Phylogeny and multiple independent whole-genome duplication events in the brassicales

Authors: MABRY, MAKENZIE - University Of Missouri; BROSE, JULIA - University Of Missouri; BLISCHAK, PAUL - University Of Arizona; SUTHERLAND, BRITTANY - University Of Arizona; DISMUKES, WADE - University Of Missouri; BOTTOMS, CHRISTOPHER - University Of Missouri; EDGER, PATRICK - Michigan State University; Washburn, Jacob; AN, HONG - University Of Missouri; HALL, JOCELYN - University Of Alberta; MCKAIN, MICHAEL - University Of Alabama; AL-SHEHBAZ, IHSAN - Missouri Botanical Garden; BARKER, MICHAEL - University Of Arizona; SCHRANZ, ERIC - Wageningen University; CONANT, GAVIN - North Carolina State University; PIRES, CHRIS - University Of Missouri

Submitted to: American Journal of Botany
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/5/2020
Publication Date: 8/24/2020
Publication URL: https://handle.nal.usda.gov/10113/7111130
Citation: Mabry, M.E., Brose, J.M., Blischak, P.D., Sutherland, B., Dismukes, W.T., Bottoms, C.A., Edger, P.P., Washburn, J.D., An, H., Hall, J.C., McKain, M.R., Al-Shehbaz, I., Barker, M.S., Schranz, E.M., Conant, G.C., Pires, C.J. 2020. Phylogeny and multiple independent whole-genome duplication events in the brassicales. American Journal of Botany. 107(8):1148-1164. https://doi.org/10.1002/ajb2.1514.
DOI: https://doi.org/10.1002/ajb2.1514

Interpretive Summary: Whole-genome duplication (WGD) events, when an organism’s genetic content is doubled, have occurred frequently in plant evolutionary history. These events may give rise to new species, or groups of species with novel characteristics. Identifying WGD events, and when and where they have occurred in evolutionary history, enables a greater understanding of how plants adapt to different environments. The plant order Brassicales, which includes important crops like canola, broccoli, cauliflower, kale, and others, is especially rich in WGD events. However, the phylogenetic locations of many of these events remain unknown. In this study, the evolutionary relationships of 74 Brassicales species were inferred. The phylogenetic placement of WGD events within the group were inferred and assessed using multiple methods. The study adds supporting evidence for previously hypothesized events, as well as putative evidence for the placement of previously unplaced events. These results provide a more complete picture of the potential role of WGD in the evolution of this economically important group of plant species.

Technical Abstract: PREMISE: Whole-genome duplications (WGDs) are prevalent throughout the evolutionary history of plants. For example, dozens of WGDs have been phylogenetically localized across the order Brassicales, specifically, within the family Brassicaceae. A WGD event has also been identified in the Cleomaceae, the sister family to Brassicaceae, yet its placement, as well as that of WGDs in other families in the order, remains unclear. METHODS: Phylo-transcriptomic data were generated and used to infer a nuclear phylogeny for 74 Brassicales taxa. Genome survey sequencing was also performed on 66 of those taxa to infer a chloroplast phylogeny. These phylogenies were used to assess and confirm relationships among the major families of the Brassicales and within Brassicaceae. Multiple WGD inference methods were then used to assess the placement of WGDs on the nuclear phylogeny. RESULTS: Well-supported chloroplast and nuclear phylogenies for the Brassicales and the putative placement of the Cleomaceae-specific WGD event Th-' are presented. This work also provides evidence for previously hypothesized WGDs, including a well-supported event shared by at least two members of the Resedaceae family, and a possible event within the Capparaceae. CONCLUSIONS: Phylogenetics and the placement of WGDs within highly polyploid lineages continues to be a major challenge. This study adds to the conversation on WGD inference difficulties by demonstrating that sampling is especially important for WGD identification and phylogenetic placement. Given its economic importance and genomic resources, the Brassicales continues to be an ideal group for assessing WGD inference methods.