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3. Expanding the triangle of U : comparative analysis of the Hirschfeldia incana genome provides insights into chromosomal evolution, phylogenomics and high photosynthesis-related traits

Author

Hoang, Nam V., Walden, Nora, Caracciolo, Ludovico, Luoni, Sofia Bengoa, Retta, Moges, Li, Run, Wolters, Felicia C., Woldu, Tina, Becker, Frank F.M., Verbaarschot, Patrick, Harbinson, Jeremy, Driever, Steven M., Struik, Paul C., van Amerongen, Herbert, de Ridder, Dick, Aarts, Mark G.M., Schranz, M.E., Hoang, Nam V., Walden, Nora, Caracciolo, Ludovico, Luoni, Sofia Bengoa, Retta, Moges, Li, Run, Wolters, Felicia C., Woldu, Tina, Becker, Frank F.M., Verbaarschot, Patrick, Harbinson, Jeremy, Driever, Steven M., Struik, Paul C., van Amerongen, Herbert, de Ridder, Dick, Aarts, Mark G.M., and Schranz, M.E.

Published
2024

4. The Gynandropsis gynandra genome provides insights into whole-genome duplications and the evolution of C4 photosynthesis in Cleomaceae

Author

Hoang, Nam V, Sogbohossou, EO Deedi, Xiong, Wei, Simpson, Conor JC, Singh, Pallavi, Walden, Nora, Van Den Bergh, Erik, Becker, Frank FM, Li, Zheng, Zhu, Xin-Guang, Brautigam, Andrea, Weber, Andreas PM, Van Haarst, Jan C, Schijlen, Elio GWM, Hendre, Prasad S, Van Deynze, Allen, Achigan-Dako, Enoch G, Hibberd, Julian M, Schranz, M Eric, Hoang, Nam V [0000-0003-0782-2835], Sogbohossou, EO Deedi [0000-0002-9034-0062], Xiong, Wei [0000-0002-4525-5969], Simpson, Conor JC [0000-0001-7055-3186], Singh, Pallavi [0000-0003-3694-6378], Walden, Nora [0000-0002-3078-6791], van den Bergh, Erik [0000-0001-9865-574X], Becker, Frank FM [0000-0002-7947-1379], Li, Zheng [0000-0001-6894-9616], Zhu, Xin-Guang [0000-0002-4435-130X], Brautigam, Andrea [0000-0002-5309-0527], Weber, Andreas PM [0000-0003-0970-4672], van Haarst, Jan C [0000-0003-0307-1245], Schijlen, Elio GWM [0000-0003-3818-2762], Hendre, Prasad S [0000-0003-1691-183X], Van Deynze, Allen [0000-0002-2093-0577], Achigan-Dako, Enoch G [0000-0002-5493-0516], Hibberd, Julian M [0000-0003-0662-7958], Schranz, M Eric [0000-0001-6777-6565], and Apollo - University of Cambridge Repository

Subjects
Information Management, Informatie Management, Arabidopsis, Cell Biology, Plant Science, PE&RC, Laboratorium voor Erfelijkheidsleer, Biosystematiek, Evolution, Molecular, Magnoliopsida, BIOS Applied Bioinformatics, Gene Duplication, IT Projectmanagement, Brassicaceae, Life Science, Biosystematics, Laboratory of Genetics, Photosynthesis, EPS, IT Project Management
Abstract

Gynandropsis gynandra (Cleomaceae) is a cosmopolitan leafy vegetable and medicinal plant, which has also been used as a model to study C4 photosynthesis due to its evolutionary proximity to C3 Arabidopsis (Arabidopsis thaliana). Here, we present the genome sequence of G. gynandra, anchored onto 17 main pseudo-molecules with a total length of 740 Mb, an N50 of 42 Mb and 30,933 well-supported gene models. The G. gynandra genome and previously released genomes of C3 relatives in the Cleomaceae and Brassicaceae make an excellent model for studying the role of genome evolution in the transition from C3 to C4 photosynthesis. Our analyses revealed that G. gynandra and its C3 relative Tarenaya hassleriana shared a whole-genome duplication event (Gg-alpha), then an addition of a third genome (Th-alpha, +1x) took place in T. hassleriana but not in G. gynandra. Analysis of syntenic copy number of C4 photosynthesis-related gene families indicates that G. gynandra generally retained more duplicated copies of these genes than C3T. hassleriana, and also that the G. gynandra C4 genes might have been under positive selection pressure. Both whole-genome and single-gene duplication were found to contribute to the expansion of the aforementioned gene families in G. gynandra. Collectively, this study enhances our understanding of the polyploidy history, gene duplication and retention, as well as their impact on the evolution of C4 photosynthesis in Cleomaceae. © The Author(s) 2023. Published by Oxford University Press on behalf of American Society of Plant Biologists.

