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Intergenomic gene transfer in diploid and allopolyploid Gossypium.

Zhao N, Grover CE, Chen Z, Wendel JF, Hua J.

BMC Plant Biol. 2019 Nov 12;19(1):492. doi: 10.1186/s12870-019-2041-2.


Reticulate evolution helps explain apparent homoplasy in floral biology and pollination in baobabs (Adansonia; Bombacoideae; Malvaceae).

Karimi N, Grover CE, Gallagher JP, Wendel JF, Ané C, Baum DA.

Syst Biol. 2019 Nov 6. pii: syz073. doi: 10.1093/sysbio/syz073. [Epub ahead of print]


Salt tolerance diversity in diploid and polyploid cotton (Gossypium) species.

Dong Y, Hu G, Yu J, Thu SW, Grover CE, Zhu S, Wendel JF.

Plant J. 2019 Oct 23. doi: 10.1111/tpj.14580. [Epub ahead of print]


The chromosome-scale reference genome of black pepper provides insight into piperine biosynthesis.

Hu L, Xu Z, Wang M, Fan R, Yuan D, Wu B, Wu H, Qin X, Yan L, Tan L, Sim S, Li W, Saski CA, Daniell H, Wendel JF, Lindsey K, Zhang X, Hao C, Jin S.

Nat Commun. 2019 Oct 16;10(1):4702. doi: 10.1038/s41467-019-12607-6.


De Novo Genome Sequence Assemblies of Gossypium raimondii and Gossypium turneri.

Udall JA, Long E, Hanson C, Yuan D, Ramaraj T, Conover JL, Gong L, Arick MA, Grover CE, Peterson DG, Wendel JF.

G3 (Bethesda). 2019 Oct 7;9(10):3079-3085. doi: 10.1534/g3.119.400392.


DNA methylation repatterning accompanying hybridization, whole genome doubling and homoeolog exchange in nascent segmental rice allotetraploids.

Li N, Xu C, Zhang A, Lv R, Meng X, Lin X, Gong L, Wendel JF, Liu B.

New Phytol. 2019 Jul;223(2):979-992. doi: 10.1111/nph.15820. Epub 2019 Apr 30.


Insights into the Evolution of the New World Diploid Cottons (Gossypium, Subgenus Houzingenia) Based on Genome Sequencing.

Grover CE, Arick MA 2nd, Thrash A, Conover JL, Sanders WS, Peterson DG, Frelichowski JE, Scheffler JA, Scheffler BE, Wendel JF.

Genome Biol Evol. 2019 Jan 1;11(1):53-71. doi: 10.1093/gbe/evy256.


A Malvaceae mystery: A mallow maelstrom of genome multiplications and maybe misleading methods?

Conover JL, Karimi N, Stenz N, Ané C, Grover CE, Skema C, Tate JA, Wolff K, Logan SA, Wendel JF, Baum DA.

J Integr Plant Biol. 2019 Jan;61(1):12-31. doi: 10.1111/jipb.12746.


Cytonuclear Coevolution following Homoploid Hybrid Speciation in Aegilops tauschii.

Li C, Sun X, Conover JL, Zhang Z, Wang J, Wang X, Deng X, Wang H, Liu B, Wendel JF, Gong L.

Mol Biol Evol. 2019 Feb 1;36(2):341-349. doi: 10.1093/molbev/msy215.


Cis-trans controls and regulatory novelty accompanying allopolyploidization.

Hu G, Wendel JF.

New Phytol. 2019 Mar;221(4):1691-1700. doi: 10.1111/nph.15515. Epub 2018 Nov 10.


Cytonuclear responses to genome doubling.

Sharbrough J, Conover JL, Tate JA, Wendel JF, Sloan DB.

Am J Bot. 2017 Sep;104(9):1277-1280. doi: 10.3732/ajb.1700293. No abstract available.


Core cis-element variation confers subgenome-biased expression of a transcription factor that functions in cotton fiber elongation.

Zhao B, Cao JF, Hu GJ, Chen ZW, Wang LY, Shangguan XX, Wang LJ, Mao YB, Zhang TZ, Wendel JF, Chen XY.

New Phytol. 2018 May;218(3):1061-1075. doi: 10.1111/nph.15063. Epub 2018 Feb 21.


