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Duplicate gene evolution, homoeologous recombination, and transcriptome characterization in allopolyploid cotton.

Flagel LE, Wendel JF, Udall JA.

BMC Genomics. 2012 Jul 6;13:302. doi: 10.1186/1471-2164-13-302.


The cytonuclear dimension of allopolyploid evolution: an example from cotton using rubisco.

Gong L, Salmon A, Yoo MJ, Grupp KK, Wang Z, Paterson AH, Wendel JF.

Mol Biol Evol. 2012 Oct;29(10):3023-36. Epub 2012 Apr 3.


Homoeologous nonreciprocal recombination in polyploid cotton.

Salmon A, Flagel L, Ying B, Udall JA, Wendel JF.

New Phytol. 2010 Apr;186(1):123-34. doi: 10.1111/j.1469-8137.2009.03093.x. Epub 2009 Nov 19.


Rate variation among nuclear genes and the age of polyploidy in Gossypium.

Senchina DS, Alvarez I, Cronn RC, Liu B, Rong J, Noyes RD, Paterson AH, Wing RA, Wilkins TA, Wendel JF.

Mol Biol Evol. 2003 Apr;20(4):633-43. Epub 2003 Apr 2.


Evolutionary rate variation, genomic dominance and duplicate gene expression evolution during allotetraploid cotton speciation.

Flagel LE, Wendel JF.

New Phytol. 2010 Apr;186(1):184-93. doi: 10.1111/j.1469-8137.2009.03107.x. Epub 2009 Nov 19.


Polyploidy and the petal transcriptome of Gossypium.

Rambani A, Page JT, Udall JA.

BMC Plant Biol. 2014 Jan 6;14:3. doi: 10.1186/1471-2229-14-3.


Insights into the evolution of cotton diploids and polyploids from whole-genome re-sequencing.

Page JT, Huynh MD, Liechty ZS, Grupp K, Stelly D, Hulse AM, Ashrafi H, Van Deynze A, Wendel JF, Udall JA.

G3 (Bethesda). 2013 Oct 3;3(10):1809-18. doi: 10.1534/g3.113.007229.


[A and D genome evolution in Gossypium revealed using SSR molecular markers].

Guo WZ, Wang K, Zhang TZ.

Yi Chuan Xue Bao. 2003 Feb;30(2):183-8. Chinese.


Duplicate gene expression in allopolyploid Gossypium reveals two temporally distinct phases of expression evolution.

Flagel L, Udall J, Nettleton D, Wendel J.

BMC Biol. 2008 Apr 16;6:16. doi: 10.1186/1741-7007-6-16.


Microcolinearity and genome evolution in the AdhA region of diploid and polyploid cotton (Gossypium).

Grover CE, Kim H, Wing RA, Paterson AH, Wendel JF.

Plant J. 2007 Jun;50(6):995-1006. Epub 2007 Apr 25.


Genome rearrangements derived from homoeologous recombination following allopolyploidy speciation in coffee.

Lashermes P, Combes MC, Hueber Y, Severac D, Dereeper A.

Plant J. 2014 May;78(4):674-85. doi: 10.1111/tpj.12505. Epub 2014 Apr 23.


Evolution and expression of MYB genes in diploid and polyploid cotton.

Cedroni ML, Cronn RC, Adams KL, Wilkins TA, Wendel JF.

Plant Mol Biol. 2003 Feb;51(3):313-25.


Proteomic profiling of developing cotton fibers from wild and domesticated Gossypium barbadense.

Hu G, Koh J, Yoo MJ, Grupp K, Chen S, Wendel JF.

New Phytol. 2013 Oct;200(2):570-82. doi: 10.1111/nph.12381. Epub 2013 Jun 25.


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.


A global assembly of cotton ESTs.

Udall JA, Swanson JM, Haller K, Rapp RA, Sparks ME, Hatfield J, Yu Y, Wu Y, Dowd C, Arpat AB, Sickler BA, Wilkins TA, Guo JY, Chen XY, Scheffler J, Taliercio E, Turley R, McFadden H, Payton P, Klueva N, Allen R, Zhang D, Haigler C, Wilkerson C, Suo J, Schulze SR, Pierce ML, Essenberg M, Kim H, Llewellyn DJ, Dennis ES, Kudrna D, Wing R, Paterson AH, Soderlund C, Wendel JF.

Genome Res. 2006 Mar;16(3):441-50. Epub 2006 Feb 14.


Characterization of duplicate gene evolution in the recent natural allopolyploid Tragopogon miscellus by next-generation sequencing and Sequenom iPLEX MassARRAY genotyping.

Buggs RJ, Chamala S, Wu W, Gao L, May GD, Schnable PS, Soltis DE, Soltis PS, Barbazuk WB.

Mol Ecol. 2010 Mar;19 Suppl 1:132-46. doi: 10.1111/j.1365-294X.2009.04469.x.


Duplication, divergence and persistence in the Phytochrome photoreceptor gene family of cottons (Gossypium spp.).

Abdurakhmonov IY, Buriev ZT, Logan-Young CJ, Abdukarimov A, Pepper AE.

BMC Plant Biol. 2010 Jun 20;10:119. doi: 10.1186/1471-2229-10-119.


Analysis of complete nucleotide sequences of 12 Gossypium chloroplast genomes: origin and evolution of allotetraploids.

Xu Q, Xiong G, Li P, He F, Huang Y, Wang K, Li Z, Hua J.

PLoS One. 2012;7(8):e37128. doi: 10.1371/journal.pone.0037128. Epub 2012 Aug 2. Erratum in: PLoS One. 2013;8(5). doi: 10.1371/annotation/47563c17-536c-465d-9b93-cd35a78f6e66.

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