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The fate of duplicated genes in a polyploid plant genome.

Roulin A, Auer PL, Libault M, Schlueter J, Farmer A, May G, Stacey G, Doerge RW, Jackson SA.

Plant J. 2013 Jan;73(1):143-53. doi: 10.1111/tpj.12026. Epub 2012 Oct 22.


Differential accumulation of retroelements and diversification of NB-LRR disease resistance genes in duplicated regions following polyploidy in the ancestor of soybean.

Innes RW, Ameline-Torregrosa C, Ashfield T, Cannon E, Cannon SB, Chacko B, Chen NW, Couloux A, Dalwani A, Denny R, Deshpande S, Egan AN, Glover N, Hans CS, Howell S, Ilut D, Jackson S, Lai H, Mammadov J, Del Campo SM, Metcalf M, Nguyen A, O'Bleness M, Pfeil BE, Podicheti R, Ratnaparkhe MB, Samain S, Sanders I, Ségurens B, Sévignac M, Sherman-Broyles S, Thareau V, Tucker DM, Walling J, Wawrzynski A, Yi J, Doyle JJ, Geffroy V, Roe BA, Maroof MA, Young ND.

Plant Physiol. 2008 Dec;148(4):1740-59. doi: 10.1104/pp.108.127902. Epub 2008 Oct 8.


A Comparative Epigenomic Analysis of Polyploidy-Derived Genes in Soybean and Common Bean.

Kim KD, El Baidouri M, Abernathy B, Iwata-Otsubo A, Chavarro C, Gonzales M, Libault M, Grimwood J, Jackson SA.

Plant Physiol. 2015 Aug;168(4):1433-47. doi: 10.1104/pp.15.00408. Epub 2015 Jul 6.


Genome sequence of the palaeopolyploid soybean.

Schmutz J, Cannon SB, Schlueter J, Ma J, Mitros T, Nelson W, Hyten DL, Song Q, Thelen JJ, Cheng J, Xu D, Hellsten U, May GD, Yu Y, Sakurai T, Umezawa T, Bhattacharyya MK, Sandhu D, Valliyodan B, Lindquist E, Peto M, Grant D, Shu S, Goodstein D, Barry K, Futrell-Griggs M, Abernathy B, Du J, Tian Z, Zhu L, Gill N, Joshi T, Libault M, Sethuraman A, Zhang XC, Shinozaki K, Nguyen HT, Wing RA, Cregan P, Specht J, Grimwood J, Rokhsar D, Stacey G, Shoemaker RC, Jackson SA.

Nature. 2010 Jan 14;463(7278):178-83. doi: 10.1038/nature08670. Erratum in: Nature. 2010 May 6;465(7294):120.


Genome duplication and gene loss affect the evolution of heat shock transcription factor genes in legumes.

Lin Y, Cheng Y, Jin J, Jin X, Jiang H, Yan H, Cheng B.

PLoS One. 2014 Jul 21;9(7):e102825. doi: 10.1371/journal.pone.0102825. eCollection 2014.


Concerted evolution of D1 and D2 to regulate chlorophyll degradation in soybean.

Fang C, Li C, Li W, Wang Z, Zhou Z, Shen Y, Wu M, Wu Y, Li G, Kong LA, Liu C, Jackson SA, Tian Z.

Plant J. 2014 Mar;77(5):700-12. doi: 10.1111/tpj.12419. Epub 2014 Feb 4.


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.


Dynamic rearrangements determine genome organization and useful traits in soybean.

Kim KD, Shin JH, Van K, Kim DH, Lee SH.

Plant Physiol. 2009 Nov;151(3):1066-76. doi: 10.1104/pp.109.141739. Epub 2009 Aug 14.


Pericentromeric effects shape the patterns of divergence, retention, and expression of duplicated genes in the paleopolyploid soybean.

Du J, Tian Z, Sui Y, Zhao M, Song Q, Cannon SB, Cregan P, Ma J.

Plant Cell. 2012 Jan;24(1):21-32. doi: 10.1105/tpc.111.092759. Epub 2012 Jan 6.


Changes in twelve homoeologous genomic regions in soybean following three rounds of polyploidy.

Severin AJ, Cannon SB, Graham MM, Grant D, Shoemaker RC.

Plant Cell. 2011 Sep;23(9):3129-36. doi: 10.1105/tpc.111.089573. Epub 2011 Sep 13.


The lipoxygenase gene family: a genomic fossil of shared polyploidy between Glycine max and Medicago truncatula.

Shin JH, Van K, Kim DH, Kim KD, Jang YE, Choi BS, Kim MY, Lee SH.

BMC Plant Biol. 2008 Dec 23;8:133. doi: 10.1186/1471-2229-8-133.


Partitioned expression of duplicated genes during development and evolution of a single cell in a polyploid plant.

Hovav R, Udall JA, Chaudhary B, Rapp R, Flagel L, Wendel JF.

Proc Natl Acad Sci U S A. 2008 Apr 22;105(16):6191-5. doi: 10.1073/pnas.0711569105. Epub 2008 Apr 17.


Molecular evidence for asymmetric evolution of sister duplicated blocks after cereal polyploidy.

Wang H, Yu L, Lai F, Liu L, Wang J.

Plant Mol Biol. 2005 Sep;59(1):63-74.


Extensive translational regulation of gene expression in an allopolyploid (Glycine dolichocarpa).

Coate JE, Bar H, Doyle JJ.

Plant Cell. 2014 Jan;26(1):136-50. doi: 10.1105/tpc.113.119966. Epub 2014 Jan 31.


Contrasting patterns of evolution following whole genome versus tandem duplication events in Populus.

Rodgers-Melnick E, Mane SP, Dharmawardhana P, Slavov GT, Crasta OR, Strauss SH, Brunner AM, Difazio SP.

Genome Res. 2012 Jan;22(1):95-105. doi: 10.1101/gr.125146.111. Epub 2011 Oct 5.


Genome-wide analysis of soybean HD-Zip gene family and expression profiling under salinity and drought treatments.

Chen X, Chen Z, Zhao H, Zhao Y, Cheng B, Xiang Y.

PLoS One. 2014 Feb 3;9(2):e87156. doi: 10.1371/journal.pone.0087156. eCollection 2014.


A comparative transcriptomic study of an allotetraploid and its diploid progenitors illustrates the unique advantages and challenges of RNA-seq in plant species.

Ilut DC, Coate JE, Luciano AK, Owens TG, May GD, Farmer A, Doyle JJ.

Am J Bot. 2012 Feb;99(2):383-96. doi: 10.3732/ajb.1100312. Epub 2012 Feb 1.


Comparative evolution of photosynthetic genes in response to polyploid and nonpolyploid duplication.

Coate JE, Schlueter JA, Whaley AM, Doyle JJ.

Plant Physiol. 2011 Apr;155(4):2081-95. doi: 10.1104/pp.110.169599. Epub 2011 Feb 2.

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