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Analysis of 142 genes resolves the rapid diversification of the rice genus
Xin-Hui Zou, Fu-Min Zhang, Jian-Guo Zhang, Li-Li Zang, Liang Tang, Jun Wang, Tao Sang, Song Ge
Genome Biol. 2008; 9(3): R49. Published online 2008 March 3. doi: 10.1186/gb-2008-9-3-r49
PMCID:
PMC2397501
Abstract Full Text PDF–466K Supplementary Material
 Is Cited by the Following 21 Articles in this Archive:
Multigenic phylogeny and analysis of tree incongruences in Triticeae (Poaceae)
Juan S Escobar, Céline Scornavacca, Alberto Cenci, Claire Guilhaumon, Sylvain Santoni, Emmanuel JP Douzery, Vincent Ranwez, Sylvain Glémin, Jacques David
BMC Evol Biol. 2011; 11: 181. Published online 2011 June 24. doi: 10.1186/1471-2148-11-181
PMCID:
PMC3142523
Abstract Full Text PDF–587K Supplementary Material
Molecular evidence for a single evolutionary origin of domesticated rice
Jeanmaire Molina, Martin Sikora, Nandita Garud, Jonathan M. Flowers, Samara Rubinstein, Andy Reynolds, Pu Huang, Scott Jackson, Barbara A. Schaal, Carlos D. Bustamante, Adam R. Boyko, Michael D. Purugganan
Proc Natl Acad Sci U S A. 2011 May 17; 108(20): 8351–8356. Published online 2011 May 2. doi: 10.1073/pnas.1104686108
PMCID:
PMC3101000
Abstract Full Text PDF–296K Supplementary Material
A multi gene sequence-based phylogeny of the Musaceae (banana) family
Pavla Christelová, Miroslav Valárik, Eva Hřibová, Edmond De Langhe, Jaroslav Doležel
BMC Evol Biol. 2011; 11: 103. Published online 2011 April 16. doi: 10.1186/1471-2148-11-103
PMCID:
PMC3102628
Abstract Full Text PDF–1.2M Supplementary Material
The performance of the Congruence Among Distance Matrices (CADM) test in phylogenetic analysis
Véronique Campbell, Pierre Legendre, François-Joseph Lapointe
BMC Evol Biol. 2011; 11: 64. Published online 2011 March 9. doi: 10.1186/1471-2148-11-64
PMCID:
PMC3065422
Abstract Full Text PDF–470K
Phylogenomic Analysis Resolves the Formerly Intractable Adaptive Diversification of the Endemic Clade of East Asian Cyprinidae (Cypriniformes)
Wenjing Tao, Ming Zou, Xuzhen Wang, Xiaoni Gan, Richard L. Mayden, Shunping He
PLoS One. 2010; 5(10): e13508. Published online 2010 October 20. doi: 10.1371/journal.pone.0013508
PMCID:
PMC2958143
Abstract Full Text PDF–1.5M Supplementary Material
Genome-wide characterization of the biggest grass, bamboo, based on 10,608 putative full-length cDNA sequences
Zhenhua Peng, Tingting Lu, Lubin Li, Xiaohui Liu, Zhimin Gao, Tao Hu, Xuewen Yang, Qi Feng, Jianping Guan, Qijun Weng, Danlin Fan, Chuanrang Zhu, Ying Lu, Bin Han, Zehui Jiang
BMC Plant Biol. 2010; 10: 116. Published online 2010 June 18. doi: 10.1186/1471-2229-10-116
PMCID:
PMC3017805
Abstract Full Text PDF–1.2M Supplementary Material
Numbers of genes in the NBS and RLK families vary by more than four-fold within a plant species and are regulated by multiple factors
Meiping Zhang, Yen-Hsuan Wu, Mi-Kyung Lee, Yun-Hua Liu, Ying Rong, Teofila S. Santos, Chengcang Wu, Fangming Xie, Randall L. Nelson, Hong-Bin Zhang
Nucleic Acids Res. 2010 October; 38(19): 6513–6525. Published online 2010 June 11. doi: 10.1093/nar/gkq524
PMCID:
PMC2965241
Abstract Full Text PDF–333K Supplementary Material
Phylogenomics with incomplete taxon coverage: the limits to inference
Michael J Sanderson, Michelle M McMahon, Mike Steel
BMC Evol Biol. 2010; 10: 155. Published online 2010 May 25. doi: 10.1186/1471-2148-10-155
PMCID:
PMC2897806
Abstract Full Text PDF–2.7M
Sequence variation and selection of small RNAs in domesticated rice
Yu Wang, Dan Shen, Shiping Bo, Huan Chen, Jian Zheng, Qian-Hao Zhu, Daguang Cai, Chris Helliwell, Longjiang Fan
BMC Evol Biol. 2010; 10: 119. Published online 2010 April 30. doi: 10.1186/1471-2148-10-119
PMCID:
PMC2887405
Abstract Full Text PDF–1008K Supplementary Material
Massive gene losses in Asian cultivated rice unveiled by comparative genome analysis
Hiroaki Sakai, Takeshi Itoh
BMC Genomics. 2010; 11: 121. Published online 2010 February 19. doi: 10.1186/1471-2164-11-121
PMCID:
PMC2831846
Abstract Full Text PDF–573K Supplementary Material
Paleogenomic Analysis of the Short Arm of Chromosome 3 Reveals the History of the African and Asian Progenitors of Cultivated Rices
Anne Roulin, Cristian Chaparro, Benoit Piégu, Scott Jackson, Olivier Panaud
Genome Biol Evol. 2010; 2: 132–139. Published online 2010 February 11. doi: 10.1093/gbe/evq005
PMCID:
PMC2839358
Abstract Full Text PDF–250K Supplementary Material
Genomic and Expression Plasticity of Polyploidy
Scott Jackson, Z. Jeffrey Chen
Curr Opin Plant Biol. Author manuscript; available in PMC 2011 April 1.
