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Items: 1 to 20 of 103


Dynamic evolution of oryza genomes is revealed by comparative genomic analysis of a genus-wide vertical data set.

Ammiraju JS, Lu F, Sanyal A, Yu Y, Song X, Jiang N, Pontaroli AC, Rambo T, Currie J, Collura K, Talag J, Fan C, Goicoechea JL, Zuccolo A, Chen J, Bennetzen JL, Chen M, Jackson S, Wing RA.

Plant Cell. 2008 Dec;20(12):3191-209. doi: 10.1105/tpc.108.063727. Epub 2008 Dec 19.


Rapid diversification of five Oryza AA genomes associated with rice adaptation.

Zhang QJ, Zhu T, Xia EH, Shi C, Liu YL, Zhang Y, Liu Y, Jiang WK, Zhao YJ, Mao SY, Zhang LP, Huang H, Jiao JY, Xu PZ, Yao QY, Zeng FC, Yang LL, Gao J, Tao DY, Wang YJ, Bennetzen JL, Gao LZ.

Proc Natl Acad Sci U S A. 2014 Nov 18;111(46):E4954-62. doi: 10.1073/pnas.1418307111. Epub 2014 Nov 3.


Spatio-temporal patterns of genome evolution in allotetraploid species of the genus Oryza.

Ammiraju JS, Fan C, Yu Y, Song X, Cranston KA, Pontaroli AC, Lu F, Sanyal A, Jiang N, Rambo T, Currie J, Collura K, Talag J, Bennetzen JL, Chen M, Jackson S, Wing RA.

Plant J. 2010 Aug;63(3):430-42. doi: 10.1111/j.1365-313X.2010.04251.x. Epub 2010 May 6.


ZINC-INDUCED FACILITATOR-LIKE family in plants: lineage-specific expansion in monocotyledons and conserved genomic and expression features among rice (Oryza sativa) paralogs.

Ricachenevsky FK, Sperotto RA, Menguer PK, Sperb ER, Lopes KL, Fett JP.

BMC Plant Biol. 2011 Jan 25;11:20. doi: 10.1186/1471-2229-11-20.


Transposable element distribution, abundance and role in genome size variation in the genus Oryza.

Zuccolo A, Sebastian A, Talag J, Yu Y, Kim H, Collura K, Kudrna D, Wing RA.

BMC Evol Biol. 2007 Aug 29;7:152.


Insights into the Musa genome: syntenic relationships to rice and between Musa species.

Lescot M, Piffanelli P, Ciampi AY, Ruiz M, Blanc G, Leebens-Mack J, da Silva FR, Santos CM, D'Hont A, Garsmeur O, Vilarinhos AD, Kanamori H, Matsumoto T, Ronning CM, Cheung F, Haas BJ, Althoff R, Arbogast T, Hine E, Pappas GJ Jr, Sasaki T, Souza MT Jr, Miller RN, Glaszmann JC, Town CD.

BMC Genomics. 2008 Jan 30;9:58. doi: 10.1186/1471-2164-9-58.


Exceptional lability of a genomic complex in rice and its close relatives revealed by interspecific and intraspecific comparison and population analysis.

Tian Z, Yu Y, Lin F, Yu Y, Sanmiguel PJ, Wing RA, McCouch SR, Ma J, Jackson SA.

BMC Genomics. 2011 Mar 8;12:142. doi: 10.1186/1471-2164-12-142.


Genome-wide analysis of heat shock transcription factor families in rice and Arabidopsis.

Guo J, Wu J, Ji Q, Wang C, Luo L, Yuan Y, Wang Y, Wang J.

J Genet Genomics. 2008 Feb;35(2):105-18. doi: 10.1016/S1673-8527(08)60016-8.


The Rice Genome Knowledgebase (RGKbase): an annotation database for rice comparative genomics and evolutionary biology.

Wang D, Xia Y, Li X, Hou L, Yu J.

Nucleic Acids Res. 2013 Jan;41(Database issue):D1199-205. doi: 10.1093/nar/gks1225. Epub 2012 Nov 28.


Whole-genome sequencing of Oryza brachyantha reveals mechanisms underlying Oryza genome evolution.

Chen J, Huang Q, Gao D, Wang J, Lang Y, Liu T, Li B, Bai Z, Luis Goicoechea J, Liang C, Chen C, Zhang W, Sun S, Liao Y, Zhang X, Yang L, Song C, Wang M, Shi J, Liu G, Liu J, Zhou H, Zhou W, Yu Q, An N, Chen Y, Cai Q, Wang B, Liu B, Min J, Huang Y, Wu H, Li Z, Zhang Y, Yin Y, Song W, Jiang J, Jackson SA, Wing RA, Wang J, Chen M.

Nat Commun. 2013;4:1595. doi: 10.1038/ncomms2596.


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.

Ammiraju JS, Luo M, Goicoechea JL, Wang W, Kudrna D, Mueller C, Talag J, Kim H, Sisneros NB, Blackmon B, Fang E, Tomkins JB, Brar D, MacKill D, McCouch S, Kurata N, Lambert G, Galbraith DW, Arumuganathan K, Rao K, Walling JG, Gill N, Yu Y, SanMiguel P, Soderlund C, Jackson S, Wing RA.

Genome Res. 2006 Jan;16(1):140-7. Epub 2005 Dec 12.


Genome evolution in diploid and tetraploid Coffea species as revealed by comparative analysis of orthologous genome segments.

Cenci A, Combes MC, Lashermes P.

Plant Mol Biol. 2012 Jan;78(1-2):135-45. doi: 10.1007/s11103-011-9852-3. Epub 2011 Nov 16.


Multifunctionality and diversity of GDSL esterase/lipase gene family in rice (Oryza sativa L. japonica) genome: new insights from bioinformatics analysis.

Chepyshko H, Lai CP, Huang LM, Liu JH, Shaw JF.

BMC Genomics. 2012 Jul 15;13:309. doi: 10.1186/1471-2164-13-309.


Rice structural variation: a comparative analysis of structural variation between rice and three of its closest relatives in the genus Oryza.

Hurwitz BL, Kudrna D, Yu Y, Sebastian A, Zuccolo A, Jackson SA, Ware D, Wing RA, Stein L.

Plant J. 2010 Sep;63(6):990-1003. doi: 10.1111/j.1365-313X.2010.04293.x.


Polymorphisms and evolutionary history of retrotransposon insertions in rice promoters.

Xu Z, Rafi S, Ramakrishna W.

Genome. 2011 Aug;54(8):629-38. doi: 10.1139/G11-030. Epub 2011 Aug 8.


New insights into Oryza genome evolution: high gene colinearity and differential retrotransposon amplification.

Zhang S, Gu YQ, Singh J, Coleman-Derr D, Brar DS, Jiang N, Lemaux PG.

Plant Mol Biol. 2007 Jul;64(5):589-600. Epub 2007 May 30.


Comparative genomics of rice and Arabidopsis. Analysis of 727 cytochrome P450 genes and pseudogenes from a monocot and a dicot.

Nelson DR, Schuler MA, Paquette SM, Werck-Reichhart D, Bak S.

Plant Physiol. 2004 Jun;135(2):756-72.


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