Publications

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2010
L. E. Flagel and Wendel, J. F., “Evolutionary rate variation, genomic dominance and duplicate gene expression evolution during allotetraploid cotton speciation”, New Phytologist, vol. 186, no. 1, pp. 184-193, 2010.
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.
T. Bureau, Hu, G., Hawkins, J. S., Grover, C. E., and Wendel, J. F., “The history and disposition of transposable elements in polyploid Gossypium”, Genome, vol. 53, no. 8, pp. 599-607, 2010.
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.
Y. Bao, Wendel, J. F., and Ge, S., “Multiple patterns of rDNA evolution following polyploidy in Oryza”, Molecular phylogenetics and evolution, vol. 55, no. 1, pp. 136-142, 2010.
J. F. Wendel, Brubaker, C. L., and Seelanan, T., “The origin and evolution of Gossypium”, in Physiology of cotton, Springer Netherlands, 2010, pp. 1-18.
L. Betancur, Singh, B., Rapp, R. A., Wendel, J. F., M Marks, D., Roberts, A. W., and Haigler, C. H., “Phylogenetically distinct cellulose synthase genes support secondary wall thickening in arabidopsis shoot trichomes and cotton fiber”, Journal of integrative plant biology, vol. 52, no. 2, pp. 205-220, 2010.
C. E. Grover and Wendel, J. F., “Recent insights into mechanisms of genome size change in plants”, Journal of Botany, vol. 2010, 2010.
J. M. Pleasants and Wendel, J. F., “Reproductive and Pollination Biology of the Endemic Hawaiian Cotton, Gossypium tomentosum (Malvaceae) 1”, Pacific Science, vol. 64, no. 1, pp. 45-55, 2010.
2009
L. E. Flagel, Chen, L., Chaudhary, B., and Wendel, J. F., “Coordinated and fine-scale control of homoeologous gene expression in allotetraploid cotton”, Journal of heredity, p. esp003, 2009.
J. F. Wendel, Brubaker, C., Álvarez, I., Cronn, R., and Stewart, J. McD., “Evolution and natural history of the cotton genus”, in Genetics and genomics of cotton, Springer US, 2009, pp. 3-22.
L. E. Flagel and Wendel, J. F., “Gene duplication and evolutionary novelty in plants”, New Phytologist, vol. 183, no. 3, pp. 557-564, 2009.
L. Schmidt, Hu, G., and Wendel, J. F., “Genetic Analysis of Seed Storage Proteins in Gossypium”, 2009.
R. A. Rapp, Udall, J. A., and Wendel, J. F., “Genomic expression dominance in allopolyploids”, Bmc Biology, vol. 7, no. 1, p. 18, 2009.
K. M. Butterworth, Adams, D. C., Horner, H. T., and Wendel, J. F., “Initiation and early development of fiber in wild and cultivated cotton”, International Journal of Plant Sciences, vol. 170, no. 5, pp. 561-574, 2009.
B. Chaudhary, Hovav, R., Flagel, L., Mittler, R., and Wendel, J. F., “Parallel expression evolution of oxidative stress-related genes in fiber from wild and domesticated diploid and polyploid cotton (Gossypium)”, Bmc Genomics, vol. 10, no. 1, p. 378, 2009.
J. S. Hawkins, Proulx, S. R., Rapp, R. A., and Wendel, J. F., “Rapid DNA loss as a counterbalance to genome expansion through retrotransposon proliferation in plants”, Proceedings of the National Academy of Sciences, vol. 106, no. 42, pp. 17811-17816, 2009.
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.
K. L. Adams, Flagel, L., and Wendel, J. F., “Responses of the cotton genome to polyploidy”, in Genetics and Genomics of Cotton, Springer US, 2009, pp. 419-429.
2008
L. Flagel, Udall, J., Nettleton, D., and Wendel, J. F., “Duplicate gene expression in allopolyploid Gossypium reveals two temporally distinct phases of expression evolution”, BMC biology, vol. 6, no. 1, p. 16, 2008.
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.
J. J. Doyle, Flagel, L. E., Paterson, A. H., Rapp, R. A., Soltis, D. E., Soltis, P. S., and Wendel, J. F., “Evolutionary genetics of genome merger and doubling in plants”, Annual review of genetics, vol. 42, pp. 443-461, 2008.
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.
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.
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.
C. E. Grover, Yu, Y., Wing, R. A., Paterson, A. H., and Wendel, J. F., “A phylogenetic analysis of indel dynamics in the cotton genus”, Molecular Biology and Evolution, vol. 25, no. 7, pp. 1415-1428, 2008.
C. Grover, Hawkins, J., and Wendel, J. F., “Phylogenetic insights into the pace and pattern of plant genome size evolution”, 2008.
L. E. Flagel, Rapp, R. A., Grover, C. E., Widrlechner, M. P., Hawkins, J., Grafenberg, J. L., Álvarez, I., Chung, G. Young, and Wendel, J. F., “Phylogenetic, morphological, and chemotaxonomic incongruence in the North American endemic genus Echinacea”, American journal of botany, vol. 95, no. 6, pp. 756-765, 2008.
