Phylogeny and Multiple Independent Whole‐Genome Duplication Events
RESEARCH ARTICLE Phylogeny and multiple independent whole-genome duplication events in the Brassicales Makenzie E. Mabry1,11 , Julia M. Brose1, Paul D. Blischak2, Brittany Sutherland2, Wade T. Dismukes1, Christopher A. Bottoms3, Patrick P. Edger4, Jacob D. Washburn5, Hong An1, Jocelyn C. Hall6, Michael R. McKain7, Ihsan Al-Shehbaz8, Michael S. Barker2, M. Eric Schranz9, Gavin C. Conant10, and J. Chris Pires1,11 Manuscript received 10 December 2019; revision accepted 5 May PREMISE: Whole-genome duplications (WGDs) are prevalent throughout the evolutionary 2020. history of plants. For example, dozens of WGDs have been phylogenetically localized 1 Division of Biological Sciences and Christopher S. Bond Life across the order Brassicales, specifically, within the family Brassicaceae. A WGD event has Sciences Center, University of Missouri, Columbia, Missouri 65211, also been identified in the Cleomaceae, the sister family to Brassicaceae, yet its placement, USA as well as that of WGDs in other families in the order, remains unclear. 2 Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85719, USA METHODS: Phylo-transcriptomic data were generated and used to infer a nuclear 3 Informatics Research Core Facility and Christopher S. Bond Life phylogeny for 74 Brassicales taxa. Genome survey sequencing was also performed on 66 Sciences Center, University of Missouri, Columbia, Missouri 65211, of those taxa to infer a chloroplast phylogeny. These phylogenies were used to assess and USA confirm relationships among the major families of the Brassicales and within Brassicaceae. 4 Department of Horticulture, Michigan State University, East Lansing, Michigan 48824, USA Multiple WGD inference methods were then used to assess the placement of WGDs on the 5 Plant Genetics Research Unit, USDA-ARS, Columbia, Missouri nuclear phylogeny.
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