| Gene functions | Gene | Gene used as a query | The number of potential orthologs | |||
|---|---|---|---|---|---|---|
| (link to tree info) | Arabidopsis thaliana | Oryza sativa | Selaginalla moellendorffii | Physcomitrella patens | ||
| Cell cycle regulation | CDKA;1 | CDKA;1 | 1 | 3 | 1 (1) | 2 |
| Cell cycle regulation | CDKB1;1 and 1;2 2) | CDKB1;1 | 2 | 1 | 2 (3) | 7 |
| Cell cycle regulation | CDKB2;1 and 2;2 | CDKB1;1 | 2 | 1 | 0 | 0 |
| Cell cycle regulation | CDKC;1 to 2 | CDKC;1 | 2 | 2 | 1 (2) | 3 |
| Cell cycle regulation | CDKD;1 to 3 2) | CDKD;1 | 3 | 1 | 1 (2) | 3 |
| Cell cycle regulation | CDKE;1/HEN3 | CDKE;1 | 1 | 1 | 1 (1) | 2 |
| Cell cycle regulation | CDKF;1 | CDKF;1 | 1 | 1 | 1 (2) | 1 |
| Cell cycle regulation | CYCA1;1 to 2, A2;1 to 4, and A3;1 to 4 2) | CYCA1;1 | 10 | 7 | 3 (6) | 8 |
| Cell cycle regulation | CYCB1;1 to 5, B2;1 to 5, and B3;1 2) | CYCB1;1 | 11 | 5 | 1 (2) | 2 |
| Cell cycle regulation | CYCD1;1, D2;1, D3;1 to 3, D4;1 to 2, D5;1, D6;1, and D7;1 2) | CYCD1;1 | 10 | 12 | 3 (5) | 2 |
| Cell cycle regulation | CYCH1;1 | CYCH1;1 | 1 | 1 | 1 (2) | 2 |
| Cell cycle regulation | KRP1 to 7 | KRP4 | 7 | 6 | 3 (6) | 1 |
| Cell cycle regulation | RBR1 | RBR1 | 1 | 2 | 2 (4) | 3 |
| Cell cycle regulation | E2FA, B, and C | E2Fa | 3 | 3 | 2 (4) | 4 |
| Cell cycle regulation | DEL1, 2, and 3 2) | DEL1 | 3 | 2 | 1 (2) | 3 |
| Cell cycle regulation | WEE1 2) | WEE1 | 1 | 1 | 2 (3) | 1 |
| Cell cycle regulation | Arath;CDC25 | ARATH;CDC25 | 1 | 2 | 1 (2) | 1 |
| Cell cycle regulation | HBT | HBT | 2 | 1 | 2 (3) | 2 |
| Cell cycle regulation | ANP1 2) | ANP1 | 3 | 2 | 1 (2) | 2 |
| Cytoskeleton | ATFH1 to 11 | ATFH8 | 11 | 9 | 1 (1) | 6 |
| Cytoskeleton | ATFH13 to 19, and 21 2) | AT2G25050 | 8 | 5 | 2 (3) | 2 |
| Cytoskeleton | ARP2/WRM | WRM | 1 | 1 | 1 (2) | 1 |
| Cytoskeleton | ARP3/DIS1 | DIS1 | 1 | 1 | 1 (2) | 2 |
| Cytoskeleton | ARPC1a and b | ARPC1b | 2 | 1 | 1 (2) | 2 |
| Cytoskeleton | ARPC2A/DIS2 and ARPC2B 2) | DIS2 | 2 | 2 | 1 (2) | 2 |
| Cytoskeleton | ARPC3 | ARPC3 | 1 | 1 | 1 (2) | 2 |
| Cytoskeleton | ARPC4 | ARPC4 | 1 | 1 | 1 (2) | 1 |
| Cytoskeleton | ARPC5/CRK | CRK | 1 | 1 | 1 (2) | 1 |
| Cytoskeleton | WAVE1 to 5/SCAR1 to 5 | WAVE5 | 5 | 3 | 2 (3) | 7 |
| Cytoskeleton | ABI1L1 | ABI1L1 | 4 | 6 | 1 (2) | 2 |
| Cytoskeleton | PIR121/KLK/SRA1 | KLK | 1 | 1 | 1 (2) | 2 |
| Cytoskeleton | NAP125/GRL | GRL | 1 | 1 | 1 (2) | 2 |
| Cytoskeleton | HSPC300/BRK1 | BRK1 | 1 | 1 | 1 (2) | 1 |
| Cytoskeleton | ADF1 | ADF1 | 12 | 10 | 3 (6) | 1 |
| Cytoskeleton | VLN1 to 4 | VLN3 | 5 | 5 | 1 (2) | 3 |
| Cytoskeleton | ATFIM1 | ATFIM1 | 5 | 3 | 2 (4) | 2 |
| Cytoskeleton | PRF1 | PRF1 | 5 | 3 | 1 (2) | 3 |
| Cytoskeleton | TUBG1 and 2 | TUBG1 | 2 | 1 | 1 (2) | 2 |
