Claude dePamphilis

Affiliate Researcher
Titles and Affiliations
Professor, Biology

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.

In the News

Research Keywords

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Projects

Recent Publications

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 journalArticlepeer-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 journalReview articlepeer-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 4 2023, In: Genome biology and evolution. 15, 1

Research output: Contribution to journalArticlepeer-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 journalArticlepeer-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 journalArticlepeer-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 3 2023, In: Genome biology and evolution. 15, 3

Research output: Contribution to journalArticlepeer-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 journalArticlepeer-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 journalArticlepeer-review

Phylogenomic resolution of order- and family-level monocot relationships using 602 single-copy nuclear genes and 1375 BUSCO genes

Timilsena, P. R., Wafula, E. K., Barrett, C. F., Ayyampalayam, S., McNeal, J. R., Rentsch, J. D., McKain, M. R., Heyduk, K., Harkess, A., Villegente, M., Conran, J. G., Illing, N., Fogliani, B., Ané, C., Pires, J. C., Davis, J. I., Zomlefer, W. B., Stevenson, D. W., Graham, S. W., Givnish, T. J., & 2 othersLeebens-Mack, J. & dePamphilis, C. W., Nov 22 2022, In: Frontiers in Plant Science. 13, 876779.

Research output: Contribution to journalArticlepeer-review

Building a foundation for gene family analysis in Rosaceae genomes with a novel workflow: A case study in Pyrus architecture genes

Zhang, H., Wafula, E. K., Eilers, J., Harkess, AE., Ralph, P. E., Timilsena, P. R., dePamphilis, C. W., Waite, J. M. & Honaas, L. A., Nov 14 2022, In: Frontiers in Plant Science. 13, 975942.

Research output: Contribution to journalArticlepeer-review

The geography of parasite local adaptation to host communities

Bellis, E. S., McLaughlin, C. M., dePamphilis, C. W. & Lasky, J. R., Aug 2021, In: Ecography. 44, 8, p. 1205-1217 13 p.

Research output: Contribution to journalArticlepeer-review

Genomic structural variants constrain and facilitate adaptation in natural populations of Theobroma cacao, the chocolate tree

Hämälä, T., Wafula, E. K., Guiltinan, M. J., Ralph, P. E., dePamphilis, C. W. & Tiffin, P., Aug 31 2021, In: Proceedings of the National Academy of Sciences of the United States of America. 118, 35, e2102914118.

Research output: Contribution to journalArticlepeer-review

Transcriptomics of Differential Ripening in ‘d’Anjou’ Pear (Pyrus communis L.)

Honaas, L., Hargarten, H., Hadish, J., Ficklin, S. P., Serra, S., Musacchi, S., Wafula, E., Mattheis, J., dePamphilis, C. W. & Rudell, D., Jun 16 2021, In: Frontiers in Plant Science. 12, 609684.

Research output: Contribution to journalArticlepeer-review

Insights into angiosperm evolution, floral development and chemical biosynthesis from the Aristolochia fimbriata genome

Qin, L., Hu, Y., Wang, J., Wang, X., Zhao, R., Shan, H., Li, K., Xu, P., Wu, H., Yan, X., Liu, L., Yi, X., Wanke, S., Bowers, J. E., Leebens-Mack, J. H., dePamphilis, C. W., Soltis, P. S., Soltis, D. E., Kong, H. & Jiao, Y., Sep 2021, In: Nature Plants. 7, 9, p. 1239-1253 15 p.

Research output: Contribution to journalArticlepeer-review

In silico identification and structure function analysis of a putative coclaurine N-methyltransferase from Aristolochia fimbriata

Ali, R., Jiao, Y., Kerr Wall, P., Patching, S. G., Ahmad, I., Lutfulla, G. & dePamphilis, C. W., Apr 2020, In: Computational Biology and Chemistry. 85, 107201.

Research output: Contribution to journalArticlepeer-review