Protein–protein interaction networks after the WGT. (A) The Arabidopsis PPI network at the root branch (bottom), and the same PPI network colored by the Brassica rapa gene retention status (top). The dark purple nodes represent retained triplets (Supplemental Code). (B) The PPI network partitioned by subgenome assignment at the root branch: (LF) red, 4249 nodes and 8454 edges; (MF1) green, 3379 nodes and 6442 edges; (MF2) blue, 3073 nodes and 4961 edges. (C) A subset of the PPI network where only nodes encoded by single copies genes and connected to other single-copy nodes are shown. Red nodes are from the LF subgenome, green nodes are from the MF1 subgenome, and blue nodes are from the MF2 subgenome.
