S3 Table. Enriched GO terms of genes commonly deregulated in seeds of reciprocal C. rubella × C. grandiflora (Cr × Cg) hybridizations and Arabidopsis WT × osd1 reciprocal interploidy hybridizations. GO terms are sorted by their P‐value (lower to higher). Only GO categories with a P‐value <0.001 are shown. Commonly down‐regulated genes in Cr × Cg and Arabidopsis WT × osd1 Molecular function GO term P‐value Number of genes Description GO:0003777 GO:0003774 GO:0019887 GO:0019207 GO:0030234 GO:0030528 GO:0016563 GO:0003700 7.72E‐14 4.72E‐12 7.01E‐10 9.01E‐10 1.25E‐07 1.21E‐05 2.29E‐04 4.99E‐04 14 14 9 9 16 45 7 37 Biological process GO term P‐value Number of genes Description GO:0007018 GO:0007017 GO:0030705 GO:0007010 GO:0051726 GO:0007049 GO:0046907 GO:0051649 GO:0051641 GO:0051244 GO:0050794 GO:0050791 GO:0050789 GO:0006810 GO:0006996 GO:0016043 GO:0051234 GO:0051179 Cellular localization GO term GO:0005875 GO:0015630 1.41E‐13 1.04E‐12 5.32E‐12 1.11E‐08 1.48E‐08 4.83E‐08 7.50E‐07 8.70E‐07 9.70E‐07 4.40E‐06 5.00E‐06 8.78E‐06 1.02E‐04 6.54E‐04 6.88E‐04 7.31E‐04 7.64E‐04 8.29E‐04 P‐value 5.79E‐13 3.67E‐12 13 15 13 15 11 13 19 19 19 46 46 46 46 46 17 28 46 46 Number of genes 13 16 F microtubule motor activity F motor activity F protein kinase regulator activity F kinase regulator activity F enzyme regulator activity F transcription regulator activity F transcriptional activator activity F transcription factor activity P microtubule‐based movement P microtubule‐based process P cytoskeleton‐dependent intracellular transport P cytoskeleton organization and biogenesis P regulation of cell cycle P cell cycle P intracellular transport P establishment of cellular localization P cellular localization P regulation of cellular physiological process P regulation of cellular process P regulation of physiological process P regulation of biological process P transport P organelle organization and biogenesis P cell organization and biogenesis P establishment of localization P localization Description C microtubule associated complex C microtubule cytoskeleton GO:0044430 GO:0005856 GO:0031225 GO:0009524 GO:0005634 1.11E‐10 9.34E‐10 1.65E‐06 7.84E‐04 8.91E‐04 16 16 14 4 46 C cytoskeletal part C cytoskeleton C anchored to membrane C phragmoplast C nucleus Commonly up‐regulated genes in Cr × Cg and Arabidopsis WT × osd1 Molecular function GO term GO:0016798 GO:0004553 P‐value 1.96E‐04 1.72E‐04 Biological process GO term GO:0005975 GO:0006355 GO:0006351 Cellular localization GO term GO:0012505 P‐value 8.00E‐04 5.36E‐04 8.24E‐04 P‐value 1.20E‐10 Number of genes 14 13 Description F hydrolase activity, acting on glycosyl bonds F hydrolase activity, hydrolyzing O‐glycosyl compounds Number of genes Description 18 P carbohydrate metabolism 22 P regulation of transcription, DNA‐dependent 22 P transcription, DNA‐dependent Number of genes Description 89 C endomembrane system Commonly down‐regulated genes in Cg × Cr and Arabidopsis osd1 × WT Cellular localization GO term GO:0012505 P‐value Number of genes Description 1.52E‐04 20 C endomembrane system Commonly up‐regulated genes in Cg × Cr and Arabidopsis osd1 × WT Biological process GO term GO:0009415 GO:0009790 P‐value Number of genes Description 8.48E‐05 3 P response to water 9.57E‐05 4 P embryonic development