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

Kasper P. Hendriks*, Christiane Kiefer, Ihsan A. Al-Shehbaz, C.D. Bailey, Alex Hooft van Huysduynen, Lachezar A. Nikolov, Lars Nauheimer, Alexandre R. Zuntini, Dmitry A. German, Andreas Franzke, Marcus A. Koch, Martin A. Lysak, Óscar Toro-Núñez, Barış Özüdoğru, Vanessa R. Invernón, Nora Walden, Olivier Maurin, Nikolai M. Hay, Philip Shushkov, Terezie MandákováEric Schranz, Mats Thulin, Michael D. Windham, Ivana Rešetnik, Stanislav Španiel, Elfy Ly, J.C. Pires, Alex Harkess, Barbara Neuffer, Robert Vogt, Christian Bräuchler, Heimo Rainer, Steven B. Janssens, Michaela Schmull, Alan Forrest, Alessia Guggisberg, Sue Zmarzty, Brendan J. Lepschi, Neville Scarlett, Fred W. Stauffer, Ines Schönberger, Peter Heenan, William J. Baker, Félix Forest, Klaus Mummenhoff*, Frederic Lens*

*Corresponding author for this work

Research output: Contribution to journalArticleAcademicpeer-review

35 Citations (Scopus)

Abstract

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.

Original languageEnglish
Pages (from-to)4052-4068.e6
JournalCurrent Biology
Volume33
Issue number19
DOIs
Publication statusPublished - 9 Oct 2023

Keywords

  • mustard family
  • phylogenomics
  • target capture sequencing
  • taxonomy
  • Tree of Life

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  • Various representative species from the mustard family (Brassicaceae). Raw sequence reads

    Hendriks, K. P. (Creator), Kiefer, C. (Creator), Al-Shehbaz, I. A. (Creator), Bailey, C. D. (Creator), Hooft van Huysduynen, A. (Creator), Nikolov, L. A. (Creator), Nauheimer, L. (Creator), Zuntini, A. R. (Creator), German, D. A. (Creator), Franzke, A. (Creator), Koch, M. A. (Creator), Lysak, M. A. (Creator), Toro-Núñez, Ó. (Creator), Özüdoğru, B. (Creator), Invernón, V. R. (Creator), Walden, N. (Creator), Maurin, O. (Creator), Hay, N. M. (Creator), Shushkov, P. (Creator), Mandáková, T. (Creator), Schranz, E. (Creator), Thulin, M. (Creator), Windham, M. D. (Creator), Rešetnik, I. (Creator), Španiel, S. (Creator), Ly, E. (Creator), Pires, J. C. (Creator), Harkess, A. (Creator), Neuffer, B. (Creator), Vogt, R. (Creator), Bräuchler, C. (Creator), Rainer, H. (Creator), Janssens, S. B. (Creator), Schmull, M. (Creator), Forrest, A. (Creator), Guggisberg, A. (Creator), Zmarzty, S. (Creator), Lepschi, B. J. (Creator), Scarlett, N. (Creator), Stauffer, F. W. (Creator), Schönberger, I. (Creator), Heenan, P. (Creator), Baker, W. J. (Creator), Forest, F. (Creator), Mummenhoff, K. (Creator) & Lens, F. (Creator), University of Osnabrück, 13 Feb 2022

    Dataset

  • Brassicaceae Woodiness raw sequencing data

    Hendriks, K. P. (Creator), Kiefer, C. (Creator), Al-Shehbaz, I. A. (Creator), Bailey, C. D. (Creator), Hooft van Huysduynen, A. (Creator), Nikolov, L. A. (Creator), Nauheimer, L. (Creator), Zuntini, A. R. (Creator), German, D. A. (Creator), Franzke, A. (Creator), Koch, M. A. (Creator), Lysak, M. A. (Creator), Toro-Núñez, Ó. (Creator), Özüdoğru, B. (Creator), Invernón, V. R. (Creator), Walden, N. (Creator), Maurin, O. (Creator), Hay, N. M. (Creator), Shushkov, P. (Creator), Mandáková, T. (Creator), Schranz, E. (Creator), Thulin, M. (Creator), Windham, M. D. (Creator), Rešetnik, I. (Creator), Španiel, S. (Creator), Ly, E. (Creator), Pires, J. C. (Creator), Harkess, A. (Creator), Neuffer, B. (Creator), Vogt, R. (Creator), Bräuchler, C. (Creator), Rainer, H. (Creator), Janssens, S. B. (Creator), Schmull, M. (Creator), Forrest, A. (Creator), Guggisberg, A. (Creator), Zmarzty, S. (Creator), Lepschi, B. J. (Creator), Scarlett, N. (Creator), Stauffer, F. W. (Creator), Schönberger, I. (Creator), Heenan, P. (Creator), Baker, W. J. (Creator), Forest, F. (Creator), Mummenhoff, K. (Creator) & Lens, F. (Creator), Naturalis, 17 Nov 2020

    Dataset

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