Publications

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Journal Article
S. Renny-Byfield, Gallagher, J. P., Grover, C. E., Szadkowski, E., Page, J. T., Udall, J. A., Wang, X., Paterson, A. H., and Wendel, J. F., “Ancient gene duplicates in Gossypium (Cotton) exhibit near-complete expression divergence”, Genome biology and evolution, vol. 6, no. 3, pp. 559-571, 2014.
L. E. Flagel, Wendel, J. F., and Udall, J. A., “Duplicate gene evolution, homoeologous recombination, and transcriptome characterization in allopolyploid cotton”, BMC genomics, vol. 13, no. 1, p. 302, 2012.
R. Hovav, Udall, J. A., Chaudhary, B., Hovav, E., Flagel, L., Hu, G., and Wendel, J. F., “The evolution of spinnable cotton fiber entailed prolonged development and a novel metabolism”, PLoS Genet, vol. 4, no. 2, p. e25, 2008.
G. Hu, Hovav, R., Grover, C. E., Faigenboim-Doron, A., Kadmon, N., Page, J. T., Udall, J. A., and Wendel, J. F., “Evolutionary Conservation and Divergence of Gene Coexpression Networks in Gossypium (Cotton) Seeds”, Genome Biology and Evolution, p. evw280, 2017.
R. A. Rapp, Haigler, C. H., Flagel, L., Hovav, R. H., Udall, J. A., and Wendel, J. F., “Gene expression in developing fibres of Upland cotton (Gossypium hirsutum L.) was massively altered by domestication”, BMC biology, vol. 8, no. 1, p. 139, 2010.
R. A. Rapp, Udall, J. A., and Wendel, J. F., “Genomic expression dominance in allopolyploids”, Bmc Biology, vol. 7, no. 1, p. 18, 2009.
B. Chaudhary, Hovav, R., Rapp, R., Verma, N., Udall, J. A., and Wendel, J. F., “Global analysis of gene expression in cotton fibers from wild and domesticated Gossypium barbadense”, Evolution & development, vol. 10, no. 5, pp. 567-582, 2008.
J. A. Udall, Swanson, J. M., Haller, K., Rapp, R. A., Sparks, M. E., Hatfield, J., Yu, Y., Wu, Y., Dowd, C., and Arpat, A. B., “A global assembly of cotton ESTs”, Genome research, vol. 16, no. 3, pp. 441-450, 2006.
A. Salmon, Flagel, L., Ying, B., Udall, J. A., and Wendel, J. F., “Homoeologous nonreciprocal recombination in polyploid cotton”, New Phytologist, vol. 186, no. 1, pp. 123-134, 2010.
S. Renny-Byfield, Page, J. T., Udall, J. A., Sanders, W. S., Peterson, D. G., Arick, M. A., Grover, C. E., and Wendel, J. F., “Independent domestication of two old world cotton species”, Genome biology and evolution, vol. 8, no. 6, pp. 1940-1947, 2016.
J. T. Page, Huynh, M. D., Liechty, Z. S., Grupp, K., Stelly, D., Hulse, A. M., Ashrafi, H., Van Deynze, A., Wendel, J. F., and Udall, J. A., “Insights into the evolution of cotton diploids and polyploids from whole-genome re-sequencing”, G3: Genes| Genomes| Genetics, vol. 3, no. 10, pp. 1809-1818, 2013.
R. Hovav, Udall, J. A., Hovav, E., Rapp, R., Flagel, L., and Wendel, J. F., “A majority of cotton genes are expressed in single-celled fiber”, Planta, vol. 227, no. 2, pp. 319-329, 2008.
J. A. Udall, Swanson, J. M., Nettleton, D., Percifield, R. J., and Wendel, J. F., “A novel approach for characterizing expression levels of genes duplicated by polyploidy”, Genetics, vol. 173, no. 3, pp. 1823-1827, 2006.
R. Hovav, Chaudhary, B., Udall, J. A., Flagel, L., and Wendel, J. F., “Parallel domestication, convergent evolution and duplicated gene recruitment in allopolyploid cotton”, Genetics, vol. 179, no. 3, pp. 1725-1733, 2008.
R. Hovav, Udall, J. A., Chaudhary, B., Rapp, R., Flagel, L., and Wendel, J. F., “Partitioned expression of duplicated genes during development and evolution of a single cell in a polyploid plant”, Proceedings of the National Academy of Sciences, vol. 105, no. 16, pp. 6191-6195, 2008.
J. A. Udall and Wendel, J. F., “Polyploidy and crop improvement”, Crop Science, vol. 46, no. Supplement_1, p. S-3-S-14, 2006.
B. Chaudhary, Flagel, L., Stupar, R. M., Udall, J. A., Verma, N., Springer, N. M., and Wendel, J. F., “Reciprocal silencing, transcriptional bias and functional divergence of homeologs in polyploid cotton (Gossypium)”, Genetics, vol. 182, no. 2, pp. 503-517, 2009.
C. E. Grover, Gallagher, J. P., Jareczek, J. J., Page, J. T., Udall, J. A., Gore, M. A., and Wendel, J. F., “Re-evaluating the phylogeny of allopolyploid Gossypium L.”, Molecular phylogenetics and evolution, vol. 92, pp. 45-52, 2015.
C. E. Grover, Gallagher, J. P., Jareczek, J. J., Page, J. T., Udall, J. A., Gore, M. A., and Wendel, J. F., “Re-evaluating the phylogeny of allopolyploid Gossypium L”, Molecular Phylogenetics and Evolution, 2015.
J. A. Udall, Flagel, L. E., Cheung, F., Woodward, A. W., Hovav, R., Rapp, R. A., Swanson, J. M., Lee, J. J., Gingle, A. R., and Nettleton, D., “Spotted cotton oligonucleotide microarrays for gene expression analysis”, Bmc Genomics, vol. 8, no. 1, p. 81, 2007.
A. Salmon, Udall, J. A., Jeddeloh, J. A., and Wendel, J. F., “Targeted capture of homoeologous coding and noncoding sequence in polyploid cotton”, G3: Genes| Genomes| Genetics, vol. 2, no. 8, pp. 921-930, 2012.