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

Author

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

Published
2023
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2. Global Brassicaceae phylogeny based on filtering of 1,000-gene dataset

Author

Hendriks, Kasper P., Kiefer, Christiane, Al-Shehbaz, Ihsan A., Bailey, C. Donovan, van Huysduynen, Alex Hooft, Nikolov, Lachezar A., Nauheimer, Lars, Zuntini, Alexandre R., German, Dmitry A., Franzke, Andreas, Koch, Marcus A., Lysak, Martin A., Toro-Nunez, Oscar, Ozudogru, Baris, Invernon, Vanessa R., Walden, Nora, Maurin, Olivier, Hay, Nikolai M., Shushkov, Philip, Mandakova, Terezie, Schranz, M. Eric, Thulin, Mats, Windham, Michael D., Resetnik, Ivana, Spaniel, Stanislav, Ly, Elfy, Pires, J. Chris, Harkess, Alex, Neuffer, Barbara, Vogt, Robert, Brauchler, Christian, Rainer, Heimo, Janssens, Steven B., Schmull, Michaela, Forrest, Alan, Guggisberg, Alessia, Zmarzty, Sue, Lepschi, Brendan J., Scarlett, Neville, Stauffer, Fred W., Schonberger, Ines, Heenan, Peter, Baker, William J., Forest, Felix, Mummenhoff, Klaus, Lens, Frederic, Hendriks, Kasper P., Kiefer, Christiane, Al-Shehbaz, Ihsan A., Bailey, C. Donovan, van Huysduynen, Alex Hooft, Nikolov, Lachezar A., Nauheimer, Lars, Zuntini, Alexandre R., German, Dmitry A., Franzke, Andreas, Koch, Marcus A., Lysak, Martin A., Toro-Nunez, Oscar, Ozudogru, Baris, Invernon, Vanessa R., Walden, Nora, Maurin, Olivier, Hay, Nikolai M., Shushkov, Philip, Mandakova, Terezie, Schranz, M. Eric, Thulin, Mats, Windham, Michael D., Resetnik, Ivana, Spaniel, Stanislav, Ly, Elfy, Pires, J. Chris, Harkess, Alex, Neuffer, Barbara, Vogt, Robert, Brauchler, Christian, Rainer, Heimo, Janssens, Steven B., Schmull, Michaela, Forrest, Alan, Guggisberg, Alessia, Zmarzty, Sue, Lepschi, Brendan J., Scarlett, Neville, Stauffer, Fred W., Schonberger, Ines, Heenan, Peter, Baker, William J., Forest, Felix, Mummenhoff, Klaus, and Lens, Frederic

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 (Bras-sicaceae 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 eval-uate 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 moder-ate. 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.

Published
2023
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3. Global Phylogeny of the Brassicaceae Provides Important Insights into Gene Discordance

Author

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

Published
2022
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4. Various representative species from the mustard family (Brassicaceae). Raw sequence reads

Author

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

Abstract

We reconstructed a phylogeny of ~95% of the genera within the angiosperm family Brassicaceae using >1,000 target genes following two publications (Johnson et al, 2019, Nikolov et al, 2019).

Published
2022

5. Global Phylogeny of the Brassicaceae Provides Important Insights into Gene Discordance

Author

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

Subjects
mustard family, Tree of Life, coalescence, taxonomy, ddc:580, Botanical sciences, Angiosperms353, phylogenomics
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 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., bioRxiv

Published
2022
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6. The best of both worlds: Combining lineage‐specific and universal bait sets in target‐enrichment hybridization reactions

Author

Hendriks, Kasper P., primary, Mandáková, Terezie, additional, Hay, Nikolai M., additional, Ly, Elfy, additional, Hooft van Huysduynen, Alex, additional, Tamrakar, Rubin, additional, Thomas, Shawn K., additional, Toro‐Núñez, Oscar, additional, Pires, J. Chris, additional, Nikolov, Lachezar A., additional, Koch, Marcus A., additional, Windham, Michael D., additional, Lysak, Martin A., additional, Forest, Félix, additional, Mummenhoff, Klaus, additional, Baker, William J., additional, Lens, Frederic, additional, and Bailey, C. Donovan, additional

Published
2021
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7. Brassicaceae Woodiness raw sequencing data

Author

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

Abstract

We study the evolution of secondary woodiness (as derived from herbaceousness) in the plant family Brassicaceae. We aim to sequence target regions following Nikolov et al. (2019) and the Angiosperms-353 bait kit (PAFTOL) using target capture sequencing (a.k.a. hyb-seq).

Published
2020

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