Publications

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2003
B. Liu and Wendel, J. F., “Epigenetic phenomena and the evolution of plant allopolyploids”, Molecular phylogenetics and evolution, vol. 29, no. 3, pp. 365-379, 2003.
M. L. Cedroni, Cronn, R. C., Adams, K. L., Wilkins, T. A., and Wendel, J. F., “Evolution and expression of MYB genes in diploid and polyploid cotton”, Plant molecular biology, vol. 51, no. 3, pp. 313-325, 2003.
K. L. Adams, Cronn, R., Percifield, R., and Wendel, J. F., “Genes duplicated by polyploidy show unequal contributions to the transcriptome and organ-specific reciprocal silencing”, Proceedings of the National Academy of Sciences, vol. 100, no. 8, pp. 4649-4654, 2003.
A. Schnabel, McDonel, P. E., and Wendel, J. F., “Phylogenetic relationships in Gleditsia (Leguminosae) based on ITS sequences”, American journal of botany, vol. 90, no. 2, pp. 310-320, 2003.
J. F. Wendel and Cronn, R. C., “Polyploidy and the evolutionary history of cotton”, Advances in agronomy, vol. 78, pp. 139-186, 2003.
D. S. Senchina, Álvarez, I., Cronn, R. C., Liu, B., Rong, J., Noyes, R. D., Paterson, A. H., Wing, R. A., Wilkins, T. A., and Wendel, J. F., “Rate variation among nuclear genes and the age of polyploidy in Gossypium”, Molecular biology and evolution, vol. 20, no. 4, pp. 633-643, 2003.
I. Álvarez and Wendel, J. F., “Ribosomal ITS sequences and plant phylogenetic inference”, Molecular phylogenetics and evolution, vol. 29, no. 3, pp. 417-434, 2003.
2004
R. Cronn and Wendel, J. F., “Cryptic trysts, genomic mergers, and plant speciation”, New Phytologist, vol. 161, no. 1, pp. 133-142, 2004.
K. L. Adams and Wendel, J. F., “Exploring the genomic mysteries of polyploidy in cotton”, Biological Journal of the Linnean Society, vol. 82, no. 4, pp. 573-581, 2004.
C. E. Grover, Kim, H. R., Wing, R. A., Paterson, A. H., and Wendel, J. F., “Incongruent patterns of local and global genome size evolution in cotton”, Genome research, vol. 14, no. 8, pp. 1474-1482, 2004.
R. L. Small, Cronn, R. C., and Wendel, J. F., “LAS Johnson Review No. 2. Use of nuclear genes for phylogeny reconstruction in plants”, Australian Systematic Botany, vol. 17, no. 2, pp. 145-170, 2004.
K. L. Adams, Percifield, R., and Wendel, J. F., “Organ-specific silencing of duplicated genes in a newly synthesized cotton allotetraploid”, Genetics, vol. 168, no. 4, pp. 2217-2226, 2004.
L. H. Rieseberg and Wendel, J. F., “Plant speciation–rise of the poor cousins”, New Phytologist, vol. 161, no. 1, pp. 3-8, 2004.
J. A. Rudgers, Strauss, S. Y., and Wendel, J. F., “Trade-offs among anti-herbivore resistance traits: insights from Gossypieae (Malvaceae)”, American Journal of Botany, vol. 91, no. 6, pp. 871-880, 2004.
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.
J. Rong, Pierce, G. J., Waghmare, V. N., Rogers, C. J., Desai, A., Chee, P. W., O May, L., Gannaway, J. R., Wendel, J. F., and Wilkins, T. A., “Genetic mapping and comparative analysis of seven mutants related to seed fiber development in cotton”, Theoretical and applied genetics, vol. 111, no. 6, pp. 1137-1146, 2005.
V. N. Waghmare, Rong, J., Rogers, C. J., Pierce, G. J., Wendel, J. F., and Paterson, A. H., “Genetic mapping of a cross between Gossypium hirsutum (cotton) and the Hawaiian endemic, Gossypium tomentosum”, Theoretical and Applied Genetics, vol. 111, no. 4, pp. 665-676, 2005.
J. F. Wendel and Adams, K. L., “Genome evolution and gene silencing in polyploid cotton”, REGNUM VEGETABILE, vol. 143, p. 271, 2005.
M. L. Ainouche and Wendel, J. F., “Genome technologies, polyploidy and evolution”, Ecole thématique CNRS “High-throughput molecular biology methods in the environmental sciences”. 2005.
J. S. Hawkins, Pleasants, J., and Wendel, J. F., “Identification of AFLP markers that discriminate between cultivated cotton and the Hawaiian island endemic, Gossypium tomentosumNuttall ex Seeman”, Genetic Resources and Crop Evolution, vol. 52, no. 8, pp. 1069-1078, 2005.
R. A. Rapp, Álvarez, I., and Wendel, J. F., “Molecular confirmation of the position of Gossypium trifurcatum Vollesen”, Genetic Resources and Crop Evolution, vol. 52, no. 6, pp. 749-753, 2005.
K. L. Adams and Wendel, J. F., “Novel patterns of gene expression in polyploid plants”, TRENDS in Genetics, vol. 21, no. 10, pp. 539-543, 2005.
I. Álvarez, Cronn, R., and Wendel, J. F., “Phylogeny of the New World diploid cottons (Gossypium L., Malvaceae) based on sequences of three low-copy nuclear genes”, Plant Systematics and Evolution, vol. 252, no. 3-4, pp. 199-214, 2005.
K. L. Adams and Wendel, J. F., “Polyploidy and genome evolution in plants”, Current opinion in plant biology, vol. 8, no. 2, pp. 135-141, 2005.
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.
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.
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.

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