Fig. 5: Gene loss in the genomes of P. guangdongensis and G. elata.

For all the investigated species, we compared the size of each gene family with the average size of a gene family through calculating the F index (Methods). The F index for gene family ranges from 0 to 1, with 0.5 representing the size of a gene family in a species to be exactly equal to its average size. We hence classified 8,423 gene families that exist in 16 out of 19 angiosperm species and have homologues from A. trichopoda into five categories: “Missing” with F index equal to 0; “Less than average” with F index greater than 0 but less than or equal to 0.45; “Around average (less)” with F index greater than 0.45 but less than or equal to 0.5; “Around average (greater)” with F index greater than 0.5 but less than or equal to 0.55; and “Greater than average” with F index greater than 0.55. The bar plot illustrates the percentage of the conserved gene families in each category and the values on the left and right sides show the percentages of the gene families that are smaller and larger than the average size, respectively. See Extended Data Fig. 2 for the number of missing gene families in each species.