Published
2023
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5. 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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8. The Gynandropsis gynandra genome provides insights into whole-genome duplications and the evolution of C4 photosynthesis in Cleomaceae

Author

Hoang, Nam V., Sogbohossou, Deedi, Xiong, Wei, Simpson, Conor J.C., Singh, Pallavi, Walden, Nora, van den Bergh, Erik, Becker, Frank F.M., Li, Zheng, Zhu, Xin-Guang, Brautigam, Andrea, Weber, Andreas P.M., van Haarst, Jan C., Schijlen, Elio G.W.M., Hendre, Prasad S., van Deynze, Allen, Achigan-Dako, Enoch G., Hibberd, Julian M., Schranz, Eric, Hoang, Nam V., Sogbohossou, Deedi, Xiong, Wei, Simpson, Conor J.C., Singh, Pallavi, Walden, Nora, van den Bergh, Erik, Becker, Frank F.M., Li, Zheng, Zhu, Xin-Guang, Brautigam, Andrea, Weber, Andreas P.M., van Haarst, Jan C., Schijlen, Elio G.W.M., Hendre, Prasad S., van Deynze, Allen, Achigan-Dako, Enoch G., Hibberd, Julian M., and Schranz, Eric

Published
2023

9. 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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11. Synteny Identifies Reliable Orthologs for Phylogenomics and Comparative Genomics of the Brassicaceae

Author

Walden, Nora, Schranz, Michael Eric, Walden, Nora, and Schranz, Michael Eric

Abstract

Large genomic data sets are becoming the new normal in phylogenetic research, but the identification of true orthologous genes and the exclusion of problematic paralogs is still challenging when applying commonly used sequencing methods such as target enrichment. Here, we compared conventional ortholog detection using OrthoFinder with ortholog detection through genomic synteny in a data set of 11 representative diploid Brassicaceae whole-genome sequences spanning the entire phylogenetic space. Then, we evaluated the resulting gene sets regarding gene number, functional annotation, and gene and species tree resolution. Finally, we used the syntenic gene sets for comparative genomics and ancestral genome analysis. The use of synteny resulted in considerably more orthologs and also allowed us to reliably identify paralogs. Surprisingly, we did not detect notable differences between species trees reconstructed from syntenic orthologs when compared with other gene sets, including the Angiosperms353 set and a Brassicaceae-specific target enrichment gene set. However, the synteny data set comprised a multitude of gene functions, strongly suggesting that this method of marker selection for phylogenomics is suitable for studies that value downstream gene function analysis, gene interaction, and network studies. Finally, we present the first ancestral genome reconstruction for the Core Brassicaceae which predating the Brassicaceae lineage diversification ∼25 million years ago.

Published
2023

14. 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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15. Parallel gene loss underlies success in a colonizing Arabidopsis lineage

Author

Fulgione, Andrea, Neto, Célia, Elfarargi, Ahmed F., Tergemina, Emmanuel, Ansari, Shifa, Göktay, Mehmet, Dinis, Herculano, Döring, Nina, Flood, Pádraic J., Rodriguez-Pacheco, Sofia, Walden, Nora, Koch, Marcus A., Roux, Fabrice, Hermisson, Joachim, Hancock, Angela M., Fulgione, Andrea, Neto, Célia, Elfarargi, Ahmed F., Tergemina, Emmanuel, Ansari, Shifa, Göktay, Mehmet, Dinis, Herculano, Döring, Nina, Flood, Pádraic J., Rodriguez-Pacheco, Sofia, Walden, Nora, Koch, Marcus A., Roux, Fabrice, Hermisson, Joachim, and Hancock, Angela M.