J. S. Hawkins, Grover, C. E., and Wendel, J. F., “Repeated big bangs and the expanding universe: Directionality in plant genome size evolution”, Plant Science, vol. 174, no. 6, pp. 557-562, 2008.
2007
P. M. Fortune, Schierenbeck, K. A., Ainouche, A. K., Jacquemin, J., Wendel, J. F., and Ainouche, M. L., “Evolutionary dynamics of Waxy and the origin of hexaploid Spartina species (Poaceae)”, Molecular phylogenetics and evolution, vol. 43, no. 3, pp. 1040-1055, 2007.
R. J. Percifield, Hawkins, J. S., McCoy, J. - A., Widrlechner, M. P., and Wendel, J. F., “Genetic diversity in Hypericum and AFLP Markers for species-specific identification of H. perforatum L.”, Planta medica, vol. 73, no. 15, p. 1614, 2007.
C. E. Grover, Kim, H. R., Wing, R. A., Paterson, A. H., and Wendel, J. F., “Microcolinearity and genome evolution in the AdhA region of diploid and polyploid cotton (Gossypium)”, The Plant Journal, vol. 50, no. 6, pp. 995-1006, 2007.
C. Grover, Kim, H., Wing, R. A., and Wendel, J. F., “Microcolinearity in the Allotetraploid Gossypium hirsutum”, Genome Exploitation: Data Mining the Genome, p. 231, 2007.
T. Bureau, Hawkins, J. S., Hu, G., Rapp, R. A., Grafenberg, J. L., and Wendel, J. F., “Phylogenetic determination of the pace of transposable element proliferation in plants: copia and LINE-like elements in Gossypium”, Genome, vol. 51, no. 1, pp. 11-18, 2007.
J. S. Hawkins, Rapp, R. A., and Wendel, J. F., “Rapid DNA loss as a counterbalance to retrotransposon proliferation in plant genome size evolution”, Transposable Elements and Genome Size Dynamics in Gossypium, p. 61, 2007.
C. E. Grover, Hawkins, J. S., and Wendel, J. F., “Tobacco genomes quickly go up in smoke”, New Phytologist, vol. 175, no. 4, pp. 599-602, 2007.
2006
I. Álvarez and Wendel, J. F., “Cryptic interspecific introgression and genetic differentiation within Gossypium aridum (Malvaceae) and its relatives”, Evolution, vol. 60, no. 3, pp. 505-517, 2006.
J. S. Hawkins, Kim, H. R., Nason, J. D., Wing, R. A., and Wendel, J. F., “Differential lineage-specific amplification of transposable elements is responsible for genome size variation in Gossypium”, Genome research, vol. 16, no. 10, pp. 1252-1261, 2006.
A. L. Keyte, Percifield, R., Liu, B., and Wendel, J. F., “Infraspecific DNA methylation polymorphism in cotton (Gossypium hirsutum L.)”, Journal of Heredity, vol. 97, no. 5, pp. 444-450, 2006.
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.
D. S. Senchina, Flagel, L. E., Wendel, J. F., and Kohut, M. L., “Phenetic comparison of sevenEchinacea species based on immunomodulatory characteristics”, Economic botany, vol. 60, no. 3, pp. 205-211, 2006.
J. A. Udall and Wendel, J. F., “Polyploidy and crop improvement”, Crop Science, vol. 46, no. Supplement_1, p. S-3-S-14, 2006.
2005
C. I. Castillo-Davis, Miller, D. J., Ball, E. E., Technau, U., Adams, K. L., Wendel, J. F., Neeman, Y., Dahary, D., Levanon, E. Y., and Sorek, R., “553 Multievidence microarray mining”, Genetics, vol. 21, no. 10, pp. 533-582, 2005.
J. F. Wendel and Doyle, J., “7 Polyploidy and evolution in plants”, Plant diversity and evolution: genotypic and phenotypic variation in higher plants, p. 97, 2005.
K. L. Adams and Wendel, J. F., “Allele-specific, bidirectional silencing of an alcohol dehydrogenase gene in different organs of interspecific diploid cotton hybrids”, Genetics, vol. 171, no. 4, pp. 2139-2142, 2005.
J. F. Wendel, “Epigenetic phenomena and the evolution of plant allopolyploids”, 中国生物学文摘, vol. 19, no. 4, pp. 8-22, 2005.
J. F. Wendel, “Epigenetics and plant evolution.”, New Phytologist, vol. 168, no. 1, pp. 81-91, 2005.
R. A. Rapp and Wendel, J. F., “Epigenetics and plant evolution”, New Phytologist, vol. 168, no. 1, pp. 81-91, 2005.
A. Salmon, Ainouche, M. L., and Wendel, J. F., “Genetic and epigenetic consequences of recent hybridization and polyploidy in Spartina (Poaceae)”, Molecular ecology, vol. 14, no. 4, pp. 1163-1175, 2005.

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