Resolving the backbone of the Brassicaceae phylogeny for investigating trait diversity
Abstract
Summary: The Brassicaceae family comprises c. 4000 species including economically important crops and the model plant Arabidopsis thaliana. Despite their importance, the relationships among major lineages in the family remain unresolved, hampering comparative research. Here, we inferred a Brassicaceae phylogeny using newly generated targeted enrichment sequence data of 1827 exons (> 940 000 bases) representing 63 species, as well as sequenced genome data of 16 species, together representing 50 of the 52 currently recognized Brassicaceae tribes. A third of the samples were derived from herbarium material, facilitating broad taxonomic coverage of the family. Six major clades formed successive sister groups to the rest of Brassicaceae. We also recovered strong support for novel relationships among tribes, and resolved the position of 16 taxa previously not assigned to a tribe. The broad utility of these phylogenetic results is illustrated through a comparative investigation of genome‐wide expression signatures that distinguish simple from complex leaves in Brassicaceae. Our study provides an easily extendable dataset for further advances in Brassicaceae systematics and a timely higher‐level phylogenetic framework for a wide range of comparative studies of multiple traits in an intensively investigated group of plants.
Additional Information
© 2019 The Authors. New Phytologist © 2019 New Phytologist Trust. This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited. Received: 9 August 2018; Accepted: 10 January 2019. We thank: Angela Hay and Laura Lagomarsino for critically reading the manuscript; Aaron Liston for advice on target capture sequencing; Bonn Botanical Garden (BONN), Harvard University Herbaria (GH and A), Berlin Botanical Garden and Botanical Museum (B), Missouri Botanical Garden (MO), the Royal Botanical Garden Kew (K), the Herbarium at the Bulgarian Academy of Sciences (SOM), BGV‐UPM 'César Gómez Campo', Laura Lagomarsino, Daniel Santamaría‐Aguilar, Mike Kintgen and Carlos Alonso‐Blanco for plant material; Asis Hallab and Baoxing Song for providing alignments of the orthologous genes used in probe design; and Alison Devault and Jake Enk at Arbor Biosciences for probe design, library preparation and capture. We are grateful to BrassiBase (http://brassibase.cos.uni-heidelberg.de) for sharing seeds and expertise. Work on crucifer development and diversity in the Tsiantis Laboratory is supported by Deutsche Forschungsgemeinschaft 'Adaptomics' grants TS 229/1‐1 and SFB (Sonderforschungbereit) 680, and core grant by the Max Planck Society. MT also acknowledges support from CEPLAS Cluster of Excellence. LAN and PS were supported by Alexander von Humboldt Research Fellowships. CDB was supported by NSF Plant Genome Research Grant 1238731. Author contributions: LAN and MT conceived and planned the study; LAN conducted all experimental work, and collected and curated sequence data; LAN and PS performed the phylogenomic analyses with input from CDB; LAN, BN and DF performed the transcriptome analyses, XG contributed sequenced genome data and bioinformatics expertise; IAAl‐S provided taxonomic expertise and advice on the biology of Brassicaceae; LAN and MT wrote the paper with input from CDB whose discussions with MT over many years were instrumental for conceiving the study; and all authors approved the manuscript. MT provided funding and directed the study.Attached Files
Published - Nikolov_et_al-2019-New_Phytologist.pdf
Supplemental Material - nph15732-sup-0001-datasets1.xlsx
Supplemental Material - nph15732-sup-0002-datasets2.zip
Supplemental Material - nph15732-sup-0003-datasets3.xlsx
Supplemental Material - nph15732-sup-0004-supinfo.pdf
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Additional details
- Eprint ID
- 92813
- Resolver ID
- CaltechAUTHORS:20190211-073502673
- TS 229/1‐1
- Deutsche Forschungsgemeinschaft (DFG)
- SFB 680
- Deutsche Forschungsgemeinschaft (DFG)
- Max Planck Society
- Cluster of Excellence on Plant Sciences (CEPLAS)
- Alexander von Humboldt Foundation
- IOS-1238731
- NSF
- Created
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2019-02-12Created from EPrint's datestamp field
- Updated
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2021-11-16Created from EPrint's last_modified field