Tribe Brassiceae RNAseq and GSS

Sequencing data generated for the publication:Thomas SK et al. 2025. Polyploidy as a taxonomic clade marker for mustard crops and relatives. Annals of Botany (In Review)In this study, we sampled across the tribe Brassiceae (55 transcriptomes and 216 concatenated plastid assemblies) and include appropriate outgroups to addresses the long-standing question of the timing and placement of an ancient polyploidy event in mustard crops and their wild relatives (tribe Brassiceae), the Br-alpha Whole Genome Triplication (WGT).Polyploidy, hybridization, and reticulate evolution often make it harder to understand the evolution of the mustard family, and in this study we advance our current understanding of ancient polyploidy in tribe Brassiceae through a confident placement and timing for the Br-alpha WGT. Despite conflicting topologies among chloroplast and nuclear phylogenies, we find tribe Brassiceae to be consistently monophyletic, however as a whole it does not share the ancient hexaploidy (Br-alpha). Instead, Br-alpha characterizes another clade, which includes most of the tribe Brassiceae, but excludes the clade containing the genera Orychophragmus and Sinalliaria. In addition, our divergence time analyses place the Br-alpha WGT between 12.1 - 10.7 Ma.Large-scale genomic events and other rare genomic characters like ancient polyploidy have indirectly influenced how we define clades but have not always been explicitly used in their circumscription. The current circumscription of tribe Brassiceae is mainly based on a few morphological characters, but species within the tribe vary in which characters they share. Depending on the species, they may contain all, some, or even none of the morphological characters, and the classification of Brassica and relatives has remained controversial since the first assignment by Linnaeus in 1753. Therefore, based on our results, we propose a re-circumscription of the tribe Brassiceae to be defined by the Br-alpha WGT. This presents a stable character, and harkens back to an older circumscription of the tribe before Orychophragmus and Sinalliaria were added.This work is important and timely because the crop species of Brassica are important agronomically and economically, and yet we still lack a complete understanding of their genomic history. In addition, using rare genomic characters as taxonomic clade markers is likely to increase, and this will be one of the first manuscripts that uses polyploidy to define an economically important clade.