The long and short of doubling down: polyploidy, epigenetics, and the temporal dynamics of genome fractionation.

Wendel JF, Lisch D, Hu G, Mason AS.

Curr Opin Genet Dev. 2018 Apr;49:1-7. doi: 10.1016/j.gde.2018.01.004. Epub 2018 Feb 10. Review.


Gene Expression Dominance in Allopolyploids: Hypotheses and Models.

Bottani S, Zabet NR, Wendel JF, Veitia RA.

Trends Plant Sci. 2018 May;23(5):393-402. doi: 10.1016/j.tplants.2018.01.002. Epub 2018 Feb 9. Review.


Comparative Genomics of an Unusual Biogeographic Disjunction in the Cotton Tribe (Gossypieae) Yields Insights into Genome Downsizing.

Grover CE, Arick MA 2nd, Conover JL, Thrash A, Hu G, Sanders WS, Hsu CY, Naqvi RZ, Farooq M, Li X, Gong L, Mudge J, Ramaraj T, Udall JA, Peterson DG, Wendel JF.

Genome Biol Evol. 2017 Dec 1;9(12):3328-3344. doi: 10.1093/gbe/evx248.


Segmental allotetraploidy generates extensive homoeologous expression rewiring and phenotypic diversity at the population level in rice.

Sun Y, Wu Y, Yang C, Sun S, Lin X, Liu L, Xu C, Wendel JF, Gong L, Liu B.

Mol Ecol. 2017 Oct;26(20):5451-5466. doi: 10.1111/mec.14297. Epub 2017 Sep 16.


Evolution of DMSP (dimethylsulfoniopropionate) biosynthesis pathway: Origin and phylogenetic distribution in polyploid Spartina (Poaceae, Chloridoideae).

Rousseau H, Rousseau-Gueutin M, Dauvergne X, Boutte J, Simon G, Marnet N, Bouchereau A, Guiheneuf S, Bazureau JP, Morice J, Ravanel S, Cabello-Hurtado F, Ainouche A, Salmon A, Wendel JF, Ainouche ML.

Mol Phylogenet Evol. 2017 Sep;114:401-414. doi: 10.1016/j.ympev.2017.07.003. Epub 2017 Jul 8.


Gene-body CG methylation and divergent expression of duplicate genes in rice.

Wang X, Zhang Z, Fu T, Hu L, Xu C, Gong L, Wendel JF, Liu B.

Sci Rep. 2017 Jun 1;7(1):2675. doi: 10.1038/s41598-017-02860-4.


Molecular evolution of the plastid genome during diversification of the cotton genus.

Chen Z, Grover CE, Li P, Wang Y, Nie H, Zhao Y, Wang M, Liu F, Zhou Z, Wang X, Cai X, Wang K, Wendel JF, Hua J.

Mol Phylogenet Evol. 2017 Jul;112:268-276. doi: 10.1016/j.ympev.2017.04.014. Epub 2017 Apr 13.


Diversity analysis of cotton (Gossypium hirsutum L.) germplasm using the CottonSNP63K Array.

Hinze LL, Hulse-Kemp AM, Wilson IW, Zhu QH, Llewellyn DJ, Taylor JM, Spriggs A, Fang DD, Ulloa M, Burke JJ, Giband M, Lacape JM, Van Deynze A, Udall JA, Scheffler JA, Hague S, Wendel JF, Pepper AE, Frelichowski J, Lawley CT, Jones DC, Percy RG, Stelly DM.

BMC Plant Biol. 2017 Feb 3;17(1):37. doi: 10.1186/s12870-017-0981-y.


Evolutionary Conservation and Divergence of Gene Coexpression Networks in Gossypium (Cotton) Seeds.

Hu G, Hovav R, Grover CE, Faigenboim-Doron A, Kadmon N, Page JT, Udall JA, Wendel JF.

Genome Biol Evol. 2016 Dec 1;8(12):3765-3783. doi: 10.1093/gbe/evw280.


An examination of nucleotypic effects in diploid and polyploid cotton.

Snodgrass SJ, Jareczek J, Wendel JF.

AoB Plants. 2017 Jan 12;9. pii: plw082. doi: 10.1093/aobpla/plw082. Print 2017 Jan.


Entire nucleotide sequences of Gossypium raimondii and G. arboreum mitochondrial genomes revealed A-genome species as cytoplasmic donor of the allotetraploid species.

