Luis F. and Gschwend, Andrea R. and Noutsos, Christos and Wu, Cheng-chieh and Kao, Shu-min and Zeng, Jhih-wun and Wei, Fu-jin and Zhao, Qiang and Feng, Qi and El Baidouri, Moaine and Carpentier, Marie-Christine and Lasserre, Eric and Cooke, Richard and Rosa Farias, Daniel da and da Maia, Luciano Carlos and dos Santos, Railson S. and Nyberg, Kevin G. and McNally, Kenneth L. and Mauleon, Ramil and Alexandrov, Nickolai and Schmutz, Jeremy and Flowers, Dave and Fan, Chuanzhu and Weigel, Detlef and Jena, Kshirod K. and Wicker, Thomas and Chen, Mingsheng and Han, Bin and Henry, Robert and Hsing, Yue-ie C. and Kurata, Nori and de Oliveira, Antonio Costa and Panaud, Olivier and Jackson, Scott A. and Machado, Carlos A. and Sanderson, Michael J. and Long, Manyuan and Ware, Doreen and Wing, Rod A.},
abstractNote = {The genus Oryza is a model system for the study of molecular evolution over time scales ranging from a few thousand to 15 million years. Using 13 reference genomes spanning the Oryza species tree, we show that despite few large-scale chromosomal rearrangements rapid species diversification is mirrored by lineage-specific emergence and turnover of many novel elements, including transposons, and potential new coding and noncoding genes. Our study resolves controversial areas of the Oryza phylogeny, showing a complex history of introgression among different chromosomes in the young 'AA' subclade containing the two domesticated species. This study highlights the prevalence of functionally coupled disease resistance genes and identifies many new haplotypes of potential use for future crop protection. Finally, this study marks a milestone in modern rice research with the release of a complete long-read assembly of IR 8 'Miracle Rice', which relieved famine and drove the Green Revolution in Asia 50 years ago.},
doi = {10.1038/s41588-018-0040-0},
journal = {Nature Genetics},
number = 2,
volume = 50,
place = {United States},
year = {Mon Jan 22 00:00:00 EST 2018},
month = {Mon Jan 22 00:00:00 EST 2018}
}
Web of Science
Works referenced in this record:
The Oryza BAC resource: a genus-wide and genome scale tool for exploring rice genome evolution and leveraging useful genetic diversity from wild relatives
journal, January 2010
- Ammiraju, Jetty S. S.; Song, Xiang; Luo, Meizhong
- Breeding Science, Vol. 60, Issue 5
Kalign – an accurate and fast multiple sequence alignment algorithm
journal, December 2005
- Lassmann, Timo; Sonnhammer, Erik LL
- BMC Bioinformatics, Vol. 6, Issue 1
The Pib gene for rice blast resistance belongs to the nucleotide binding and leucine-rich repeat class of plant disease resistance genes
journal, July 1999
- Wang, Zi-Xuan; Yano, Masahiro; Yamanouchi, Utako
- The Plant Journal, Vol. 19, Issue 1
DAGchainer: a tool for mining segmental genome duplications and synteny
journal, July 2004
- Haas, B. J.; Delcher, A. L.; Wortman, J. R.
- Bioinformatics, Vol. 20, Issue 18
genoPlotR: comparative gene and genome visualization in R
journal, July 2010
- Guy, L.; Roat Kultima, J.; Andersson, S. G. E.
- Bioinformatics, Vol. 26, Issue 18
CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
journal, January 1994
- Thompson, Julie D.; Higgins, Desmond G.; Gibson, Toby J.
- Nucleic Acids Research, Vol. 22, Issue 22, p. 4673-4680
Gramene 2013: comparative plant genomics resources
journal, November 2013
- Monaco, Marcela K.; Stein, Joshua; Naithani, Sushma
- Nucleic Acids Research, Vol. 42, Issue D1
TreeFam: 2008 Update
journal, December 2007
- Ruan, J.; Li, H.; Chen, Z.
- Nucleic Acids Research, Vol. 36, Issue Database
Gene tree discordance, phylogenetic inference and the multispecies coalescent
journal, June 2009
- Degnan, James H.; Rosenberg, Noah A.
- Trends in Ecology & Evolution, Vol. 24, Issue 6
“Out of Pollen” Hypothesis for Origin of New Genes in Flowering Plants: Study from Arabidopsis thaliana
journal, September 2014
- Wu, Dong-Dong; Wang, Xin; Li, Yan
- Genome Biology and Evolution, Vol. 6, Issue 10
Durable panicle blast-resistance gene Pb1 encodes an atypical CC-NBS-LRR protein and was generated by acquiring a promoter through local genome duplication: Durable panicle blast resistance gene Pb1
journal, October 2010
- Hayashi, Nagao; Inoue, Haruhiko; Kato, Takahiro
- The Plant Journal, Vol. 64, Issue 3
Database resources of the National Center for Biotechnology Information
journal, December 2007
- Wheeler, D. L.; Barrett, T.; Benson, D. A.
- Nucleic Acids Research, Vol. 36, Issue Database
Genome-Wide Patterns of Nucleotide Polymorphism in Domesticated Rice
journal, January 2005
- Caicedo, Ana; Williamson, Scott; Hernandez, Ryan D.
- PLoS Genetics, Vol. preprint, Issue 2007
Gramene database in 2010: updates and extensions
journal, November 2010
- Youens-Clark, K.; Buckler, E.; Casstevens, T.
- Nucleic Acids Research, Vol. 39, Issue Database
UVB sensitivity and cyclobutane pyrimidine dimer (CPD) photolyase genotypes in cultivated and wild rice species
journal, January 2008
- Iwamatsu, Yutaka; Aoki, Chizuru; Takahashi, Masaaki
- Photochemical & Photobiological Sciences, Vol. 7, Issue 3
A recent duplication revisited: phylogenetic analysis reveals an ancestral duplication highly-conserved throughout the Oryza genus and beyond
journal, January 2009
- Jacquemin, Julie; Laudié, Michèle; Cooke, Richard
- BMC Plant Biology, Vol. 9, Issue 1
The map-based sequence of the rice genome
journal, August 2005
- ,
- Nature, Vol. 436, Issue 7052, p. 793-800
Genome and Comparative Transcriptomics of African Wild Rice Oryza longistaminata Provide Insights into Molecular Mechanism of Rhizomatousness and Self-Incompatibility
journal, November 2015
- Zhang, Yesheng; Zhang, Shilai; Liu, Hui
- Molecular Plant, Vol. 8, Issue 11
Tandem and segmental gene duplication and recombination in the evolution of plant disease resistance genes
journal, March 2004
- Leister, Dario
- Trends in Genetics, Vol. 20, Issue 3
MAKER-P: A Tool Kit for the Rapid Creation, Management, and Quality Control of Plant Genome Annotations
journal, December 2013
- Campbell, Michael S.; Law, MeiYee; Holt, Carson
- Plant Physiology, Vol. 164, Issue 2
Mugsy: fast multiple alignment of closely related whole genomes
journal, December 2010
- Angiuoli, Samuel V.; Salzberg, Steven L.
