In our lab we work on the fascinating connections between molecular evolutionary processes and genotypic/phenotypic diversity.  Our many research projects explore various aspects of  molecular and genome evolution, phylogenetics, and phenotypic evolution of higher plants.  We use a diverse set of technologies and approaches to explore the manner in which genomes change over evolutionary time, as well as the relationship between these events and morphological change. We have a particular interest in the mysterious and common phenomenon of genome doubling, or polyploidy, with a special focus on the cotton genus (Gossypium).   Read more about

Research

Polyploid speciation is exceptionally common in plants, often operating sympatrically to saltationally generate new lineages.

Comparative evolutionary genomics and domestication genomics are among the most active areas of research in the lab. Please check back here often for updates on our massive genomic resequencing effort, our comparative molecular evolutionary analyses, and our work on domestication genomics.

Somewhat remarkably, given its importance in human commence, new species of cotton continue to be discovered.  Our lab is among the few worldwide that maintains an active interest in fundamental plant exploration and discovery in the cotton genus.

One of the important realizations to emerge from numerous studies of polyploid plants is that polyploid creates massive alterations in gene expression. 

Recent Publications

Garcia, S., J.F.Wendel, N. Borowska-Zuchowska, M. Aïnouche, J. Lunerova and A. Kovarik. 2020. The utility of graph clustering for the identification of evolutionary fates of 5S rDNA homoeologs in plant allopolyploids and hybrids. Frontiers in Plant Science 11:41.

Grover, C. E., M. Yoo, M. A. Gore, D. B. Harker, R. L. Byers, A. E. Lipka, G. Hu, D. Yuan, J. L. Conover, J. A. Udall, A. H. Paterson, and J. F. Wendel. 2020. Genetic analysis of the transition from wild to domesticated cotton (G. hirsutum). Genes, Genomes, and Genetics 10:731-754.

Rousseau-Guetin, M. and J. F. Wendel. 2020. Barbara McClintock, a pioneer in the study of polyploidy. In Perspectives on Nobel Laureate Barbara McClintock's publications (1926-1984): A Companion Volume (Lee B. Kass, Ed.)

Dong, Y., G. Hu, J. Yu, S. W. Thu, C. E. Grover, S. Zhu, and J. F. Wendel. 2020. Salt tolerance in diploid and polyploid cotton (Gossypium) species. The Plant Journal 101: 1135-1151.

Grover, C. E., M. Pan, D. Yuan, M. A. Arick, G. Hu, L. Brase, D.Stelly, Z. Lu, R. J. Schmitz, D. G. Peterson, J. F. Wendel, and J. A. Udall. 2020. The Gossypium longicalyx genome as a resource and implications for cotton breeding and evolution. Genes, Genomes, and Genetics doi:10.1534/g3.120.401050.

Hu, G., C. E. Grover, M. A. Arick, M. Liu, D. G. Peterson, and J. F. Wendel. 2020. Homoeologous gene expression and co-expression network analyses and evolutionary inference in allopolyploids. Briefings in Bioinformatics doi: 10.1093/bib/bbaa035.

Karimi, N., C. E. Grover, J. P. Gallagher, J. F. Wendel, C. Ané, and D. A. Baum. Reticulate evolution helps explain apparent homoplasy in floral biology and pollination in baobabs (Adansonia; Bombacoideae; Malvaceae). 2020. Systematic Biology 69: 462–478, 2020.

Chen, Z. J., A. Sreedasyam, A. Ando, Q. Song, L. M. De Santiago, A. M. Hulse-Kemp, M. Ding, W. Ye, R. C. Kirkbride, J. Jenkins, C. Plott, J. Lovell, Y.-M. Lin, R. Vaughn, B. Liu, L. Wen, S. Simpson, B. E. Scheffler, C. A. Saski, C. E. Grover, G. Hu, J. Conover, J. Carlson, S. Shu, L. B. Boston, M. Williams, D. G. Peterson, K. McGee, D. C. Jones, J. F. Wendel, D. M. Stelly, J. Grimwood, and J. Schmutz. 2020. Genomic diversifications of five Gossypium allopolyploid species and their impact on cotton improvement. Nature Genetics  https://doi.org/10.1038/s41588-020-0614-5.

Cao J.-F., Zhao B., Huang C.-C., Chen Z.-W., Zhao T., Liu H.-R., Hu G.-J., Shangguan X.-X., Shan C.-M., Wang L.-J., Zhang T.-Z., Wendel J.F., Guan X.-Y., and Chen X.-Y. 2020. The miR319-targeted ghtcp4 promotes the transition from cell elongation to wall thickening in cotton fiber. Molecular Plant 13: 1063–1077.

Chen, Z., J. Zhao, J. Qiao, W. Li, J. Li, R. Xu, Z. Liu, B. Xing, J. F. Wendel, and C. E. Grover. 2020. Comparative analysis of codon usage between Gossypium hirsutum and G. barbadense mitochondrial genomes. Mitochondrial DNA, part B, 56: 2500–2506.