Chen Z, Nie H, Grover CE, Wang Y, Li P, Wang M, Pei H, Zhao Y, Li S, Wendel JF, Hua J.

Plant Biol (Stuttg). 2017 May;19(3):484-493. doi: 10.1111/plb.12536. Epub 2017 Feb 2.


Rapid proliferation and nucleolar organizer targeting centromeric retrotransposons in cotton.

Han J, Masonbrink RE, Shan W, Song F, Zhang J, Yu W, Wang K, Wu Y, Tang H, Wendel JF, Wang K.

Plant J. 2016 Dec;88(6):992-1005. doi: 10.1111/tpj.13309. Epub 2016 Nov 1.


Chloroplast DNA Structural Variation, Phylogeny, and Age of Divergence among Diploid Cotton Species.

Chen Z, Feng K, Grover CE, Li P, Liu F, Wang Y, Xu Q, Shang M, Zhou Z, Cai X, Wang X, Wendel JF, Wang K, Hua J.

PLoS One. 2016 Jun 16;11(6):e0157183. doi: 10.1371/journal.pone.0157183. eCollection 2016.


Independent Domestication of Two Old World Cotton Species.

Renny-Byfield S, Page JT, Udall JA, Sanders WS, Peterson DG, Arick MA 2nd, Grover CE, Wendel JF.

Genome Biol Evol. 2016 Jul 2;8(6):1940-7. doi: 10.1093/gbe/evw129.


Insights into the Ecology and Evolution of Polyploid Plants through Network Analysis.

Gallagher JP, Grover CE, Hu G, Wendel JF.

Mol Ecol. 2016 Jun;25(11):2644-60. doi: 10.1111/mec.13626. Epub 2016 May 11. Review.


Evolution of plant genome architecture.

Wendel JF, Jackson SA, Meyers BC, Wing RA.

Genome Biol. 2016 Mar 1;17:37. doi: 10.1186/s13059-016-0908-1. Review.


Rapid evolutionary divergence of Gossypium barbadense and G. hirsutum mitochondrial genomes.

Tang M, Chen Z, Grover CE, Wang Y, Li S, Liu G, Ma Z, Wendel JF, Hua J.

BMC Genomics. 2015 Oct 12;16:770. doi: 10.1186/s12864-015-1988-0.


The wondrous cycles of polyploidy in plants.

Wendel JF.

Am J Bot. 2015 Nov;102(11):1753-6. doi: 10.3732/ajb.1500320. Epub 2015 Oct 8. No abstract available.


Multiple rounds of ancient and recent hybridizations have occurred within the Aegilops-Triticum complex.

Li LF, Liu B, Olsen KM, Wendel JF.

New Phytol. 2015 Oct;208(1):11-2. doi: 10.1111/nph.13563. Epub 2015 Jul 6. No abstract available.


Re-evaluating the phylogeny of allopolyploid Gossypium L.

Grover CE, Gallagher JP, Jareczek JJ, Page JT, Udall JA, Gore MA, Wendel JF.

Mol Phylogenet Evol. 2015 Nov;92:45-52. doi: 10.1016/j.ympev.2015.05.023. Epub 2015 Jun 4.


Unraveling the fabric of polyploidy.

Paterson AH, Wendel JF.

Nat Biotechnol. 2015 May;33(5):491-3. doi: 10.1038/nbt.3217. No abstract available.


Gene-expression novelty in allopolyploid cotton: a proteomic perspective.

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

Genetics. 2015 May;200(1):91-104. doi: 10.1534/genetics.115.174367. Epub 2015 Mar 2.


A re-evaluation of the homoploid hybrid origin of Aegilops tauschii, the donor of the wheat D-subgenome.

Li LF, Liu B, Olsen KM, Wendel JF.

New Phytol. 2015 Oct;208(1):4-8. doi: 10.1111/nph.13294. Epub 2015 Jan 21. No abstract available.


Persistence of subgenomes in paleopolyploid cotton after 60 my of evolution.

Renny-Byfield S, Gong L, Gallagher JP, Wendel JF.

Mol Biol Evol. 2015 Apr;32(4):1063-71. doi: 10.1093/molbev/msv001. Epub 2015 Jan 7.


CenH3 evolution in diploids and polyploids of three angiosperm genera.