- Bioinformatics, Vol. 27, Issue 3
Rice Pi5 -Mediated Resistance to Magnaporthe oryzae Requires the Presence of Two Coiled-Coil–Nucleotide-Binding–Leucine-Rich Repeat Genes
journal, January 2009
- Lee, Sang-Kyu; Song, Min-Young; Seo, Young-Su
- Genetics, Vol. 181, Issue 4
Genome-Wide Patterns of Nucleotide Polymorphism in Domesticated Rice
journal, January 2007
- Caicedo, Ana L.; Williamson, Scott H.; Hernandez, Ryan D.
- PLoS Genetics, Vol. 3, Issue 9
Transposable Elements Are Major Contributors to the Origin, Diversification, and Regulation of Vertebrate Long Noncoding RNAs
journal, April 2013
- Kapusta, Aurélie; Kronenberg, Zev; Lynch, Vincent J.
- PLoS Genetics, Vol. 9, Issue 4
Molecular evidence for a single evolutionary origin of domesticated rice
journal, May 2011
- Molina, J.; Sikora, M.; Garud, N.
- Proceedings of the National Academy of Sciences, Vol. 108, Issue 20
The life cycle of Drosophila orphan genes
text, January 2014
- Palmieri, Nicola; Kosiol, Carolin; Schlötterer, Christian
- arXiv
A maximum pseudo-likelihood approach for estimating species trees under the coalescent model
journal, January 2010
- Liu, Liang; Yu, Lili; Edwards, Scott V.
- BMC Evolutionary Biology, Vol. 10, Issue 1
MRBAYES: Bayesian inference of phylogenetic trees
journal, August 2001
- Huelsenbeck, J. P.; Ronquist, F.
- Bioinformatics, Vol. 17, Issue 8
Comparative analysis of plant immune receptor architectures uncovers host proteins likely targeted by pathogens
journal, February 2016
- Sarris, Panagiotis F.; Cevik, Volkan; Dagdas, Gulay
- BMC Biology, Vol. 14, Issue 1
Analyses of LTR-Retrotransposon Structures Reveal Recent and Rapid Genomic DNA Loss in Rice
journal, May 2004
- Ma, J.
- Genome Research, Vol. 14, Issue 5
Transposable elements reveal a stem cell-specific class of long noncoding RNAs
journal, January 2012
- Kelley, David; Rinn, John
- Genome Biology, Vol. 13, Issue 11
M-Coffee: combining multiple sequence alignment methods with T-Coffee
journal, March 2006
- Wallace, I. M.
- Nucleic Acids Research, Vol. 34, Issue 6
Plant F-Box Protein Evolution Is Determined by Lineage-Specific Timing of Major Gene Family Expansion Waves
journal, July 2013
- Navarro-Quezada, Aura; Schumann, Nadine; Quint, Marcel
- PLoS ONE, Vol. 8, Issue 7
LEA proteins: IDPs with versatile functions in cellular dehydration tolerance
journal, September 2012
- Hincha, Dirk K.; Thalhammer, Anja
- Biochemical Society Transactions, Vol. 40, Issue 5
Basic local alignment search tool
journal, October 1990
- Altschul, Stephen F.; Gish, Warren; Miller, Webb
- Journal of Molecular Biology, Vol. 215, Issue 3, p. 403-410
Could abiotic stress tolerance in wild relatives of rice be used to improve Oryza sativa?
journal, February 2014
- Atwell, Brian J.; Wang, Han; Scafaro, Andrew P.
- Plant Science, Vol. 215-216
De Novo Next Generation Sequencing of Plant Genomes
journal, March 2009
- Rounsley, Steve; Marri, Pradeep Reddy; Yu, Yeisoo
- Rice, Vol. 2, Issue 1
Phylogeny and biogeography of the rice tribe (Oryzeae): Evidence from combined analysis of 20 chloroplast fragments
journal, January 2010
- Tang, Liang; Zou, Xin-hui; Achoundong, Gaston
- Molecular Phylogenetics and Evolution, Vol. 54, Issue 1
Evolutionary origins of Brassicaceae specific genes in Arabidopsis thaliana
journal, February 2011
- Donoghue, Mark TA; Keshavaiah, Channa; Swamidatta, Sandesh H.
- BMC Evolutionary Biology, Vol. 11, Issue 1
Genome Alignment Spanning Major Poaceae Lineages Reveals Heterogeneous Evolutionary Rates and Alters Inferred Dates for Key Evolutionary Events
journal, June 2015
- Wang, Xiyin; Wang, Jinpeng; Jin, Dianchuan
- Molecular Plant, Vol. 8, Issue 6
Reference-guided assembly of four diverse Arabidopsis thaliana genomes
journal, June 2011
- Schneeberger, K.; Ossowski, S.; Ott, F.
- Proceedings of the National Academy of Sciences, Vol. 108, Issue 25
agriGO: a GO analysis toolkit for the agricultural community
journal, April 2010
- Du, Zhou; Zhou, Xin; Ling, Yi
- Nucleic Acids Research, Vol. 38, Issue suppl_2
PAML 4: Phylogenetic Analysis by Maximum Likelihood
journal, April 2007
- Yang, Z.
- Molecular Biology and Evolution, Vol. 24, Issue 8
Gene family evolution in green plants with emphasis on the origination and evolution of Arabidopsis thaliana genes
journal, January 2013
- Guo, Ya-Long
- The Plant Journal, Vol. 73, Issue 6
Nested Retrotransposons in the Intergenic Regions of the Maize Genome
journal, November 1996
- SanMiguel, P.; Tikhonov, A.; Jin, Y. -K.
- Science, Vol. 274, Issue 5288
Genome-wide investigation on the genetic variations of rice disease resistance genes
journal, August 2006
- Yang, Sihai; Feng, Zhumei; Zhang, Xiuyan
- Plant Molecular Biology, Vol. 62, Issue 1-2
Phylogenetic relationships and genome divergence among the AA- genome species of the genus Oryza as revealed by 53 nuclear genes and 16 intergenic regions
journal, January 2014
- Zhu, Ting; Xu, Ping-Zhen; Liu, Jiang-Peng
- Molecular Phylogenetics and Evolution, Vol. 70
Development and Mapping of 2240 New SSR Markers for Rice (Oryza sativa L.)
journal, January 2002
- McCouch, S. R.
- DNA Research, Vol. 9, Issue 6
MODELTEST: testing the model of DNA substitution
journal, October 1998
- Posada, D.; Crandall, K. A.
- Bioinformatics, Vol. 14, Issue 9
Rapid diversification of five Oryza AA genomes associated with rice adaptation
journal, November 2014
- Zhang, Qun-Jie; Zhu, Ting; Xia, En-Hua
- Proceedings of the National Academy of Sciences, Vol. 111, Issue 46
A Receptor Kinase-Like Protein Encoded by the Rice Disease Resistance Gene, Xa21
journal, December 1995
- Song, W. -Y.; Wang, G. -L.; Chen, L. -L.
