Publications

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2015
C. E. Grover, Gallagher, J. P., and Wendel, J. F., “Candidate Gene Identification of Flowering Time Genes in Cotton”, The Plant Genome, 2015.
L. Gong, Masonbrink, R. E., Grover, C. E., Renny-Byfield, S., and Wendel, J. F., “A Cluster of Recently Inserted Transposable Elements Associated with siRNAs in”, The Plant Genome, 2015.
G. Hu, Koh, J., Yoo, M. - J., Chen, S., and Wendel, J. F., “Gene-Expression Novelty in Allopolyploid Cotton: A Proteomic Perspective”, Genetics, 2015.
G. Hu, Koh, J., Yoo, M. - J., Chen, S., and Wendel, J. F., “Gene-Expression Novelty in Allopolyploid Cotton: A Proteomic Perspective”, Genetics, vol. 200, no. 1, pp. 91-104, 2015.
J. McD. Stewart, Craven, L. A., Brubaker, C., and Wendel, J. F., “Gossypium anapoides (Malvaceae), a new species from Western Australia”, Novon, vol. 23, no. 4, pp. 447-451, 2015.
L. ‐F. Li, Liu, B., Olsen, K. M., and Wendel, J. F., “Multiple rounds of ancient and recent hybridizations have occurred within the Aegilops–Triticum complex”, New Phytologist, 2015.
S. Renny-Byfield, Gong, L., Gallagher, J. P., and Wendel, J. F., “Persistence of Subgenomes in Paleopolyploid Cotton after 60 My of Evolution”, Molecular biology and evolution, vol. 32, no. 4, pp. 1063-1071, 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, 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.
L. ‐F. Li, Liu, B., Olsen, K. M., and Wendel, J. F., “A re‐evaluation of the homoploid hybrid origin of Aegilops tauschii, the donor of the wheat D‐subgenome”, New Phytologist, 2015.
J. F. Wendel and Grover, C. E., “Taxonomy and Evolution of the Cotton Genus, Gossypium”, Cotton, no. agronmonogr57, 2015.
R. Hovav, Faigenboim-Doron, A., Kadmon, N., Hu, G., Zhang, X., Gallagher, J. P., and Wendel, J. F., “A Transcriptome Profile for Developing Seed of Polyploid Cotton”, The Plant Genome, vol. 8, no. 1, 2015.
A. H. Paterson and Wendel, J. F., “Unraveling the fabric of polyploidy”, Nature Biotechnology, vol. 33, no. 5, pp. 491-493, 2015.
A. H. Paterson and Wendel, J. F., “Unraveling the fabric of polyploidy”, Nature biotechnology, vol. 33, no. 5, pp. 491-493, 2015.
2014
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.
R. E. Masonbrink, Gallagher, J. P., Jareczek, J. J., Renny-Byfield, S., Grover, C. E., Gong, L., and Wendel, J. F., “CenH3 evolution in diploids and polyploids of three angiosperm genera”, BMC plant biology, vol. 14, no. 1, p. 383, 2014.
M. - J. Yoo and Wendel, J. F., “Comparative evolutionary and developmental dynamics of the cotton (Gossypium hirsutum) fiber transcriptome”, 2014.
D. J. Crawford, Doyle, J. J., Soltis, D. E., Soltis, P. S., and Wendel, J. F., “Contemporary and future studies in plant speciation”, 2014.
D. J. Crawford, Doyle, J. J., Soltis, D. E., Soltis, P. S., and Wendel, J. F., “Contemporary and future studies in plant speciation, morphological/floral evolution and polyploidy: honouring the scientific contributions of Leslie D. Gottlieb to plant evolutionary biology”, Philosophical Transactions of the Royal Society B: Biological Sciences, vol. 369, no. 1648, p. 20130341, 2014.
L. Gong, Olson, M., and Wendel, J. F., “Cytonuclear evolution of rubisco in four allopolyploid lineages”, Molecular biology and evolution, vol. 31, no. 10, pp. 2624-2636, 2014.
S. Renny-Byfield and Wendel, J. F., “Doubling down on genomes: polyploidy and crop plants”, American journal of botany, vol. 101, no. 10, pp. 1711-1725, 2014.
O. Panaud, Jackson, S. A., and Wendel, J. F., “Drivers and dynamics of diversity in plant genomes”, New Phytologist, vol. 202, no. 1, pp. 15-18, 2014.
C. Xu, Bai, Y., Lin, X., Zhao, N., Hu, L., Gong, Z., Wendel, J. F., and Liu, B., “Genome-wide disruption of gene expression in allopolyploids but not hybrids of rice subspecies”, Molecular biology and evolution, vol. 31, no. 5, pp. 1066-1076, 2014.
J. E. Coate, Buggs, R. J. A., Wendel, J. F., Doyle, J. J., Soltis, D. E., and Soltis, P. S., “The legacy of diploid progenitors in allopolyploid gene”, 2014.
R. J. A. Buggs, Wendel, J. F., Doyle, J. J., Soltis, D. E., Soltis, P. S., and Coate, J. E., “The legacy of diploid progenitors in allopolyploid gene expression patterns”, Philosophical Transactions of the Royal Society B: Biological Sciences, vol. 369, no. 1648, p. 20130354, 2014.
C. E. Grover, Zhu, X., Grupp, K. K., Jareczek, J. J., Gallagher, J. P., Szadkowski, E., Seijo, J. G., and Wendel, J. F., “Molecular confirmation of species status for the allopolyploid cotton species, Gossypium ekmanianum Wittmack”, Genetic Resources and Crop Evolution, vol. 62, no. 1, pp. 103-114, 2014.
