Data from: Improved transcriptome sampling pinpoints 26 ancient and more recent polyploidy events in Caryophyllales, including two allopolyploidy events

• Studies of the macroevolutionary legacy of polyploidy are limited by an
incomplete sampling of these events across the tree of life. To better
locate and understand these events, we need comprehensive taxonomic
sampling as well as homology inference methods that accurately reconstruct
the frequency and location of gene duplications. • We assembled a dataset
of transcriptomes and genomes from 169 species in Caryophyllales, of which
43 were newly generated for this study, representing one of the densest
sampled genomic-scale datasets available. We carried out phylogenomic
analyses using a modified phylome strategy to reconstruct the species
tree. We mapped phylogenetic distribution of polyploidy events by both
tree-based and distance-based methods, and explicitly tested scenarios for
allopolyploidy. • We identified twenty-six ancient and more recent
polyploidy events distributed throughout Caryophyllales. Two of these
events were inferred to be allopolyploidy. • Through dense phylogenomic
sampling, we show the propensity of polyploidy throughout the evolutionary
history of Caryophyllales. We also provide a framework for utilizing
transcriptome data to detect allopolyploidy, which is important as it may
have different macro-evolutionary implications compared to autopolyploidy.