- Science, Vol. 270, Issue 5243
Genome sequencing and analysis of the model grass Brachypodium distachyon
journal, February 2010
- ,
- Nature, Vol. 463, Issue 7282, p. 763-768
The Sorghum bicolor genome and the diversification of grasses
text, January 2009
- H., Paterson, A.; E., Bowers, J.; R., Bruggmann,
- Nature Publishing Group
Rice pollen hybrid incompatibility caused by reciprocal gene loss of duplicated genes
journal, November 2010
- Mizuta, Y.; Harushima, Y.; Kurata, N.
- Proceedings of the National Academy of Sciences, Vol. 107, Issue 47
Database resources of the National Center for Biotechnology Information
journal, January 2009
- Sayers, E. W.; Barrett, T.; Benson, D. A.
- Nucleic Acids Research, Vol. 37, Issue Database
Extensive sequence divergence between the reference genomes of two elite indica rice varieties Zhenshan 97 and Minghui 63
journal, August 2016
- Zhang, Jianwei; Chen, Ling-Ling; Xing, Feng
- Proceedings of the National Academy of Sciences, Vol. 113, Issue 35
The Rice Resistance Protein Pair RGA4/RGA5 Recognizes the Magnaporthe oryzae Effectors AVR-Pia and AVR1-CO39 by Direct Binding
journal, April 2013
- Cesari, Stella; Thilliez, Gaëtan; Ribot, Cécile
- The Plant Cell, Vol. 25, Issue 4
The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools
journal, December 2011
- Lamesch, Philippe; Berardini, Tanya Z.; Li, Donghui
- Nucleic Acids Research, Vol. 40, Issue D1
A novel conserved mechanism for plant NLR protein pairs: the “integrated decoy†hypothesis
journal, November 2014
- Cesari, Stella; Bernoux, Maud; Moncuquet, Philippe
- Frontiers in Plant Science, Vol. 5
Database resources of the National Center for Biotechnology Information
journal, January 2006
- Wheeler, D. L.
- Nucleic Acids Research, Vol. 34, Issue 90001
Phylogenomic Analysis of BAC-end Sequence Libraries in <I>Oryza</I> (Poaceae)
journal, September 2010
- Cranston, Karen A.; Hurwitz, Bonnie; Sanderson, Michael J.
- Systematic Botany, Vol. 35, Issue 3
Insertion–deletion biases and the evolution of genome size
journal, January 2004
- Gregory, T. Ryan
- Gene, Vol. 324
Past, present and future of rice blast management
journal, July 2014
- Pooja, Kapoor; Katoch, Abhishek
- Plant Science Today, Vol. 1, Issue 3
High Rate of Chimeric Gene Origination by Retroposition in Plant Genomes
journal, July 2006
- Wang, Wen; Zheng, Hongkun; Fan, Chuanzhu
- The Plant Cell, Vol. 18, Issue 8
A Rice Gene of De Novo Origin Negatively Regulates Pathogen-Induced Defense Response
journal, February 2009
- Xiao, Wenfei; Liu, Hongbo; Li, Yu
- PLoS ONE, Vol. 4, Issue 2
BEDTools: a flexible suite of utilities for comparing genomic features
journal, January 2010
- Quinlan, Aaron R.; Hall, Ira M.
- Bioinformatics, Vol. 26, Issue 6
Semi-dominant mutations in the CC-NB-LRR-type R gene, NLS1, lead to constitutive activation of defense responses in rice: R protein mutations cause activation of defense responses
journal, April 2011
- Tang, Jiuyou; Zhu, Xudong; Wang, Yiqin
- The Plant Journal, Vol. 66, Issue 6
Phylogenetic patterns of emergence of new genes support a model of frequent de novo evolution
journal, January 2013
- Neme, Rafik; Tautz, Diethard
- BMC Genomics, Vol. 14, Issue 1
BLAST+: architecture and applications
journal, January 2009
- Camacho, Christiam; Coulouris, George; Avagyan, Vahram
- BMC Bioinformatics, Vol. 10, Issue 1
How should gaps be treated in parsimony? A comparison of approaches using simulation
journal, March 2007
- Ogden, T. Heath; Rosenberg, Michael S.
- Molecular Phylogenetics and Evolution, Vol. 42, Issue 3
Dynamic Evolution of Oryza Genomes Is Revealed by Comparative Genomic Analysis of a Genus-Wide Vertical Data Set
journal, December 2008
- Ammiraju, Jetty S. S.; Lu, Fei; Sanyal, Abhijit
- The Plant Cell, Vol. 20, Issue 12
Evolutionary dynamics of an ancient retrotransposon family provides insights into evolution of genome size in the genus Oryza: Evolutionary dynamics of ancient retrotransposon family
journal, August 2007
- Ammiraju, Jetty S. S.; Zuccolo, Andrea; Yu, Yeisoo
- The Plant Journal, Vol. 52, Issue 2
High-resolution mapping, cloning and molecular characterization of the Pi-k h gene of rice, which confers resistance to Magnaporthe grisea
journal, October 2005
- Sharma, T. R.; Madhav, M. S.; Singh, B. K.
- Molecular Genetics and Genomics, Vol. 274, Issue 6
Spip and Squiq, two novel rice non-autonomous LTR retro-element families related to RIRE3 and RIRE8
journal, January 2007
- Vitte, Clementine; Chaparro, Cristian; Quesneville, Hadi
- Plant Science, Vol. 172, Issue 1
Comparative sequence analysis of MONOCULM1 -orthologous regions in 14 Oryza genomes
journal, January 2009
- Lu, Fei; Ammiraju, Jetty S. S.; Sanyal, Abhijit
- Proceedings of the National Academy of Sciences, Vol. 106, Issue 6
Doubling genome size without polyploidization: Dynamics of retrotransposition-driven genomic expansions in Oryza australiensis, a wild relative of rice
journal, October 2006
- Piegu, B.; Guyot, R.; Picault, N.
- Genome Research, Vol. 16, Issue 10
High Occurrence of Functional New Chimeric Genes in Survey of Rice Chromosome 3 Short Arm Genome Sequences
journal, May 2013
- Zhang, Chengjun; Wang, Jun; Marowsky, Nicholas C.
- Genome Biology and Evolution, Vol. 5, Issue 5
The Sorghum bicolor genome and the diversification of grasses
journal, January 2009
- Paterson, Andrew H.; Bowers, John E.; Bruggmann, Rémy
- Nature, Vol. 457, Issue 7229
Pack-MULE transposable elements mediate gene evolution in plants
journal, September 2004
- Jiang, Ning; Bao, Zhirong; Zhang, Xiaoyu
- Nature, Vol. 431, Issue 7008
The genome sequence of African rice (Oryza glaberrima) and evidence for independent domestication
journal, July 2014
- Wang, Muhua; Yu, Yeisoo; Haberer, Georg
- Nature Genetics, Vol. 46, Issue 9
Genome-wide identification of NBS genes in japonica rice reveals significant expansion of divergent non-TIR NBS-LRR genes
journal, May 2004
- Wang, Y.; Chen, J. -Q.; Araki, H.