Masonbrink RE, Gallagher JP, Jareczek JJ, Renny-Byfield S, Grover CE, Gong L, Wendel JF.

BMC Plant Biol. 2014 Dec 30;14:383. doi: 10.1186/s12870-014-0383-3.


Control of cotton fibre elongation by a homeodomain transcription factor GhHOX3.

Shan CM, Shangguan XX, Zhao B, Zhang XF, Chao LM, Yang CQ, Wang LJ, Zhu HY, Zeng YD, Guo WZ, Zhou BL, Hu GJ, Guan XY, Chen ZJ, Wendel JF, Zhang TZ, Chen XY.

Nat Commun. 2014 Nov 21;5:5519. doi: 10.1038/ncomms6519.


Proteomics profiling of fiber development and domestication in upland cotton (Gossypium hirsutum L.).

Hu G, Koh J, Yoo MJ, Pathak D, Chen S, Wendel JF.

Planta. 2014 Dec;240(6):1237-51. doi: 10.1007/s00425-014-2146-7. Epub 2014 Aug 26.


Doubling down on genomes: polyploidy and crop plants.

Renny-Byfield S, Wendel JF.

Am J Bot. 2014 Oct;101(10):1711-25. doi: 10.3732/ajb.1400119. Epub 2014 Aug 3. Review.


Cytonuclear evolution of rubisco in four allopolyploid lineages.

Gong L, Olson M, Wendel JF.

Mol Biol Evol. 2014 Oct;31(10):2624-36. doi: 10.1093/molbev/msu207. Epub 2014 Jul 10.


Evolution of the BBAA component of bread wheat during its history at the allohexaploid level.

Zhang H, Zhu B, Qi B, Gou X, Dong Y, Xu C, Zhang B, Huang W, Liu C, Wang X, Yang C, Zhou H, Kashkush K, Feldman M, Wendel JF, Liu B.

Plant Cell. 2014 Jul;26(7):2761-76. doi: 10.1105/tpc.114.128439. Epub 2014 Jul 2.


The legacy of diploid progenitors in allopolyploid gene expression patterns.

Buggs RJ, Wendel JF, Doyle JJ, Soltis DE, Soltis PS, Coate JE.

Philos Trans R Soc Lond B Biol Sci. 2014 Aug 5;369(1648). pii: 20130354. doi: 10.1098/rstb.2013.0354. Review.


Contemporary and future studies in plant speciation, morphological/floral evolution and polyploidy: honouring the scientific contributions of Leslie D. Gottlieb to plant evolutionary biology.

Crawford DJ, Doyle JJ, Soltis DE, Soltis PS, Wendel JF.

Philos Trans R Soc Lond B Biol Sci. 2014 Aug 5;369(1648). pii: 20130341. doi: 10.1098/rstb.2013.0341. No abstract available.


Genome-wide disruption of gene expression in allopolyploids but not hybrids of rice subspecies.

Xu C, Bai Y, Lin X, Zhao N, Hu L, Gong Z, Wendel JF, Liu B.

Mol Biol Evol. 2014 May;31(5):1066-76. doi: 10.1093/molbev/msu085. Epub 2014 Feb 27.


Drivers and dynamics of diversity in plant genomes.

Panaud O, Jackson SA, Wendel JF.

New Phytol. 2014 Apr;202(1):15-8. doi: 10.1111/nph.12633. No abstract available.


Ancient gene duplicates in Gossypium (cotton) exhibit near-complete expression divergence.

Renny-Byfield S, Gallagher JP, Grover CE, Szadkowski E, Page JT, Udall JA, Wang X, Paterson AH, Wendel JF.

Genome Biol Evol. 2014 Mar;6(3):559-71. doi: 10.1093/gbe/evu037.


Comparative evolutionary and developmental dynamics of the cotton (Gossypium hirsutum) fiber transcriptome.

Yoo MJ, Wendel JF.

PLoS Genet. 2014 Jan;10(1):e1004073. doi: 10.1371/journal.pgen.1004073. Epub 2014 Jan 2.


Composition and expression of conserved microRNA genes in diploid cotton (Gossypium) species.

Gong L, Kakrana A, Arikit S, Meyers BC, Wendel JF.

Genome Biol Evol. 2013;5(12):2449-59. doi: 10.1093/gbe/evt196.


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.

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