Li, C., X. Wang, Y. Xiao, X. Sun, J. Wang, X. Yang, Y. Sun, Y. Sha, R. Lv, Y. Yu, B. Ding, Z. Zhang, N. Li, T. Wang, J. F. Wendel, B. Liu, and L. Gong. 2020. Cytonuclear co-evolution of rubisco small subunits and plastid translocons accompanying sequential allopolyploidy events in Triticum. Molecular Biology and Evolution https://doi.org/10.1093/molbev/msaa158.

Nieto-Feliner, G., J. Casacuberta, and J. F. Wendel. 2020. Genomics of evolutionary novelty in hybrids and polyploids. Frontiers in Genetics doi: 10.3389/fgene.2020.00792.

Escudero, M. and J. F. Wendel. 2020. The grand sweep of chromosomal evolution in angiosperms. The New Phytologist https://doi.org/10.1111/nph.16802.

Gallagher, J. P., G. Hu, C. E. Grover, J.J. Jareczek and J. F. Wendel. 2020. Effects of genome duplication and domestication on the fiber gene coexpression network of Gossypium hirsutum L. Genes, Genomes and Genetics 10: 2879-2892.

Cao, J., J. Huang, C. Huang, X. Zhang, X. Shangguan, L. Wang, J. F. Wendel, C. E. Grover and Z. Chen. 2020. Genome-wide characterization of the miR396-targeted GRF family genes and their roles in response to salt stresses in Gossypium hirsutum. BMG Genomics 21:575, https://doi.org/10.1186/s12864-020-06986-0.

Mason, A.S., and J. F. Wendel. 2020. Homoeologous exchanges, segmental allopolyploidy and polyploid diversification. Frontiers in Genetics 11:1014, doi: 10.3389/fgene.2020.01014

Hu, G. and J. F. Wendel. 2019. Cis-trans controls and regulatory novelty accompanying allopolyploidization. New Phytologist 221: 1691–1700.

Li, C., X. Sun, J. L. Conover, Z. Zhang, J. Wang, X. Wang, X. Deng, H. Wang, B. Liu, J. F. Wendel and L. Gong. 2019. Cytonuclear coevolution following homoploid hybrid speciation in Aegilops tauschii. Molecular Biology and Evolution 36:341–349  https://doi.org/10.1093/molbev/msy215.

Grover, C. E., M. A. Arick, A. Thrash, J. L. Conover, W. S. Sanders, D. G. Peterson, J. E. Frelichowski, J. A. Scheffler, B. E. Scheffler, and J. F. Wendel. 2019. Insights into the evolution of the New World diploid cottons (Gossypium, subgenus Houzingenia) based on genome sequencing. Genome Biology and Evolution 11: 53–71.

Conover, J. L., N. Karimi, N. Stenz, C. Ané, C. E. Grover, C. Skema, J. A. Tate, K. Wolff, S. Logan, J. F. Wendel, and D. A. Baum. 2019. A Malvaceae mystery: a mallow maelstrom of genome multiplications and maybe misleading methods? Journal of Integrative Plant Biology 61:12-31.

Li, N., C. Xu, A. Zhang, R. Liu, X. Meng, X. Lin, L. Gong, J. F. Wendel and B. Liu. 2019. DNA methylation due to repatterning accompanying separate and combined effects of hybridization, whole genome doubling and homoeolog exchange in nascent segmental rice allotetraploids. The New Phytologist 223: 979–992.

Hu, L., Z. Xu, M. Wang, D. Yuan, R. Fan, B. Wu, H. Wu, X. Qin, L. Yan, L. Tan, S. Sim, W. Li, C. A. Saski, H. Daniell, J. F. Wendel, K. Lindsey, X. Zhang, C. Hao and S. Jin. The chromosome-scale reference genome of black pepper (Piper nigrum L.) provides further insight into piperine biosynthesis. 2019. Nature Communications 10: 4702, doi.org/10.1038/s41467-019-12607-6.

Udall, J.A., E. Long, C. Hanson, D. Yuan, T. Ramaraj, J. L. Conover, L. Gong, M. A. Arick, C. E. Grover, D. G. Peterson, and J. F. Wendel. 2019. De novo genome sequence assemblies of Gossypium raimondii and G. turneri. Genes, Genomes, and Genomics 9: 3079-3085.

Hu, G., C. E. Grover, D. Yuan, Y. Dong, E. Miller, J. L. Conover, J. F. Wendel. 2019. Evolution and diversity of the cotton genome. In: Cotton Precision Breeding (Mehboob-ur-Rahman, Yusuf Zafar and Tianzhen Zhang, Eds.), Springer.

Karimi, N., C. E. Grover, C. Ané, J. P. Gallagher, J. F. Wendel, D. A. Baum. Species networks and ancient introgression in the baobabs, Adansonia (Bombacoideae; Malvaceae). 2019. Systematic Biology https://doi.org/10.1093/sysbio/syz073.