- Molecular Genetics and Genomics, Vol. 271, Issue 4
Genes from scratch – the evolutionary fate of de novo genes
journal, April 2015
- Schlötterer, Christian
- Trends in Genetics, Vol. 31, Issue 4
Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation
journal, May 2010
- Trapnell, Cole; Williams, Brian A.; Pertea, Geo
- Nature Biotechnology, Vol. 28, Issue 5
Orthologous Comparisons of the Hd1 Region across Genera Reveal Hd1 Gene Lability within Diploid Oryza Species and Disruptions to Microsynteny in Sorghum
journal, June 2010
- Sanyal, A.; Ammiraju, J. S. S.; Lu, F.
- Molecular Biology and Evolution, Vol. 27, Issue 11
A Draft Sequence of the Neandertal Genome
journal, May 2010
- Green, R. E.; Krause, J.; Briggs, A. W.
- Science, Vol. 328, Issue 5979
Rapid recent growth and divergence of rice nuclear genomes
journal, July 2004
- Ma, J.; Bennetzen, J. L.
- Proceedings of the National Academy of Sciences, Vol. 101, Issue 34
The Oryza bacterial artificial chromosome library resource: Construction and analysis of 12 deep-coverage large-insert BAC libraries that represent the 10 genome types of the genus Oryza
journal, December 2005
- Ammiraju, J. S. S.
- Genome Research, Vol. 16, Issue 1
The Eight Amino-Acid Differences Within Three Leucine-Rich Repeats Between Pi2 and Piz-t Resistance Proteins Determine the Resistance Specificity to Magnaporthe grisea
journal, November 2006
- Zhou, Bo; Qu, Shaohong; Liu, Guifu
- Molecular Plant-Microbe Interactions, Vol. 19, Issue 11
Comparative Physical Mapping Between Oryza sativa (AA Genome Type) and O. punctata (BB Genome Type)
journal, March 2007
- Kim, HyeRan; Miguel, Phillip San; Nelson, William
- Genetics, Vol. 176, Issue 1
Integration of decoy domains derived from protein targets of pathogen effectors into plant immune receptors is widespread
journal, February 2016
- Kroj, Thomas; Chanclud, Emilie; Michel-Romiti, Corinne
- New Phytologist, Vol. 210, Issue 2
Phylogenomics Reveals Three Sources of Adaptive Variation during a Rapid Radiation
journal, February 2016
- Pease, James B.; Haak, David C.; Hahn, Matthew W.
- PLOS Biology, Vol. 14, Issue 2
Loss of Karma transposon methylation underlies the mantled somaclonal variant of oil palm
journal, September 2015
- Ong-Abdullah, Meilina; Ordway, Jared M.; Jiang, Nan
- Nature, Vol. 525, Issue 7570
Gene Trees in Species Trees
journal, September 1997
- Maddison, Wayne P.
- Systematic Biology, Vol. 46, Issue 3
Fifteen Million Years of Evolution in the Oryza Genus Shows Extensive Gene Family Expansion
journal, April 2014
- Jacquemin, Julie; Ammiraju, Jetty S. S.; Haberer, Georg
- Molecular Plant, Vol. 7, Issue 4
Transposon-derived small RNA is responsible for modified function of WRKY45 locus
journal, February 2016
- Zhang, Haitao; Tao, Zeng; Hong, Hanming
- Nature Plants, Vol. 2, Issue 3
The life cycle of Drosophila orphan genes
journal, February 2014
- Palmieri, Nicola; Kosiol, Carolin; Schlötterer, Christian
- eLife, Vol. 3
The universal distribution of evolutionary rates of genes and distinct characteristics of eukaryotic genes of different apparent ages
journal, April 2009
- Wolf, Y. I.; Novichkov, P. S.; Karev, G. P.
- Proceedings of the National Academy of Sciences, Vol. 106, Issue 18
A new look at the statistical model identification
journal, December 1974
- Akaike, H.
- IEEE Transactions on Automatic Control, Vol. 19, Issue 6
The in Silico Map-Based Cloning of Pi36 , a Rice Coiled-Coil–Nucleotide-Binding Site–Leucine-Rich Repeat Gene That Confers Race-Specific Resistance to the Blast Fungus
journal, May 2007
- Liu, Xinqiong; Lin, Fei; Wang, Ling
- Genetics, Vol. 176, Issue 4
A Novel Protein RLS1 with NB–ARM Domains Is Involved in Chloroplast Degradation during Leaf Senescence in Rice
journal, January 2012
- Jiao, Bin-Bin; Wang, Jian-Jun; Zhu, Xu-Dong
- Molecular Plant, Vol. 5, Issue 1
The International Oryza Map Alignment Project: development of a genus-wide comparative genomics platform to help solve the 9 billion-people question
journal, May 2013
- Jacquemin, Julie; Bhatia, Dharminder; Singh, Kuldeep
- Current Opinion in Plant Biology, Vol. 16, Issue 2
Ancestral grass karyotype reconstruction unravels new mechanisms of genome shuffling as a source of plant evolution
journal, September 2010
- Murat, F.; Xu, J. -H.; Tannier, E.
- Genome Research, Vol. 20, Issue 11
From The Cover: An algorithm for progressive multiple alignment of sequences with insertions
journal, July 2005
- Loytynoja, A.; Goldman, N.
- Proceedings of the National Academy of Sciences, Vol. 102, Issue 30
The variant call format and VCFtools
journal, June 2011
- Danecek, P.; Auton, A.; Abecasis, G.
- Bioinformatics, Vol. 27, Issue 15
Expression of Xa1, a bacterial blight-resistance gene in rice, is induced by bacterial inoculation
journal, February 1998
- Yoshimura, S.; Yamanouchi, U.; Katayose, Y.
- Proceedings of the National Academy of Sciences, Vol. 95, Issue 4
Coordination of Leaf Photosynthesis, Transpiration, and Structural Traits in Rice and Wild Relatives (Genus Oryza)
journal, May 2013
- Giuliani, R.; Koteyeva, N.; Voznesenskaya, E.
- PLANT PHYSIOLOGY, Vol. 162, Issue 3
Improvement of the Oryza sativa Nipponbare reference genome using next generation sequence and optical map data
journal, January 2013
- Kawahara, Yoshihiro; de la Bastide, Melissa; Hamilton, John P.
