Gene duplications provide raw material for the emergence of novel traits. The two primary mechanisms for gene duplication are polyploidy events, which result in whole genome duplications or triplications (WGD, WGT), and small-scale duplications (SSD). Together, these processes play a crucial role in plant evolution. Mustard crops (Brassica) such as bok choy, broccoli, cabbage, and canola belong to the tribe Brassiceae within the mustard family (Brassicaceae), nested in the larger order Brassicales. These crops share a relatively recent Br-α WGT, which has influenced their domestication, phenotypic plasticity, and secondary metabolism. However, the precise timing and placement of this event on the mustard phylogeny remain unclear.

To resolve this, sequence and fossil data are used to determine when and where the Br-α WGT occurred in Chapter 2. These findings have important implications for understanding the evolution and taxonomy of this group. While extensive research has explored gene duplications in mustard crop species, their wild relatives within tribe Brassiceae remain largely unstudied. A combination of ionomics, metabolomics, and comparative genomics is applied in Chapter 3 to investigate salt and heavy metal stress responses in the mustard crop wild relative Cakile maritima. These analyses identify retained duplicate genes likely contributing to stress adaptation, highlighting the roles of both WGT- and SSD-derived duplications in environmental resilience. These findings highlight the value of crop wild relatives in understanding adaptation and identifying genetic targets for improving stress tolerance in crops.

Beyond tribe Brassiceae, the Br-α WGT is only one of several ancient polyploidies in Brassicales. The At-β WGD is shared by most Brassicales species, but its exact placement remains uncertain. To address this, the first haplotype-resolved genome assembly of Moringa oleifera is generated in Chapter 4, providing a foundation for studying trait evolution following ancient polyploidy. This genome, in combination with other genomic resources, also supports future crop improvement efforts in the species.

Overall, this research advances the understanding of mustard crop evolution and their wild relatives. Studying the evolution of crops and their wild relatives provides valuable insights into agronomically important traits, contributing to the development of sustainable agriculture.

Select Publications

*See Shawn K. Thomas's Google Scholar profile for a full list of his publications.

Thomas SK, Hoek KV, Ogoti T, Duong H, Angelovici R, Pires JC, Mendoza-Cozatl D, Washburn JD, Schenck CA. (2024). Halophytes and heavy metals: A multi-omics approach to understand the role of gene and genome duplication in abiotic stress tolerance of Cakile maritima. American Journal of Botany, 111(8), e16310.

Mabry ME, et al. (2024). Complementing model species with model clades. The Plant Cell, 36(5),1205-1226.

Ruppel M, Nelson SK, Sidberry G, Mitchell M, Kick DR, Thomas SK, Guill KE, Oliver ME, Washburn JD. (2023) RootBot: High-Throughput Root Stress Phenotyping Robot. Applications in Plant Sciences, 11(6), e11541.

Thomas SK, An H, Pires JC. (2023). Mangroves and Multiplications: Influence of genome duplications on salt tolerance. Molecular Ecology, 32(2): 275-277. 

Doctoral Program Committee

• Dr. J Chris Pires, Co-chair
• Dr. Jacob Washburn, Co-chair
• Dr. Jim Birchler
• Dr. David Mendoza-Cozatl