Resolving the backbone of the Brassicaceae phylogeny for investigating trait diversity
Open Access
- 30 April 2019
- journal article
- research article
- Published by Wiley in New Phytologist
- Vol. 222 (3), 1638-1651
- https://doi.org/10.1111/nph.15732
Abstract
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.Keywords
Funding Information
- Deutsche Forschungsgemeinschaft (TS 229/1‐1, SFB 680)
- Alexander von Humboldt-Stiftung
- National Science Foundation (1238731)
This publication has 71 references indexed in Scilit:
- VarScan 2: Somatic mutation and copy number alteration discovery in cancer by exome sequencingGenome Research, 2012
- Normalization, testing, and false discovery rate estimation for RNA-sequencing dataBiostatistics, 2011
- Full-length transcriptome assembly from RNA-Seq data without a reference genomeNature Biotechnology, 2011
- Evolution of Gene Regulatory Networks Controlling Body Plan DevelopmentCell, 2011
- CRL4s: the CUL4-RING E3 ubiquitin ligasesTrends in Biochemical Sciences, 2009
- The Sequence Alignment/Map format and SAMtoolsBioinformatics, 2009
- Fast and accurate short read alignment with Burrows–Wheeler transformBioinformatics, 2009
- PAML 4: Phylogenetic Analysis by Maximum LikelihoodMolecular Biology and Evolution, 2007
- BLAT—The BLAST-Like Alignment ToolGenome Research, 2002
- Multiple Comparisons of Log-Likelihoods with Applications to Phylogenetic InferenceMolecular Biology and Evolution, 1999