- Rice, Vol. 6, Issue 1
The EMBL-EBI bioinformatics web and programmatic tools framework
journal, April 2015
- Li, Weizhong; Cowley, Andrew; Uludag, Mahmut
- Nucleic Acids Research, Vol. 43, Issue W1
New Gene Evolution: Little Did We Know
journal, November 2013
- Long, Manyuan; VanKuren, Nicholas W.; Chen, Sidi
- Annual Review of Genetics, Vol. 47, Issue 1
MUSCLE: multiple sequence alignment with high accuracy and high throughput
journal, March 2004
- Edgar, R. C.
- Nucleic Acids Research, Vol. 32, Issue 5, p. 1792-1797
Skillful statistical models to predict seasonal wind speed and solar radiation in a Yangtze River estuary case study
journal, May 2020
- Zeng, Peng; Sun, Xun; Farnham, David J.
- Scientific Reports, Vol. 10, Issue 1
Evolution's cauldron: Duplication, deletion, and rearrangement in the mouse and human genomes
journal, September 2003
- Kent, W. J.; Baertsch, R.; Hinrichs, A.
- Proceedings of the National Academy of Sciences, Vol. 100, Issue 20
Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads
journal, June 2009
- Ye, K.; Schulz, M. H.; Long, Q.
- Bioinformatics, Vol. 25, Issue 21
MAFFT: Iterative Refinement and Additional Methods
book, January 2013
- Katoh, Kazutaka; Standley, Daron M.
- Methods in Molecular Biology
LTR retrotransposons in rice (Oryza sativa, L.): recent burst amplifications followed by rapid DNA loss
journal, January 2007
- Vitte, Clémentine; Panaud, Olivier; Quesneville, Hadi
- BMC Genomics, Vol. 8, Issue 1
Versatile and open software for comparing large genomes
journal, January 2004
- Kurtz, Stefan; Phillippy, Adam; Delcher, Arthur L.
- Genome Biology, Vol. 5, Issue 2, R12
Extensive introgression in a malaria vector species complex revealed by phylogenomics
journal, November 2014
- Fontaine, Michael C.; Pease, James B.; Steele, Aaron
- Science, Vol. 347, Issue 6217
Consistent over-estimation of gene number in complex plant genomes
journal, December 2004
- Bennetzen, Jeffrey L.; Coleman, Craig; Liu, Renyi
- Current Opinion in Plant Biology, Vol. 7, Issue 6
A Single Amino Acid Difference Distinguishes Resistant and Susceptible Alleles of the Rice Blast Resistance Gene Pi-ta
journal, November 2000
- Bryan, Gregory T.; Wu, Kun-Sheng; Farrall, Leonard
- The Plant Cell, Vol. 12, Issue 11
A Draft Sequence of the Rice Genome (Oryza sativa L. ssp. indica)
journal, April 2002
- Yu, Jun
- Science, Vol. 296, Issue 5565, p. 79-92
Deep Transcriptome Sequencing of Wild Halophyte Rice, Porteresia coarctata, Provides Novel Insights into the Salinity and Submergence Tolerance Factors
journal, October 2013
- Garg, R.; Verma, M.; Agrawal, S.
- DNA Research, Vol. 21, Issue 1
Long-Range and Targeted Ectopic Recombination between the Two Homeologous Chromosomes 11 and 12 in Oryza Species
journal, May 2011
- Jacquemin, J.; Chaparro, C.; Laudie, M.
- Molecular Biology and Evolution, Vol. 28, Issue 11
The Broad-Spectrum Blast Resistance Gene Pi9 Encodes a Nucleotide-Binding Site–Leucine-Rich Repeat Protein and Is a Member of a Multigene Family in Rice
journal, December 2005
- Qu, Shaohong; Liu, Guifu; Zhou, Bo
- Genetics, Vol. 172, Issue 3
Selective Acquisition and Retention of Genomic Sequences by Pack- Mutator -Like Elements Based on Guanine-Cytosine Content and the Breadth of Expression
journal, September 2013
- Ferguson, Ann A.; Zhao, Dongyan; Jiang, Ning
- Plant Physiology, Vol. 163, Issue 3
Recent developments in the MAFFT multiple sequence alignment program
journal, March 2008
- Katoh, K.; Toh, H.
- Briefings in Bioinformatics, Vol. 9, Issue 4
A Draft Sequence of the Rice Genome (Oryza sativa L. ssp. japonica)
journal, April 2002
- Goff, S. A.
- Science, Vol. 296, Issue 5565
The Blast Resistance Gene Pi37 Encodes a Nucleotide Binding Site–Leucine-Rich Repeat Protein and Is a Member of a Resistance Gene Cluster on Rice Chromosome 1
journal, October 2007
- Lin, Fei; Chen, Shen; Que, Zhiqun
- Genetics, Vol. 177, Issue 3
Disentangling Methodological and Biological Sources of Gene Tree Discordance on Oryza (Poaceae) Chromosome 3
journal, April 2014
- Zwickl, Derrick J.; Stein, Joshua C.; Wing, Rod A.
- Systematic Biology, Vol. 63, Issue 5
Domestication history and geographical adaptation inferred from a SNP map of African rice
journal, August 2016
- Meyer, Rachel S.; Choi, Jae Young; Sanches, Michelle
- Nature Genetics, Vol. 48, Issue 9
Retrotransposons Control Fruit-Specific, Cold-Dependent Accumulation of Anthocyanins in Blood Oranges
journal, March 2012
- Butelli, Eugenio; Licciardello, Concetta; Zhang, Yang
- The Plant Cell, Vol. 24, Issue 3
Are orphan genes protein-coding, prediction artifacts, or non-coding RNAs?
journal, May 2016
- Prabh, Neel; Rödelsperger, Christian
- BMC Bioinformatics, Vol. 17, Issue 1
Identification of a New Rice Blast Resistance Gene, Pid3 , by Genomewide Comparison of Paired Nucleotide-Binding Site–Leucine-Rich Repeat Genes and Their Pseudogene Alleles Between the Two Sequenced Rice Genomes
journal, June 2009
- Shang, Junjun; Tao, Yong; Chen, Xuewei
- Genetics, Vol. 182, Issue 4
A multifaceted genomics approach allows the isolation of the rice Pia-blast resistance gene consisting of two adjacent NBS-LRR protein genes: Rice Pia R gene
journal, March 2011
- Okuyama, Yudai; Kanzaki, Hiroyuki; Abe, Akira
- The Plant Journal, Vol. 66, Issue 3
The Bioperl Toolkit: Perl Modules for the Life Sciences
journal, October 2002
- Stajich, J. E.
- Genome Research, Vol. 12, Issue 10
Two Adjacent Nucleotide-Binding Site–Leucine-Rich Repeat Class Genes Are Required to Confer Pikm -Specific Rice Blast Resistance
journal, October 2008
- Ashikawa, Ikuo; Hayashi, Nagao; Yamane, Hiroko
- Genetics, Vol. 180, Issue 4
The species of the genus Oryza and transfer of useful genes from wild species into cultivated rice, O. sativa
journal, January 2010
- Jena, Kshirod K.
