Global Brassicaceae phylogeny based on filtering of 1,000-gene dataset

Global Brassicaceae phylogeny based on filtering of 1,000-gene dataset

Hendriks, Kasper P. (University of Osnabrück; Naturalis Biodiversity Center)
Al-Shehbaz, Ihsan A. (Missouri Botanical Garden)
Bailey, C. Donovan (New Mexico State Univ.)
Hooft van Huysduynen, Alex (Naturalis Biodiversity Center; Universiteit Antwerpen)
Nauheimer, Lars (Australian Tropical Herbarium)
Zuntini, Alexandre R. (Royal Botanic Gardens, Kew)
Franzke, Andreas (University of Heidelberg)
Schranz, M. Eric (Wageningen University & Research)
Ly, E. (TU Delft BT/Environmental Biotechnology; Naturalis Biodiversity Center; Wetsus, Centre for Sustainable Water Technology)

2023

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 phylogenetic trees of the family are incompletely sampled and often contain poorly supported branches. Here, we present the most complete Brassicaceae genus-level family phylogenies to date (Brassicaceae Tree of Life or BrassiToL) based on nuclear (1,081 genes, 319 of the 349 genera; 57 of the 58 tribes) and plastome (60 genes, 265 genera; all tribes) data. We found cytonuclear discordance between the two, which is likely a result of rampant hybridization among closely and more distantly related lineages. To evaluate the impact of such hybridization on the nuclear phylogeny reconstruction, we performed five different gene sampling routines, which increasingly removed putatively paralog genes. Our cleaned subset of 297 genes revealed high support for the tribes, whereas support for the main lineages (supertribes) was moderate. Calibration based on the 20 most clock-like nuclear genes suggests a late Eocene to late Oligocene origin of the family. Finally, our results strongly support a recently published new family classification, dividing the family into two subfamilies (one with five supertribes), together representing 58 tribes. This includes five recently described or re-established tribes, including Arabidopsideae, a monogeneric tribe accommodating Arabidopsis without any close relatives. With a worldwide community of thousands of researchers working on Brassicaceae and its diverse members, our new genus-level family phylogeny will be an indispensable tool for studies on biodiversity and plant biology.

mustard family
phylogenomics
target capture sequencing
taxonomy
Tree of Life

http://resolver.tudelft.nl/uuid:d839216e-fb24-46e6-9246-1b0dedaad3c8

https://doi.org/10.1016/j.cub.2023.08.026

0960-9822

Current Biology, 33 (19), 4052-4068

Institutional Repository

journal article

© 2023 Kasper P. Hendriks, Ihsan A. Al-Shehbaz, C. Donovan Bailey, Alex Hooft van Huysduynen, Lars Nauheimer, Alexandre R. Zuntini, Andreas Franzke, M. Eric Schranz, E. Ly, More Authors