Published in final edited form as: Curr Opin Plant Biol. 2010 April; 13(2): 153–159. Published online 2009 December 22. doi: 10.1016/j.pbi.2009.11.004
PMCID:
PMC2880571
Abstract Full Text PDF–713K
A recent duplication revisited: phylogenetic analysis reveals an ancestral duplication highly-conserved throughout the Oryza genus and beyond
Julie Jacquemin, Michèle Laudié, Richard Cooke
BMC Plant Biol. 2009; 9: 146. Published online 2009 December 10. doi: 10.1186/1471-2229-9-146
PMCID:
PMC2797015
Abstract Full Text PDF–887K Supplementary Material
Fine-Scale Phylogenetic Discordance across the House Mouse Genome
Michael A. White, Cécile Ané, Colin N. Dewey, Bret R. Larget, Bret A. Payseur
PLoS Genet. 2009 November; 5(11): e1000729. Published online 2009 November 20. doi: 10.1371/journal.pgen.1000729
PMCID:
PMC2770633
Abstract Full Text PDF–410K Supplementary Material
Polyploid evolution in Oryza officinalis complex of the genus Oryza
Baosheng Wang, Zhuoya Ding, Wei Liu, Jin Pan, Changbao Li, Song Ge, Daming Zhang
BMC Evol Biol. 2009; 9: 250. Published online 2009 October 14. doi: 10.1186/1471-2148-9-250
PMCID:
PMC2770061
Abstract Full Text PDF–1.2M Supplementary Material
Do potatoes and tomatoes have a single evolutionary history, and what proportion of the genome supports this history?
Flor Rodriguez, Feinan Wu, Cécile Ané, Steve Tanksley, David M Spooner
BMC Evol Biol. 2009; 9: 191. Published online 2009 August 7. doi: 10.1186/1471-2148-9-191
PMCID:
PMC3087518
Abstract Full Text PDF–727K Supplementary Material
A Rice Gene of De Novo Origin Negatively Regulates Pathogen-Induced Defense Response
Wenfei Xiao, Hongbo Liu, Yu Li, Xianghua Li, Caiguo Xu, Manyuan Long, Shiping Wang
PLoS ONE. 2009; 4(2): e4603. Published online 2009 February 25. doi: 10.1371/journal.pone.0004603
PMCID:
PMC2643483
Abstract Full Text PDF–731K Supplementary Material
Comparative sequence analysis of MONOCULM1-orthologous regions in 14 Oryza genomes
Fei Lu, Jetty S. S. Ammiraju, Abhijit Sanyal, Shengli Zhang, Rentao Song, Jinfeng Chen, Guisheng Li, Yi Sui, Xiang Song, Zhukuan Cheng, Antonio Costa de Oliveira, Jeffrey L. Bennetzen, Scott A. Jackson, Rod A. Wing, Mingsheng Chen
Proc Natl Acad Sci U S A. 2009 February 10; 106(6): 2071–2076. Published online 2009 January 22. doi: 10.1073/pnas.0812798106
PMCID:
PMC2629783
Abstract Full Text PDF–513K Supplementary Material
Dynamic Evolution of Oryza Genomes Is Revealed by Comparative Genomic Analysis of a Genus-Wide Vertical Data Set
Jetty S.S. Ammiraju, Fei Lu, Abhijit Sanyal, Yeisoo Yu, Xiang Song, Ning Jiang, Ana Clara Pontaroli, Teri Rambo, Jennifer Currie, Kristi Collura, Jayson Talag, Chuanzhu Fan, Jose Luis Goicoechea, Andrea Zuccolo, Jinfeng Chen, Jeffrey L. Bennetzen, Mingsheng Chen, Scott Jackson, Rod A. Wing
Plant Cell. 2008 December; 20(12): 3191–3209. doi: 10.1105/tpc.108.063727
PMCID:
PMC2630430
Abstract Full Text PDF–905K Supplementary Material
Intergenic Locations of Rice Centromeric Chromatin
Huihuang Yan, Paul B Talbert, Hye-Ran Lee, Jamie Jett, Steven Henikoff, Feng Chen, Jiming Jiang
PLoS Biol. 2008 November; 6(11): e286. Published online 2008 November 25. doi: 10.1371/journal.pbio.0060286
PMCID:
PMC2586382
Abstract Full Text PDF–879K Supplementary Material
Human-Mediated Emergence as a Weed and Invasive Radiation in the Wild of the CD Genome Allotetraploid Rice Species (Oryza, Poaceae) in the Neotropics
Gérard Second, Germinal Rouhan
PLoS ONE. 2008; 3(7): e2613. Published online 2008 July 2. doi: 10.1371/journal.pone.0002613
PMCID:
PMC2434201
Abstract Full Text PDF–2.1M Supplementary Material
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