- Breeding Science, Vol. 60, Issue 5
Refunctionalization of the ancient rice blast disease resistance gene Pit by the recruitment of a retrotransposon as a promoter
journal, February 2009
- Hayashi, Keiko; Yoshida, Hitoshi
- The Plant Journal, Vol. 57, Issue 3
Testing for Ancient Admixture between Closely Related Populations
journal, February 2011
- Durand, Eric Y.; Patterson, Nick; Reich, David
- Molecular Biology and Evolution, Vol. 28, Issue 8
Ancestry deconvolution and partial polygenic score can improve susceptibility predictions in recently admixed individuals
journal, April 2020
- Marnetto, Davide; Pärna, Katri; Läll, Kristi
- Nature Communications, Vol. 11, Issue 1
Estimating Divergence Times in Large Phylogenetic Trees
journal, October 2007
- Britton, Tom; Anderson, Cajsa Lisa; Jacquet, David
- Systematic Biology, Vol. 56, Issue 5
The Interaction between Rice Genotype and Magnaporthe oryzae Regulates the Assembly of Rice Root-Associated Microbiota
journal, May 2021
- Tian, Dagang; Chen, Zaijie; Lin, Yan
- Rice, Vol. 14, Issue 1
Coming of age: orphan genes in plants
journal, November 2014
- Arendsee, Zebulun W.; Li, Ling; Wurtele, Eve Syrkin
- Trends in Plant Science, Vol. 19, Issue 11
Páramo is the world's fastest evolving and coolest biodiversity hotspot
journal, January 2013
- Madriñán, Santiago; Cortés, Andrés J.; Richardson, James E.
- Frontiers in Genetics, Vol. 4
The Functional Role of Pack-MULEs in Rice Inferred from Purifying Selection and Expression Profile
journal, January 2009
- Hanada, Kousuke; Vallejo, Veronica; Nobuta, Kan
- The Plant Cell, Vol. 21, Issue 1
Shared Subgenome Dominance Following Polyploidization Explains Grass Genome Evolutionary Plasticity from a Seven Protochromosome Ancestor with 16K Protogenes
journal, December 2013
- Murat, Florent; Zhang, Rongzhi; Guizard, Sébastien
- Genome Biology and Evolution, Vol. 6, Issue 1
High-resolution mapping, cloning and molecular characterization of the Pi-k h gene of rice, which confers resistance to Magnaporthe grisea
journal, November 2005
- Sharma, T. R.; Madhav, M. S.; Singh, B. K.
- Molecular Genetics and Genomics, Vol. 274, Issue 6
Proto-genes and de novo gene birth
journal, June 2012
- Carvunis, Anne-Ruxandra; Rolland, Thomas; Wapinski, Ilan
- Nature, Vol. 487, Issue 7407
EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates
journal, December 2008
- Vilella, A. J.; Severin, J.; Ureta-Vidal, A.
- Genome Research, Vol. 19, Issue 2
Factors that Contribute to Variation in Evolutionary Rate among Arabidopsis Genes
journal, March 2011
- Yang, L.; Gaut, B. S.
- Molecular Biology and Evolution, Vol. 28, Issue 8
A High-Density Rice Genetic Linkage Map with 2275 Markers Using a Single F2 Population
journal, January 1998
- Harushima, Yoshiaki; Yano, Masahiro; Shomura, Ayahiko
- Genetics, Vol. 148, Issue 1
Works referencing / citing this record:
Advances in Molecular Genetics and Genomics of African Rice (Oryza glaberrima Steud)
journal, September 2019
- Wambugu, Peterson W.; Ndjiondjop, Marie-Noelle; Henry, Robert
- Plants, Vol. 8, Issue 10
Population Genetics of the Highly Polymorphic RPP8 Gene Family
journal, September 2019
- MacQueen, Alice; Tian, Dacheng; Chang, Wenhan
- Genes, Vol. 10, Issue 9
Domestication of Oryza species eco-evolutionarily shapes bacterial and fungal communities in rice seed
journal, February 2020
- Kim, Hyun; Lee, Kiseok Keith; Jeon, Jongbum
- Microbiome, Vol. 8, Issue 1
Demography and its effects on genomic variation in crop domestication
journal, July 2018
- Gaut, Brandon S.; Seymour, Danelle K.; Liu, Qingpo
- Nature Plants, Vol. 4, Issue 8
Advances in Molecular Genetics and Genomics of African Rice (Oryza glaberrima Steud)
journal, September 2019
- Wambugu, Peterson W.; Ndjiondjop, Marie-Noelle; Henry, Robert
- Plants, Vol. 8, Issue 10
The Combined Strategy for iron uptake is not exclusive to domesticated rice (Oryza sativa)
journal, November 2019
- Wairich, Andriele; de Oliveira, Ben Hur Neves; Arend, Ezequiel Barth
- Scientific Reports, Vol. 9, Issue 1
Sketch distance-based clustering of chromosomes for large genome database compression
journal, December 2019
- Tang, Tao; Liu, Yuansheng; Zhang, Buzhong
- BMC Genomics, Vol. 20, Issue S10
Gene duplication and evolution in recurring polyploidization–diploidization cycles in plants
journal, February 2019
- Qiao, Xin; Li, Qionghou; Yin, Hao
- Genome Biology, Vol. 20, Issue 1
Engineering meiotic recombination pathways in rice
journal, June 2019
- Fayos, Ian; Mieulet, Delphine; Petit, Julie
- Plant Biotechnology Journal, Vol. 17, Issue 11
Genomic variation in 3,010 diverse accessions of Asian cultivated rice
journal, April 2018
- Wang, Wensheng; Mauleon, Ramil; Hu, Zhiqiang
- Nature, Vol. 557, Issue 7703
Gene duplication and transposition of mobile elements drive evolution of the Rpv3 resistance locus in grapevine
journal, November 2019
- Foria, Serena; Copetti, Dario; Eisenmann, Birgit
- The Plant Journal, Vol. 101, Issue 3
Segregation Distortion Observed in the Progeny of Crosses Between Oryza sativa and O. meridionalis Caused by Abortion During Seed Development
journal, October 2019
- Toyomoto, Daiki; Uemura, Masato; Taura, Satoru
- Plants, Vol. 8, Issue 10
The draft genome sequence of an upland wild rice species, Oryza granulata
journal, April 2020
- Shi, Cong; Li, Wei; Zhang, Qun-Jie
- Scientific Data, Vol. 7, Issue 1
The potentiality of rice microsatellite markers in assessment of cross-species transferability and genetic diversity of rice and its wild relatives
journal, May 2019
- Ngangkham, Umakanta; Dash, Sofini; Parida, Madhuchhanda
- 3 Biotech, Vol. 9, Issue 6
Tracking the origin of two genetic components associated with transposable element bursts in domesticated rice
journal, February 2019
- Chen, Jinfeng; Lu, Lu; Benjamin, Jazmine
- Nature Communications, Vol. 10, Issue 1
De Novo, Divergence, and Mixed Origin Contribute to the Emergence of Orphan Genes inPristionchusNematodes
journal, July 2019
- Prabh, Neel; Rödelsperger, Christian
