Orthogroup inference

Orthogroups were inferred with OrthoFinder version 0.4.0. Since orthogroups are defined as the set of genes that are descended from a single gene in the last common ancestor of all the species being considered, they can comprise orthologous as well as paralogous genes. Our analysis included proteomes of selected species from the Eurosid clade: Arabidopsis thaliana (Brassicaceae, Brassicales) and Eucalyptus grandis (Myrtaceae, Myrtales) from the Malvid clade; Populus trichocarpa (Salicaeae, Malpighiales), legumes Medicago truncatula, and Glycine max (Fabaceae, Fabales), Fragaria vesca (Rosaceae, Rosales), P. andersonii, and T. orientalis (Cannabaceae, Rosales) from the Fabid clade. Sequences were retrieved from phytozome (www.phytozome.net).