Mesopolyploidy as a taxonomic clade marker for Brassica and relatives (tribe Brassiceae)

Authors: THOMAS, SHAWN - University Of Missouri; ABRAHAMS, R. SHAWN - Purdue University; Kick, Daniel; WALDEN, NORA - University Of Heidelberg; CONANT, GAVIN - North Carolina State University; MCKAIN, MICHAEL - University Of Alabama; AN, HONG - University Of Missouri; ARIAS, TATIANA - Marie Selby Botanical Gardens; EDGAR, PATRICK - Michigan State University; HARKESS, ALEX - Hudsonalpha Institute For Biotechnology; HENDRIKS, KASPER - Naturalis Biodiversity Center; KOCH, MARCUS - University Of Heidelberg; LENS, FREDERIC - Leiden University; LYSAK, MARTIN - Masaryk University; MCALVAY, ALEX - New York Botanical Garden; MUMMENHOFF, KLAUS - University Of Osnabruck; AL-SHEHBAZ, IHSAN - Missouri Botanical Garden; Washburn, Jacob; PIRES, CHRIS - Colorado State University

Submitted to: Annals of Botany
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/23/2025
Publication Date: 8/2/2026
Citation: Thomas, S.K., Abrahams, R., Kick, D.R., Walden, N., Conant, G., Mckain, M.R., An, H., Arias, T., Edgar, P.P., Harkess, A., Hendriks, K.P., Koch, M.A., Lens, F., Lysak, M.A., Mcalvay, A., Mummenhoff, K., Al-Shehbaz, I.A., Washburn, J.D., Pires, C.J. 2026. Mesopolyploidy as a taxonomic clade marker for Brassica and relatives (tribe Brassiceae). Annals of Botany. https://doi.org/10.1093/aob/mcaf170.
DOI: https://doi.org/10.1093/aob/mcaf170

Interpretive Summary: The genetic relationship between different crop species are important for plant breeding and crop improvement. In some groups of species, like mustard family (tribe Brassiceae) which includes economically important crops like canola; radish; broccoli; and others, these relationships are complicated and remain unclear. This project investigated these relationships including better defining species group boundaries and dating the timing of divergence between these groups. This information helps scientists better understand the relationships between species and inform future research and breeding efforts in this important crop family.

Technical Abstract: Whole Genome Duplications (WGD) are rampant in flowering plant genomes. Within Brassicaceae, the genus Brassica (including crop mustards) and relatives (tribe Brassiceae) are hypothesized to share an ancient mesohexaploidy, or whole genome triplication (WGT), resulting from two WGD events (Br-a WGT). However, the phylogenetic boundaries of the Br-a WGT remain unknown. We use phylogenomic assessments and divergence time analyses to place and date Br-a WGT. We see conflicting topologies among the plastid and nuclear trees putatively due to polyploidy, hybridization, and reticulate evolution. Despite this, we find Brassiceae to be monophyletic in both trees. As currently circumscribed, Brassiceae does not share the Br-a WGT. The sister clade to the rest of the tribe, containing the genera Orychophragmus and Sinalliaria, shows no evidence of Br-a WGT. Based on this placement, divergence time analyses indicate that Br-a WGT would have occurred between 12.1-10.7 million years ago. We propose a new taxonomic revision for Brassiceae based on the shared characteristics of the Br-a WGT. This presents a stable characteristic for the tribe, which was not the case in previous taxonomies based on morphological characters. These findings help clarify the history of the mustard crops and their relatives and resolve long-standing issues with the circumscription of the tribe Brassiceae.