M. L. Ainouche and Wendel, J. F., “Polyploid speciation and genome evolution: Lessons from recent allopolyploids”, in Evolutionary Biology: Genome Evolution, Speciation, Coevolution and Origin of Life, Springer International Publishing, 2014, pp. 87-113.
G. Hu, Koh, J., Yoo, M. - J., Pathak, D., Chen, S., and Wendel, J. F., “Proteomics profiling of fiber development and domestication in upland cotton (Gossypium hirsutum L.)”, Planta, vol. 240, no. 6, pp. 1237-1251, 2014.
2013
K. M. Olsen and Wendel, J. F., “A bountiful harvest: genomic insights into crop domestication phenotypes”, Annual Review of Plant Biology, vol. 64, pp. 47-70, 2013.
L. Gong, Kakrana, A., Arikit, S., Meyers, B. C., and Wendel, J. F., “Composition and expression of conserved microRNA genes in diploid cotton (Gossypium) species”, Genome biology and evolution, vol. 5, no. 12, pp. 2449-2459, 2013.
K. M. Olsen and Wendel, J. F., “Crop plants as models for understanding plant adaptation and diversification”, Frontiers in plant science, vol. 4, 2013.
K. L. Adams and Wendel, J. F., “Dynamics of duplicated gene expression in Polyploid Cotton”, Polyploid and hybrid genomics, pp. 187-194, 2013.
A. Madlung and Wendel, J. F., “Genetic and epigenetic aspects of polyploid evolution in plants”, Cytogenetic and genome research, vol. 140, no. 2-4, pp. 270-285, 2013.
M. J. Yoo, Szadkowski, E., and Wendel, J. F., “Homoeolog expression bias and expression level dominance in allopolyploid cotton”, Heredity, vol. 110, no. 2, pp. 171-180, 2013.
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.
J. F. Wendel, “Jeans, Genes, and The Independent Domestications Of Cotton”, Plant and Animal Genome XXI Conference. Plant and Animal Genome, 2013.
G. Hu, Koh, J., Yoo, M. ‐J., Grupp, K., Chen, S., and Wendel, J. F., “Proteomic profiling of developing cotton fibers from wild and domesticated Gossypium barbadense”, New Phytologist, vol. 200, no. 2, pp. 570-582, 2013.
2012
C. E. Grover, Grupp, K. K., Wanzek, R. J., and Wendel, J. F., “Assessing the monophyly of polyploid Gossypium species”, Plant systematics and evolution, vol. 298, no. 6, pp. 1177-1183, 2012.
L. Gong, Salmon, A., Yoo, M. - J., Grupp, K. K., Wang, Z., Paterson, A. H., and Wendel, J. F., “The cytonuclear dimension of allopolyploid evolution: an example from cotton using rubisco”, Molecular biology and evolution, vol. 29, no. 10, pp. 3023-3036, 2012.
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.
C. E. Grover, Gallagher, J. P., Szadkowski, E. P., Yoo, M. J., Flagel, L. E., and Wendel, J. F., “Homoeolog expression bias and expression level dominance in allopolyploids”, New Phytologist, vol. 196, no. 4, pp. 966-971, 2012.
J. F. Wendel, Flagel, L. E., and Adams, K. L., “Jeans, genes, and genomes: cotton as a model for studying polyploidy”, in Polyploidy and genome evolution, Springer Berlin Heidelberg, 2012, pp. 181-207.
J. Greilhuber, Dolezel, J., Leitch, I. J., and Wendel, J. F., Plant Genome Diversity: Vol. 1: Plant Genomes, Their Residents, and Their Evolutionary Dynamics. Springer, 2012.
I. J. Leitch, Greilhuber, J., Dolezel, J., and Wendel, J. F., Plant Genome Diversity Volume 2: Physical Structure, Behaviour and Evolution of Plant Genomes, vol. 2. Springer Science & Business Media, 2012.
A. H. Paterson, Wendel, J. F., Gundlach, H., Guo, H., Jenkins, J., Jin, D., Llewellyn, D., Showmaker, K. C., Shu, S., and Udall, J., “Repeated polyploidization of Gossypium genomes and the evolution of spinnable cotton fibres”, Nature, vol. 492, no. 7429, pp. 423-427, 2012.
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.
C. E. Grover, Salmon, A., and Wendel, J. F., “Targeted sequence capture as a powerful tool for evolutionary analysis1”, American journal of botany, vol. 99, no. 2, pp. 312-319, 2012.
2011
G. Hu, Houston, N. L., Pathak, D., Schmidt, L., Thelen, J. J., and Wendel, J. F., “Genomically biased accumulation of seed storage proteins in allopolyploid cotton”, Genetics, vol. 189, no. 3, pp. 1103-1115, 2011.
C. L. Richards and Wendel, J. F., “The hairy problem of epigenetics in evolution”, New Phytologist, vol. 191, no. 1, pp. 7-9, 2011.
Y. Bao, Hu, G., Flagel, L. E., Salmon, A., Bezanilla, M., Paterson, A. H., Wang, Z., and Wendel, J. F., “Parallel up-regulation of the profilin gene family following independent domestication of diploid and allopolyploid cotton (Gossypium)”, Proceedings of the National Academy of Sciences, vol. 108, no. 52, pp. 21152-21157, 2011.

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