- G3 Genes|Genomes|Genetics, Vol. 9, Issue 7
Evolutionary Analysis of GH3 Genes in Six Oryza Species/Subspecies and Their Expression under Salinity Stress in Oryza sativa ssp. japonica
journal, January 2019
- Kong, Weilong; Zhong, Hua; Deng, Xiaoxiao
- Plants, Vol. 8, Issue 2
Segregation Distortion Observed in the Progeny of Crosses Between Oryza sativa and O. meridionalis Caused by Abortion During Seed Development
journal, October 2019
- Toyomoto, Daiki; Uemura, Masato; Taura, Satoru
- Plants, Vol. 8, Issue 10
Tracking the origin of two genetic components associated with transposable element bursts in domesticated rice
journal, February 2019
- Chen, Jinfeng; Lu, Lu; Benjamin, Jazmine
- Nature Communications, Vol. 10, Issue 1
Genetic innovations: Transposable element recruitment and de novo formation lead to the birth of orphan genes in the rice genome
journal, December 2019
- Jin, Gui‐Hua; Zhou, Yan‐Li; Yang, Hong
- Journal of Systematics and Evolution, Vol. 59, Issue 2
Assembling the genome of the African wild rice Oryza longistaminata by exploiting synteny in closely related Oryza species
journal, October 2018
- Reuscher, Stefan; Furuta, Tomoyuki; Bessho-Uehara, Kanako
- Communications Biology, Vol. 1, Issue 1
The Combined Strategy for iron uptake is not exclusive to domesticated rice (Oryza sativa)
journal, November 2019
- Wairich, Andriele; de Oliveira, Ben Hur Neves; Arend, Ezequiel Barth
- Scientific Reports, Vol. 9, Issue 1
Genetic characterization of the chromosome single-segment substitution lines of O. glumaepatula and O. barthii and identification of QTLs for yield-related traits
journal, March 2019
- Zhao, Hanwei; Sun, Lingling; Xiong, Tianyi
- Molecular Breeding, Vol. 39, Issue 4
Evolutionary dynamics and impacts of chromosome regions carrying R-gene clusters in rice
journal, January 2020
- Mizuno, Hiroshi; Katagiri, Satoshi; Kanamori, Hiroyuki
- Scientific Reports, Vol. 10, Issue 1
Nanopore sequencing-based genome assembly and evolutionary genomics of circum-basmati rice
journal, February 2020
- Choi, Jae Young; Lye, Zoe N.; Groen, Simon C.
- Genome Biology, Vol. 21, Issue 1
Divergent evolution of rice blast resistance Pi54 locus in the genus Oryza
journal, December 2018
- Zhang, Lin; Nakagomi, Yusuke; Endo, Takashi
- Rice, Vol. 11, Issue 1
The Versatility of SMRT Sequencing
journal, January 2019
- Hestand, Matthew S.; Ameur, Adam
- Genes, Vol. 10, Issue 1
Rapid gene cloning in cereals
journal, October 2018
- Bettgenhaeuser, Jan; Krattinger, Simon G.
- Theoretical and Applied Genetics, Vol. 132, Issue 3
The Earth BioGenome project: opportunities and challenges for plant genomics and conservation
journal, January 2020
- Exposito‐Alonso, Moises; Drost, Hajk‐Georg; Burbano, Hernán A.
- The Plant Journal, Vol. 102, Issue 2
The complex geography of domestication of the African rice Oryza glaberrima
journal, March 2019
- Choi, Jae Young; Zaidem, Maricris; Gutaker, Rafal
- PLOS Genetics, Vol. 15, Issue 3
Characterization of the transcriptional divergence between the subspecies of cultivated rice (Oryza sativa)
journal, June 2020
- Campbell, Malachy T.; Du, Qian; Liu, Kan
- BMC Genomics, Vol. 21, Issue 1
Australian Wild Rice Populations: A Key Resource for Global Food Security
journal, October 2019
- Henry, Robert J.
- Frontiers in Plant Science, Vol. 10
Genome assembly and characterization of a complex zfBED-NLR gene-containing disease resistance locus in Carolina Gold Select rice with Nanopore sequencing
journal, January 2020
- Read, Andrew C.; Moscou, Matthew J.; Zimin, Aleksey V.
- PLOS Genetics, Vol. 16, Issue 1
RiceRelativesGD: a genomic database of rice relatives for rice research
journal, January 2019
- Mao, Lingfeng; Chen, Meihong; Chu, Qinjie
- Database, Vol. 2019
Salinity tolerance in Australian wild Oryza species varies widely and matches that observed in O. sativa
journal, December 2018
- Yichie, Yoav; Brien, Chris; Berger, Bettina
- Rice, Vol. 11, Issue 1
Genetic architecture of subspecies divergence in trace mineral accumulation and elemental correlations in the rice grain
journal, November 2019
- Tan, Yongjun; Sun, Liang; Song, Qingnan
- Theoretical and Applied Genetics, Vol. 133, Issue 2
Parallel Seed Color Adaptation during Multiple Domestication Attempts of an Ancient New World Grain
journal, December 2019
- Stetter, Markus G.; Vidal-Villarejo, Mireia; Schmid, Karl J.
- Molecular Biology and Evolution, Vol. 37, Issue 5
Evaluation of rice wild relatives as a source of traits for adaptation to iron toxicity and enhanced grain quality
journal, January 2020
- Bierschenk, Birgit; Tagele, Melle Tilahun; Ali, Basharat
- PLOS ONE, Vol. 15, Issue 1
Genetic strategies for improving crop yields.
text, January 2019
- Bailey-Serres, Julia; Parker, Jane E.; Ainsworth, Elizabeth A.
- Apollo - University of Cambridge Repository
Whole Genome Sequencing and Comparative Genomic Analysis Reveal Allelic Variations Unique to a Purple Colored Rice Landrace (Oryza sativa ssp. indica cv. Purpleputtu)
journal, May 2019
- Lachagari, V. B. Reddy; Gupta, Ravi; Lekkala, Sivarama Prasad
- Frontiers in Plant Science, Vol. 10
Genome-wide identification of the peptide transporter family in rice and analysis of the PTR expression modulation in two near-isogenic lines with different nitrogen use efficiency
journal, May 2020
- Yang, Xinghai; Xia, Xiuzhong; Zeng, Yu
- BMC Plant Biology, Vol. 20, Issue 1
Applications and challenges for efficient exploration of omics interventions for the enhancement of nutritional quality in rice (Oryza sativa L.)
text, January 2019
- Rana, Nitika; Rahim, Mohammed Saba; Kaur, Gazaldeep
- Taylor & Francis
Comparative study of the mycorrhizal root transcriptomes of wild and cultivated rice in response to the pathogen Magnaporthe oryzae
journal, May 2019
- Tian, Lei; Chang, Chunling; Ma, Lina
- Rice, Vol. 12, Issue 1
Nanopore sequencing-based genome assembly and evolutionary genomics of circum-basmati rice
journal, February 2020
- Choi, Jae Young; Lye, Zoe N.; Groen, Simon C.
