Research Summary
Evolution of the flower and the floral developmental program, the study of parasitic plants, chloroplast genome and phylogenomic evolution and Floral Genome Project.
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Research Keywords
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Projects
Recent Publications
Chromosome level assembly and annotation of Cuscuta campestris Yunck. (“field dodder”), a model parasitic plant
Cerda-Herrera, J. D., Zhang, H., Wafula, E. K., Adhikari, S., Park, S. Y., Carey, S. B., Harkess, A., Ralph, P. E., Westwood, J. H., Axtell, M. J. & DePamphilis, C. W., Oct 1 2025, In: Annals of the Entomological Society of America. 15, 10, jkaf193.Research output: Contribution to journal › Article › peer-review
The floral ABCs of Hydnora, one of the most bizarre parasitic plants in the world, and its autotrophic relatives of the order Piperales
Pabón-Mora, N., González, F., dePamphilis, C. W., Bolin, J. F., Neinhuis, C., Alzate, J. F. & Wanke, S., Dec 2025, In: EvoDevo. 16, 1, 16.Research output: Contribution to journal › Article › peer-review
Local gene duplications drive extensive NLR copy number variation across multiple genotypes of Theobroma cacao
Winters, N. P., Wafula, E. K., Timilsena, P. R., Ralph, P. E., Maximova, S. N., De Pamphilis, C. W., Guiltinan, M. J. & Marden, J. H., Sep 2025, In: G3: Genes, Genomes, Genetics. 15, 9, jkaf147.Research output: Contribution to journal › Article › peer-review
A record-setting mitogenome in the holoparasitic plant Balanophorayakushimensis accompanied by exceptional loss of organellar DNA repair and recombination genes
Yu, R., Zhi, X., Ceriotti, L. F., Skippington, E., Rice, D. W., Su, H. J., Barkman, T. J., Sun, C., Liu, Y., Fang, D., Chen, X., dePamphilis, C. W., Mower, J. P., Sanchez-Puerta, M. V., Palmer, J. D. & Zhou, R., Dec 2025, In: BMC Biology. 23, 1, 344.Research output: Contribution to journal › Article › peer-review
Correction to: Variations and reduction of plastome are associated with the evolution of parasitism in Convolvulaceae (Plant Molecular Biology, (2024), 114, 3, (40), 10.1007/s11103-024-01440-1)
Chen, L. Q., Li, X., Yao, X., Li, D. Z., Barrett, C., dePamphilis, C. W. & Yu, W. B., Jun 2024, In: Plant molecular biology. 114, 3, 58.Research output: Contribution to journal › Comment/debate › peer-review
Variations and reduction of plastome are associated with the evolution of parasitism in Convolvulaceae
Chen, L. Q., Li, X., Yao, X., Li, D. Z., Barrett, C., dePamphilis, C. W. & Yu, W. B., Jun 2024, In: Plant molecular biology. 114, 3, 40.Research output: Contribution to journal › Article › peer-review
The cacao gene atlas: a transcriptome developmental atlas reveals highly tissue-specific and dynamically-regulated gene networks in Theobroma cacao L
Kulesza, E., Thomas, P., Prewitt, S. F., Shalit-Kaneh, A., Wafula, E., Knollenberg, B., Winters, N., Esteban, E., Pasha, A., Provart, N., Praul, C., Landherr, L., dePamphilis, C., Maximova, S. N. & Guiltinan, M. J., Dec 2024, In: BMC plant biology. 24, 1, 601.Research output: Contribution to journal › Article › peer-review
A combination of conserved and diverged responses underlies Theobroma cacao’s defense response to Phytophthora palmivora
Winters, N. P., Wafula, E. K., Knollenberg, B. J., Hämälä, T., Timilsena, P. R., Perryman, M., Zhang, D., Sheaffer, L. L., Praul, C. A., Ralph, P. E., Prewitt, S., Leandro-Muñoz, M. E., Delgadillo-Duran, D. A., Altman, N. S., Tiffin, P., Maximova, S. N., dePamphilis, C. W., Marden, J. H. & Guiltinan, M. J., Dec 2024, In: BMC Biology. 22, 1, 38.Research output: Contribution to journal › Article › peer-review
Extra-large G proteins have extra-large effects on agronomic traits and stress tolerance in maize and rice
Cantos, C. F., dePamphilis, C. W. & Assmann, S. M., Sep 2023, In: Trends in Plant Science. 28, 9, p. 1033-1044 12 p.Research output: Contribution to journal › Review article › peer-review
Phylotranscriptomic Analyses of Mycoheterotrophic Monocots Show a Continuum of Convergent Evolutionary Changes in Expressed Nuclear Genes From Three Independent Nonphotosynthetic Lineages
Timilsena, P. R., Barrett, C. F., Piñeyro-Nelson, A., Wafula, E. K., Ayyampalayam, S., McNeal, J. R., Yukawa, T., Givnish, T. J., Graham, S. W., Pires, J. C., Davis, J. I., Ané, C., Stevenson, D. W., Leebens-Mack, J., Martínez-Salas, E., Álvarez-Buylla, E. R. & dePamphilis, C. W., Jan 1 2023, In: Genome biology and evolution. 15, 1, evac183.Research output: Contribution to journal › Article › peer-review
PlantTribes2: Tools for comparative gene family analysis in plant genomics
Wafula, E. K., Zhang, H., Von Kuster, G., Leebens-Mack, J. H., Honaas, L. A. & dePamphilis, C. W., Jan 31 2023, In: Frontiers in Plant Science. 13, 1011199.Research output: Contribution to journal › Article › peer-review
Transcriptomic approach to uncover dynamic events in the development of mid-season sunburn in apple fruit
Waite, J. M., Kelly, E. A., Zhang, H., Hargarten, H. L., Waliullah, S., Altman, N. S., dePamphilis, C. W., Honaas, L. A. & Kalcsits, L., Aug 2023, In: G3: Genes, Genomes, Genetics. 13, 8, jkad120.Research output: Contribution to journal › Article › peer-review
De novo Assembly and Comparative Analyses of Mitochondrial Genomes in Piperales
Yu, R., Chen, X., Long, L., Jost, M., Zhao, R., Liu, L., Mower, J. P., DePamphilis, C. W., Wanke, S. & Jiao, Y., Mar 1 2023, In: Genome biology and evolution. 15, 3, evad041.Research output: Contribution to journal › Article › peer-review
Pervasive Phylogenomic Incongruence Underlies Evolutionary Relationships in Eyebrights (Euphrasia, Orobanchaceae)
Garrett, P., Becher, H., Gussarova, G., dePamphilis, C. W., Ness, R. W., Gopalakrishnan, S. & Twyford, A. D., May 27 2022, In: Frontiers in Plant Science. 13, 869583.Research output: Contribution to journal › Article › peer-review
A derived ZW chromosome system in Amborella trichopoda, representing the sister lineage to all other extant flowering plants
Käfer, J., Bewick, A., Andres-Robin, A., Lapetoule, G., Harkess, A., Caïus, J., Fogliani, B., Gâteblé, G., Ralph, P., dePamphilis, C. W., Picard, F., Scutt, C., Marais, G. A. B. & Leebens-Mack, J., Feb 2022, In: New Phytologist. 233, 4, p. 1636-1642 7 p.Research output: Contribution to journal › Article › peer-review