<p>Data associated with the manuscript "<a href="https://doi.org/10.1038/s41559-022-01838-4" target="_blank">Global patterns and rates of habitat transitions across the eukaryotic tree of life</a>". It includes the custom PR2-transitions database, annotated 18S and 28S OTU sequences, clustered short-read metabarcoding sequences, and phylogenetic trees generated in this study. </p>