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PGDD: a database of gene and genome duplication in plants.

Lee TH, Tang H, Wang X, Paterson AH.

Nucleic Acids Res. 2013 Jan;41(Database issue):D1152-8. doi: 10.1093/nar/gks1104. Epub 2012 Nov 24.


Identification of shared single copy nuclear genes in Arabidopsis, Populus, Vitis and Oryza and their phylogenetic utility across various taxonomic levels.

Duarte JM, Wall PK, Edger PP, Landherr LL, Ma H, Pires JC, Leebens-Mack J, dePamphilis CW.

BMC Evol Biol. 2010 Feb 24;10:61. doi: 10.1186/1471-2148-10-61.


Unravelling angiosperm genome evolution by phylogenetic analysis of chromosomal duplication events.

Bowers JE, Chapman BA, Rong J, Paterson AH.

Nature. 2003 Mar 27;422(6930):433-8.


Prevalent role of gene features in determining evolutionary fates of whole-genome duplication duplicated genes in flowering plants.

Jiang WK, Liu YL, Xia EH, Gao LZ.

Plant Physiol. 2013 Apr;161(4):1844-61. doi: 10.1104/pp.112.200147. Epub 2013 Feb 8.


Floral gene resources from basal angiosperms for comparative genomics research.

Albert VA, Soltis DE, Carlson JE, Farmerie WG, Wall PK, Ilut DC, Solow TM, Mueller LA, Landherr LL, Hu Y, Buzgo M, Kim S, Yoo MJ, Frohlich MW, Perl-Treves R, Schlarbaum SE, Bliss BJ, Zhang X, Tanksley SD, Oppenheimer DG, Soltis PS, Ma H, DePamphilis CW, Leebens-Mack JH.

BMC Plant Biol. 2005 Mar 30;5:5.


Unraveling ancient hexaploidy through multiply-aligned angiosperm gene maps.

Tang H, Wang X, Bowers JE, Ming R, Alam M, Paterson AH.

Genome Res. 2008 Dec;18(12):1944-54. doi: 10.1101/gr.080978.108. Epub 2008 Oct 2.


Genome and gene duplications and gene expression divergence: a view from plants.

Wang Y, Wang X, Paterson AH.

Ann N Y Acad Sci. 2012 May;1256:1-14. doi: 10.1111/j.1749-6632.2011.06384.x. Epub 2012 Jan 18. Review.


Buffering of crucial functions by paleologous duplicated genes may contribute cyclicality to angiosperm genome duplication.

Chapman BA, Bowers JE, Feltus FA, Paterson AH.

Proc Natl Acad Sci U S A. 2006 Feb 21;103(8):2730-5. Epub 2006 Feb 8.


Gene duplication as a major force in evolution.

Magadum S, Banerjee U, Murugan P, Gangapur D, Ravikesavan R.

J Genet. 2013 Apr;92(1):155-61. Review.


Comparing Arabidopsis to other flowering plants.

Barnes S.

Curr Opin Plant Biol. 2002 Apr;5(2):128-34. Review.


Extensive divergence in alternative splicing patterns after gene and genome duplication during the evolutionary history of Arabidopsis.

Zhang PG, Huang SZ, Pin AL, Adams KL.

Mol Biol Evol. 2010 Jul;27(7):1686-97. doi: 10.1093/molbev/msq054. Epub 2010 Feb 25.


MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity.

Wang Y, Tang H, Debarry JD, Tan X, Li J, Wang X, Lee TH, Jin H, Marler B, Guo H, Kissinger JC, Paterson AH.

Nucleic Acids Res. 2012 Apr;40(7):e49. doi: 10.1093/nar/gkr1293. Epub 2012 Jan 4.


Complete plastid genome sequence of Daucus carota: implications for biotechnology and phylogeny of angiosperms.

Ruhlman T, Lee SB, Jansen RK, Hostetler JB, Tallon LJ, Town CD, Daniell H.

BMC Genomics. 2006 Aug 31;7:222.


The impact of outgroup choice and missing data on major seed plant phylogenetics using genome-wide EST data.

de la Torre-Bárcena JE, Kolokotronis SO, Lee EK, Stevenson DW, Brenner ED, Katari MS, Coruzzi GM, DeSalle R.

PLoS One. 2009 Jun 2;4(6):e5764. doi: 10.1371/journal.pone.0005764.


Modeling gene and genome duplications in eukaryotes.

Maere S, De Bodt S, Raes J, Casneuf T, Van Montagu M, Kuiper M, Van de Peer Y.

Proc Natl Acad Sci U S A. 2005 Apr 12;102(15):5454-9. Epub 2005 Mar 30.


Screening synteny blocks in pairwise genome comparisons through integer programming.

Tang H, Lyons E, Pedersen B, Schnable JC, Paterson AH, Freeling M.

BMC Bioinformatics. 2011 Apr 18;12:102. doi: 10.1186/1471-2105-12-102.


The plastid genomes of flowering plants.

Ruhlman TA, Jansen RK.

Methods Mol Biol. 2014;1132:3-38. doi: 10.1007/978-1-62703-995-6_1.


Architecture and evolution of a minute plant genome.

Ibarra-Laclette E, Lyons E, Hernández-Guzmán G, Pérez-Torres CA, Carretero-Paulet L, Chang TH, Lan T, Welch AJ, Juárez MJ, Simpson J, Fernández-Cortés A, Arteaga-Vázquez M, Góngora-Castillo E, Acevedo-Hernández G, Schuster SC, Himmelbauer H, Minoche AE, Xu S, Lynch M, Oropeza-Aburto A, Cervantes-Pérez SA, de Jesús Ortega-Estrada M, Cervantes-Luevano JI, Michael TP, Mockler T, Bryant D, Herrera-Estrella A, Albert VA, Herrera-Estrella L.

Nature. 2013 Jun 6;498(7452):94-8. doi: 10.1038/nature12132. Epub 2013 May 12.


Synteny and collinearity in plant genomes.

Tang H, Bowers JE, Wang X, Ming R, Alam M, Paterson AH.

Science. 2008 Apr 25;320(5875):486-8. doi: 10.1126/science.1153917.

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