Abstract

Loss of flowering time genes in parallel in two islands underlies adaptation to new environment

Published
2022

16. 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

17. Gynandropsis gynandra cultivar:GYN Genome sequencing and assembly

Author

Hoang, Nam V., Sogbohossou, Deedi, Xiong, Wei, Simpson, Conor J.C., Singh, Pallavi, Walden, Nora, van den Bergh, Erik, Becker, Frank F.M., Li, Zheng, Zhu, Xin-Guang, Brautigam, Andrea, Weber, Andreas P.M., van Haarst, Jan C., Schijlen, Elio G.W.M., Hendre, Prasad S., van Deynze, Allen, Achigan-Dako, Enoch G., Hibberd, Julian M., Schranz, Eric, Hoang, Nam V., Sogbohossou, Deedi, Xiong, Wei, Simpson, Conor J.C., Singh, Pallavi, Walden, Nora, van den Bergh, Erik, Becker, Frank F.M., Li, Zheng, Zhu, Xin-Guang, Brautigam, Andrea, Weber, Andreas P.M., van Haarst, Jan C., Schijlen, Elio G.W.M., Hendre, Prasad S., van Deynze, Allen, Achigan-Dako, Enoch G., Hibberd, Julian M., and Schranz, Eric

Abstract

Genome sequencing and assembly of Gynandropsis gynandra, a C4 model species., Genome sequencing and assembly of Gynandropsis gynandra, a C4 model species.

Published
2022

18. 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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19. The Gynandropsis gynandra genome provides insights into whole-genome duplications and the evolution of C4 photosynthesis in Cleomaceae.

Author

Hoang, Nam V, Sogbohossou, E O Deedi, Xiong, Wei, Simpson, Conor J C, Singh, Pallavi, Walden, Nora, van den Bergh, Erik, Becker, Frank F M, Li, Zheng, Zhu, Xin-Guang, Brautigam, Andrea, Weber, Andreas P M, Haarst, Jan C van, Schijlen, Elio G W M, Hendre, Prasad S, Deynze, Allen Van, Achigan-Dako, Enoch G, Hibberd, Julian M, and Schranz, M Eric

Published
2023
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20. Parallel reduction in flowering time from de novo mutations enabled evolutionary rescue in colonizing lineages

Author

Fulgione, Andrea, Neto, Célia, Elfarargi, Ahmed F., Tergemina, Emmanuel, Ansari, Shifa, Göktay, Mehmet, Dinis, Herculano, Döring, Nina, Flood, Pádraic J., Rodriguez-Pacheco, Sofia, Walden, Nora, Koch, Marcus A., Roux, Fabrice, Hermisson, Joachim, Hancock, Angela M., Fulgione, Andrea, Neto, Célia, Elfarargi, Ahmed F., Tergemina, Emmanuel, Ansari, Shifa, Göktay, Mehmet, Dinis, Herculano, Döring, Nina, Flood, Pádraic J., Rodriguez-Pacheco, Sofia, Walden, Nora, Koch, Marcus A., Roux, Fabrice, Hermisson, Joachim, and Hancock, Angela M.

Abstract

Populations subject to abrupt environmental change must adapt quickly to avoid extinction. Understanding how populations adapt to abrupt environmental change is necessary to predict responses to future challenges, but identifying specific adaptive variants, quantifying their responses to selection and reconstructing their detailed histories is challenging in natural populations. Here, we use Arabidopsis from the Cape Verde Islands as a model to investigate the mechanisms of adaptation after a sudden shift to a more arid climate. We find genome-wide evidence of adaptation after a multivariate change in selection pressures. In particular, time to flowering is reduced in parallel across islands, substantially increasing fitness. This change was mediated by convergent de novo loss of function of two core flowering time genes: FRI on one island and FLC on the other. Evolutionary reconstructions reveal a case where expansion of the new populations coincided with the emergence and proliferation of these variants, consistent with models of rapid adaptation and evolutionary rescue.

Published
2021

23. 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

24. Genomic Blocks in Aethionema arabicum Support Arabideae as Next Diverging Clade in Brassicaceae

Author

Walden, Nora, Nguyen, Thu Phuong, Mandáková, Terezie, Lysak, Martin A., Schranz, Michael Eric, Walden, Nora, Nguyen, Thu Phuong, Mandáková, Terezie, Lysak, Martin A., and Schranz, Michael Eric

Abstract

The tribe Aethionemeae is sister to all other crucifers, making it a crucial group for unraveling genome evolution and phylogenetic relationships within the crown group Brassicaceae. In this study, we extend the analysis of Brassicaceae genomic blocks (GBs) to Aethionema whereby we identified unique block boundaries shared only with the tribe Arabideae. This was achieved using bioinformatic methods to analyze synteny between the recently updated genome sequence of Aethionema arabicum and other high-quality Brassicaceae genome sequences. We show that compared to the largely conserved genomic structure of most non-polyploid Brassicaceae lineages, GBs are highly rearranged in Aethionema. Furthermore, we detected similarities between the genomes of Aethionema and Arabis alpina, in which also a high number of genomic rearrangements compared to those of other Brassicaceae was found. These similarities suggest that tribe Arabideae, a clade showing conflicting phylogenetic position between studies, may have diverged before diversification of the other major lineages, and highlight the potential of synteny information for phylogenetic inference.