- Genome Biology, Vol. 21, Issue 1
The rice genome revolution: from an ancient grain to Green Super Rice
journal, June 2018
- Wing, Rod A.; Purugganan, Michael D.; Zhang, Qifa
- Nature Reviews Genetics, Vol. 19, Issue 8
A new reference genome for Sorghum bicolor reveals high levels of sequence similarity between sweet and grain genotypes: implications for the genetics of sugar metabolism
journal, May 2019
- Cooper, Elizabeth A.; Brenton, Zachary W.; Flinn, Barry S.
- BMC Genomics, Vol. 20, Issue 1
Applications and challenges for efficient exploration of omics interventions for the enhancement of nutritional quality in rice ( Oryza sativa L.)
journal, November 2019
- Rana, Nitika; Rahim, Mohammed Saba; Kaur, Gazaldeep
- Critical Reviews in Food Science and Nutrition
Evolutionary dynamics and impacts of chromosome regions carrying R-gene clusters in rice
journal, January 2020
- Mizuno, Hiroshi; Katagiri, Satoshi; Kanamori, Hiroyuki
- Scientific Reports, Vol. 10, Issue 1
Hidden Rice Diversity in the Guianas
journal, September 2019
- Van Andel, Tinde; Veltman, Margaretha A.; Bertin, Alice
- Frontiers in Plant Science, Vol. 10
Detection of mPing mobilization in transgenic rice plants
journal, November 2019
- Park, Doori; Choi, Ik-Young; Kim, Nam-Soo
- Genes & Genomics, Vol. 42, Issue 1
Back to the Wild: On a Quest for Donors Toward Salinity Tolerant Rice
journal, March 2020
- Solis, Celymar A.; Yong, Miing T.; Vinarao, Ricky
- Frontiers in Plant Science, Vol. 11
Genetic control of seed shattering during African rice domestication
journal, June 2018
- Lv, Shuwei; Wu, Wenguang; Wang, Muhua
- Nature Plants, Vol. 4, Issue 6
Deep taxon sampling reveals the evolutionary dynamics of novel gene families in Pristionchus nematodes
journal, September 2018
- Prabh, Neel; Roeseler, Waltraud; Witte, Hanh
- Genome Research, Vol. 28, Issue 11
Evaluation of rice wild relatives as a source of traits for adaptation to iron toxicity and enhanced grain quality
journal, January 2020
- Bierschenk, Birgit; Tagele, Melle Tilahun; Ali, Basharat
- PLOS ONE, Vol. 15, Issue 1
An asymmetric allelic interaction drives allele transmission bias in interspecific rice hybrids
journal, June 2019
- Xie, Yongyao; Tang, Jintao; Xie, Xianrong
- Nature Communications, Vol. 10, Issue 1
Assembling the genome of the African wild rice Oryza longistaminata by exploiting synteny in closely related Oryza species
journal, October 2018
- Reuscher, Stefan; Furuta, Tomoyuki; Bessho-Uehara, Kanako
- Communications Biology, Vol. 1, Issue 1
A set of AP2-like genes is associated with inflorescence branching and architecture in domesticated rice
journal, June 2019
- Harrop, Thomas W. R.; Mantegazza, Otho; Luong, Ai My
- Journal of Experimental Botany, Vol. 70, Issue 20
The complex geography of domestication of the African rice Oryza glaberrima
journal, March 2019
- Choi, Jae Young; Zaidem, Maricris; Gutaker, Rafal
- PLOS Genetics, Vol. 15, Issue 3
Young genes have distinct gene structure, epigenetic profiles, and transcriptional regulation
journal, September 2018
- Werner, Michael S.; Sieriebriennikov, Bogdan; Prabh, Neel
- Genome Research, Vol. 28, Issue 11
Structural variants in 3000 rice genomes
journal, April 2019
- Fuentes, Roven Rommel; Chebotarov, Dmytro; Duitama, Jorge
- Genome Research, Vol. 29, Issue 5
Divergent evolution of rice blast resistance Pi54 locus in the genus Oryza
journal, December 2018
- Zhang, Lin; Nakagomi, Yusuke; Endo, Takashi
- Rice, Vol. 11, Issue 1
A new reference genome for Sorghum bicolor reveals high levels of sequence similarity between sweet and grain genotypes: implications for the genetics of sugar metabolism
journal, May 2019
- Cooper, Elizabeth A.; Brenton, Zachary W.; Flinn, Barry S.
- BMC Genomics, Vol. 20, Issue 1
Insights into the Evolution of the New World Diploid Cottons ( Gossypium , Subgenus Houzingenia ) Based on Genome Sequencing
journal, November 2018
- Grover, Corrinne E.; Arick, Mark A.; Thrash, Adam
- Genome Biology and Evolution, Vol. 11, Issue 1
Genomic variation in 3,010 diverse accessions of Asian cultivated rice
journal, April 2018
- Wang, Wensheng; Mauleon, Ramil; Hu, Zhiqiang
- Nature, Vol. 557, Issue 7703
Agrobacterium-Mediated Genetic Transformation of Wild Oryza Species Using Immature Embryos
journal, June 2020
- Shimizu-Sato, Sae; Tsuda, Katsutoshi; Nosaka-Takahashi, Misuzu
- Rice, Vol. 13, Issue 1
Receptor networks underpin plant immunity
journal, June 2018
- Wu, Chih-Hang; Derevnina, Lida; Kamoun, Sophien
- Science, Vol. 360, Issue 6395
Comparative study of the mycorrhizal root transcriptomes of wild and cultivated rice in response to the pathogen Magnaporthe oryzae
journal, May 2019
- Tian, Lei; Chang, Chunling; Ma, Lina
- Rice, Vol. 12, Issue 1
Rapid evolution of protein diversity by de novo origination in Oryza
journal, March 2019
- Zhang, Li; Ren, Yan; Yang, Tao
- Nature Ecology & Evolution, Vol. 3, Issue 4
Diversifying Evolution of the Ubiquitin-26S Proteasome System in Brassicaceae and Poaceae
journal, June 2019
- Hua,
- International Journal of Molecular Sciences, Vol. 20, Issue 13
Salinity tolerance in Australian wild Oryza species varies widely and matches that observed in O. sativa
journal, December 2018
- Yichie, Yoav; Brien, Chris; Berger, Bettina
- Rice, Vol. 11, Issue 1
The Versatility of SMRT Sequencing
journal, January 2019
- Hestand, Matthew S.; Ameur, Adam
- Genes, Vol. 10, Issue 1
Advances in legume research in the genomics era
journal, January 2019
- Egan, Ashley N.; Vatanparast, Mohammad
- Australian Systematic Botany