Windham, M. | Search bioRxiv

bioRxiv2025

Boechera or not? Genomic insights and taxonomic reassessment of the misclassified Asian species B. calcarea (Brassicaceae)

The genus Boechera (Brassicaceae) serves as a model system for studying apomictic reproduction and ecological adaptations, with most species concentrated in North America. Rare occurrences of Boechera species beyond their typical range offers unique opportunities to investigate genome evolution in extralimital environments. One such species, B. calcarea, was described from the Chandalaz Range in northeastern Asia (Russia). This study aimed to investigate the genome structure and evolutionary history of B. calcarea. However, our analyses reveal that the species does not belong to Boechera. Instead, an integrative approach combining cytogenetic, phylogenetic and repeatome analyses identified the species as a member of an ancestral clades within the tribe Arabideae. The diploid Parryodes calcarea (Dudkin) D.A.German & Lysak (2n = 16) exhibits Arabideae-specific chromosomal signatures, including multiple centromere repositionings. These findings clarify the misattribution of P. calcarea to Boechera, leaving Boechera falcata and Borodinia macrophylla as the only Old World representatives of the Boechereae. This study highlights the importance of integrative methodologies in resolving taxonomic ambiguities and provides new insights into the diversification of the largest cruciferous tribe, Arabideae.

plant biology↗

bioRxiv2022

Global Phylogeny of the Brassicaceae Provides Important Insights into Gene Discordance

The mustard family (Brassicaceae) is a scientifically and economically important family, containing the model plant Arabidopsis thaliana and numerous crop species that feed billions worldwide. Despite its relevance, most published family phylogenies are incompletely sampled, generally contain massive polytomies, and/or show incongruent topologies between datasets. Here, we present the most complete Brassicaceae genus-level family phylogenies to date (Brassicaceae Tree of Life, or BrassiToL) based on nuclear (>1,000 genes, almost all 349 genera and 53 tribes) and plastome (60 genes, 79% of the genera, all tribes) data. We found cytonuclear discordance between nuclear and plastome-derived phylogenies, which is likely a result of rampant hybridisation among closely and more distantly related species, and highlight rogue taxa. To evaluate the impact of this rampant hybridisation on the nuclear phylogeny reconstruction, we performed four different sampling routines that increasingly removed variable data and likely paralogs. Our resulting cleaned subset of 297 nuclear genes revealed high support for the tribes, while support for the main lineages remained relatively low. Calibration based on the 20 most clock-like nuclear genes suggests a late Eocene to late Oligocene icehouse origin of the family. Finally, we propose five new or re-established tribes, including the recognition of Arabidopsideae, a monotypic tribe to accommodate Arabidopsis. With a worldwide community of thousands of researchers working on this family, our new, densely sampled family phylogeny will be an indispensable tool to further highlight Brassicaceae as an excellent model family for studies on biodiversity and plant biology.

evolutionary biology↗