Published
2020

26. What drives species’ distributions along elevational gradients? Macroecological and ‐evolutionary insights from Brassicaceae of the central Alps

Author

Patsiou, Theofania-Sotiria, Walden, Nora, Willi, Yvonne, and Bates, Amanda

Subjects
13. Climate action, 15. Life on land, 580 Plants (Botany)
Abstract

Aim Geographic distribution limits of organisms are often affected by climate, but little is known of how the impacts of climate evolve within sets of related taxa. Here we identified the climate variables most closely associated with low‐elevation limits, optimal elevations, and high‐elevation limits of plant species’ distributions and compared evolutionary lability of niche values predicting the three aspects of distribution best. Location Central Alps. Time period Current. Major taxa studied The plant family Brassicaceae. Methods We modelled the occurrence of 110 brassicaceous species in the central European Alps and used response curves of predicted occurrence on climatic variables to reveal those variables most strongly associated with elevational distribution. We produced a phylogeny of the species, applied phylogenetic comparative analysis and tested whether niche values predicting the low and high limits and the optimum of elevational distribution were similar among related taxa. Results Upper limits were closely associated with the length of the vegetation season for the majority of species, while summer or spring temperatures were strongly allied with both the occurrence optimum and the lower limit. Furthermore, niche values predicting the upper limit and the optimum of elevational distribution were less conserved in contrast to niche values predicting the lower limit of distribution. Main conclusions These results highlight constraints on adaptation at the warm end of the climate niche and may explain observed range retractions at warm range edges due to ongoing climate change.

27. Expanding the Triangle of U: Comparative analysis of the Hirschfeldia incana genome provides insights into chromosomal evolution, phylogenomics and high photosynthesis-related traits.

Author

Hoang NV, Walden N, Caracciolo L, Luoni SB, Retta M, Li R, Wolters FC, Woldu T, Becker FFM, Verbaarschot P, Harbinson J, Driever SM, Struik PC, van Amerongen H, de Ridder D, Aarts MGM, and Schranz ME

Abstract

Background and Aims: The Brassiceae tribe encompasses many economically important crops and exhibits high intraspecific and interspecific phenotypic variation. After a shared whole-genome triplication (WGT) event (Br-α, ~15.9 million years ago), differential lineage diversification and genomic changes contributed to an array of divergence in morphology, biochemistry, and physiology underlying photosynthesis-related traits. Here, the C3 species Hirschfeldia incana is studied as it displays high photosynthetic rates under high-light conditions. Our aim was to elucidate the evolution that gave rise to the genome of H. incana and its high-photosynthesis traits., Methods: We reconstructed a chromosome-level genome assembly for H. incana (Nijmegen, v2.0) using nanopore and chromosome conformation capture (Hi-C) technologies, with 409Mb in size and an N50 of 52Mb (a 10× improvement over the previously published scaffold-level v1.0 assembly). The updated assembly and annotation was subsequently employed to investigate the WGT history of H. incana in a comparative phylogenomic framework from the Brassiceae ancestral genomic blocks and related diploidized crops., Key Results: Hirschfeldia incana (x=7) shares extensive genome collinearity with Raphanus sativus (x=9). These two species share some commonalities with Brassica rapa and B. oleracea (A genome, x=10 and C genome, x=9, respectively) and other similarities with B. nigra (B genome, x=8). Phylogenetic analysis revealed that H. incana and R. sativus form a monophyletic clade in between the Brassica A/C and B genomes. We postulate that H. incana and R. sativus genomes are results of hybridization or introgression of the Brassica A/C and B genome types. Our results might explain the discrepancy observed in published studies regarding phylogenetic placement of H. incana and R. sativus in relation to the "Triangle of U" species. Expression analysis of WGT retained gene copies revealed sub-genome expression divergence, likely due to neo- or sub-functionalization. Finally, we highlighted genes associated with physio-biochemical-anatomical adaptive changes observed in H. incana which likely facilitate its high-photosynthesis traits under high light., Conclusions: The improved H. incana genome assembly, annotation and results presented in this work will be a valuable resource for future research to unravel the genetic basis of its ability to maintain a high photosynthetic efficiency in high-light conditions and thereby improve photosynthesis for enhanced agricultural production., (© The Author(s) 2024. Published by Oxford University Press on behalf of the Annals of Botany Company.)

Published
2024
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