Zhao, N., C. E. Grover, Z. Chen, J. F. Wendel, and J. Hua. Intergenomic gene transfer (IGT) and allopolyploidization in Gossypium. 2019. BMC Plant Biology 19:492.

Udall, J.A., E. Long, T. Ramaraj, J. L. Conover, D. Yuan, C. E. Grover, L. Gong, M. A. Arick, R. E. Masonbrink, D. G. Peterson, and J. F. Wendel. 2019. Comparative genomics implicates a breakage-fusion-bridge mechanism for descending dysploidy in plants. Frontiers in Plant Science 10:1541.

Dong, Y., G. Hu, J. Yu, S. W. Thu, C. E. Grover, S. Zhu, and J. F. Wendel. 2019. Salt tolerance in diploid and polyploid cotton (Gossypium) species. The Plant Journal doi: 10.1111/tpj.14580.

Bao, Y., G. Hu, C.E. Grover, J. Conover, D. Yuan, and J. F. Wendel. 2019. Unraveling cis and trans regulatory evolution during cotton domestication. Nature Communications 10.1038/s41467-019-13386-w.

Cao, J., J. Huang, C. Huang, X. Zhang, X. Shangguan, L. Wang, J. F. Wendel, C. E. Grover and Z. Chen. 2020. Genome-wide characterization of the miR396-targeted GRF family genes and their roles in response to salt stresses in Gossypium hirsutum. BMG Genomics (in review).

Garcia, S., J.F.Wendel, N. Borowska-Zuchowska, M. Aïnouche, J. Lunerova and A. Kovarik. 2020. The utility of graph clustering for the identification of evolutionary fates of 5S rDNA homoeologs in plant allopolyploids and hybrids. Frontiers in Plant Science .

Grover, C. E., M. Pan, D. Yuan, M. A. Arick, G. Hu, L. Brase, D.Stelly, Z. Lu, R. J. Schmitz, D. G. Peterson, J. F. Wendel, and J. A. Udall. The Gossypium longicalyx genome as a resource and implications for cotton breeding and evolution. Genes, Genomes, and Genomics (in review).

Grover, C. E., M. Yoo, M. A. Gore, D. B. Harker, R. L. Byers, A. E. Lipka, G. Hu, D. Yuan, J. L. Conover, J. A. Udall, A. H. Paterson, and J. F. Wendel. 2020. Genetic analysis of the transition from wild to domesticated cotton (G. hirsutum). Genes, Genomes, and Genomics doi:10.1534/g3.119.400909

X. Chen; J.-Feng Cao; B. Zhao; C. Huang; Z. Chen; T. Zhao; H. Liu; G. Hu; X. Shangguan; C. Shan; L. Wang; T. Zhang; J. F. Wendel; X. Guan. 2020. Molecular Plant (in review). GhTCP4 promotes the transition from cell elongation to wall thickening in cotton fiber.

Rousseau-Guetin, M. and J. F. Wendel. 2020. Barbara McClintock, a pioneer in the study of polyploidy. In Perspectives on Nobel Laureate Barbara McClintock's publications (1926-1984): A Companion Volume (Lee B. Kass, Ed.)

Hu, G., C. E. Grover, M. A. Arick, M. Liu, D. G. Peterson, and J. F. Wendel. 2020. Homoeologous gene expression and co-expression network analyses and evolutionary inference in allopolyploids. Briefings in Bioinformatics (in review).

Wendel, J. F., D. Lisch, G. Hu,  and A. S. Mason. 2018. The long and short of doubling down: polyploidy, epigenetics, and the temporal dynamics of genome fractionation. Current Opinion in Genetics and Development 49:1–7.

Zhao, B., J.-F. Cao, G. Hu, Z. W. Chen, L.-Y. Wang, X.-X. Shangguan, L.-J. Wang, Y.-B. Mao, T. Zhang, J. F. Wendel, and X.-Y. Chen. 2018. Core cis-element variation confers subgenome-biased expression of a transcription factor that functions in cotton fiber elongation. New Phytologist 18: 1061-1075.

Bottani, S.,  N. Radu Zabet, J. F. Wendel and R. A. Veitia. 2018. Gene expression dominance in allopolyploids: hypotheses and models. Trends in Plant Science https://doi.org/10.1016/j.tplants.2018.01.002.

Wang, K., J. F. Wendel, and J. Hua. 2018. Designations for individual genomes and chromosomes in Gossypium. Journal of Cotton Research 1:3-7, https://doi.org/10.1186/s42397-018-0002-1.

Hu, G. and J. F. Wendel. 2018. Cis-trans controls and regulatory novelty accompanying allopolyploidization. New Phytologist doi.org/10.1111/nph.15515.

Li, C., X. Sun, J. L. Conover, Z. Zhang, J. Wang, X. Wang, X. Deng, H. Wang, B. Liu, J. F. Wendel and L. Gong. 2018. Cytonuclear coevolution following homoploid hybrid speciation in Aegilops tauschii. Molecular Biology and Evolution https://doi.org/10.1093/molbev/msy215.

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