RT Journal Article
SR Electronic
T1 Phylogeny and Multiple Independent Whole-Genome Duplication Events in the Brassicales
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 789040
DO 10.1101/789040
A1 Makenzie E. Mabry
A1 Julia M. Brose
A1 Paul D. Blischak
A1 Brittany Sutherland
A1 Wade T. Dismukes
A1 Christopher A. Bottoms
A1 Patrick P. Edger
A1 Jacob D. Washburn
A1 Hong An
A1 Jocelyn C. Hall
A1 Michael R. McKain
A1 Ihsan Al-Shehbaz
A1 Michael S. Barker
A1 M. Eric Schranz
A1 Gavin C. Conant
A1 J. Chris Pires
YR 2019
UL http://biorxiv.org/content/early/2019/10/01/789040.abstract
AB 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. However, while its sister family, Cleomaceae, has also been characterized by a WGD, its placement, as well as that of other WGD events in other families in the order, remains unclear. Using phylo-transcriptomics from 74 taxa and genome survey sequencing for 66 of those taxa, we infer nuclear and chloroplast phylogenies to assess relationships among the major families of the Brassicales and within the Brassicaceae. We then use multiple methods of WGD inference to assess placement of WGD events. We not only present well-supported chloroplast and nuclear phylogenies for the Brassicales, but we also putatively place Th-α and provide evidence for previously unknown events, including one shared by at least two members of the Resedaceae, which we name Rs-α. Given its economic importance and many genomic resources, the Brassicales are an ideal group to continue assessing WGD inference methods. We add to the current conversation on WGD inference difficulties, by demonstrating that sampling is especially important for WGD identification.