| Cytoskeleton | ATSPC97 | AT5G17410 | 1 | 1 | 1 (2) | 3 |
| Cytoskeleton | ATSPC98 | ATSPC98 | 1 | 1 | 1 (2) | 3 |
| Cytoskeleton | ATGCP4 | AT3G53760 | 1 | 1 | 1 (2) | 1 |
| Cytoskeleton | ATGCP5/EMB1427 | AT1G80260 | 2 | 2 | 1 (2) | 1 |
| Cytoskeleton | ATGCP6 | OSJNBa0005N02.6 4) | 1 | 1 | 1 (2) | 1 |
| Cytoskeleton | ATNEDD1 | AT5G05970 | 1 | 1 | 2 (3) | 4 |
| Cytoskeleton | ERH3/FRA2 | ERH3 | 1 | 2 | 1 (2) | 2 |
| Cytoskeleton | MOR1/GEM1 | MOR1 | 1 | 1 | 1 (2) | 2 |
| Cytoskeleton | ATEB1A | ATEB1A | 3 | 2 | 3 (6) | 3 |
| Cytoskeleton | SPR1/SKU6 3) | SPR1 | 5 | 4 | 2 (4) | 4 |
| Cytoskeleton | SPR2/TOR1 3) | SPR2 | 6 | 4 | 2 (4) | 4 |
| Cytoskeleton | ATMAP65-1 to 9 2) | ATMAP65-1 | 9 | 11 | 5 (8) | 5 |
| Cytoskeleton | ROP1 to 11 2) | ROP2 | 11 | 7 | 2 (4) | 4 |
| Cytoskeleton | FASS/TON2 | FASS | 1 | 1 | 1 (2) | 1 |
| Phosphoinositides | COB | COB | 5 | 7 | 3 (6) | 3 |
| Phosphoinositides | SOS5 1) | SOS5 | 1 | 1 | 0 | 0 |
| Phosphoinositides | SKU5 | SKU5 | 4 | 4 | 1 (2) | 1 |
| Phosphoinositides | SETH1 | SETH1 | 1 | 1 | 1 (2) | 1 |
| Phosphoinositides | SETH2 | SETH2 | 1 | 1 | 1 (2) | 1 |
| Phosphoinositides | PLDP1 and 2 | PLDP1 | 2 | 2 | 1 (2) | 2 |
| Phosphoinositides | DGK1 and 2 | DGK1 | 2 | 3 | 1 (2) | 0 |
| Phosphoinositides | DGK3, 4, and 7 | DGK7 | 3 | 2 | 1 (2) | 2 |
| Phosphoinositides | DGK5 and 6 | DGK7 | 2 | 3 | 2 (4) | 1 |
| Phosphoinositides | TAG1 | TAG1 | 1 | 2 | 1 (2) | 2 |
| Phosphoinositides | TOR | TOR | 1 | 1 | 1 (2) | 1 |
| Phosphoinositides | ATSAC1 | ATSAC1 | 1 | 2 | 1 (2) | 4 |
| Phosphoinositides | IPK2a | IPK2a | 2 | 1 | 1 (1) | 1 |
| Phosphoinositides | PTEN | PTEN | 1 | 0 | 1 (2) | 0 |
| Epigenetic gene regulation | ATX1/SDG27 and ATX2/SDG30 | ATX1 | 2 | 1 | 1 (2) | 3 |
| Epigenetic gene regulation | SDG3, 9, 11, 17, 19, 21 to 23, 32, and 33 2) | SDG3 | 12 | 12 | 6 (11) | 6 |
| Epigenetic gene regulation | HDT1 to 4 | HDT2 | 4 | 3 | 1 (2) | 3 |
| Epigenetic gene regulation | HDA6 and 7 | HDA6 | 2 | 1 | 0 | 0 |
| Epigenetic gene regulation | HDA19 | HDA19 | 1 | 3 | 1 (2) | 2 |
| Epigenetic gene regulation | HDA9 and 17 | HDA9 | 2 | 1 | 1 (2) | 1 |
| Epigenetic gene regulation | HAG1 | HAG1 | 1 | 1 | 1 (2) | 1 |
| Epigenetic gene regulation | MET1 to 4 | MET1 | 4 | 2 | 1 (2) | 1 |
| Epigenetic gene regulation | CMT1 to 3 | CMT3 | 3 | 3 | 1 (2) | 1 |
| Epigenetic gene regulation | DRM1 to 3 | DRM2 | 3 | 4 | 3 (6) | 2 |
| Epigenetic gene regulation | DME1 | DME1 | 4 | 4 | 1 (2) | 3 |
| Epigenetic gene regulation | MBD11 | MBD11 | 2 | 1 | 2 (4) | 7 |
| Epigenetic gene regulation | NFF2/NFB2/FAS1 | FAS1 | 1 | 2 | 1 (2) | 1 |
| Epigenetic gene regulation | NFB1/MUB3/FAS2 | FAS2 | 1 | 1 | 1 (2) | 1 |
| Epigenetic gene regulation | MSI2 and 3 | MSI1 | 2 | 1 | 0 | 0 |
| Epigenetic gene regulation | MSI4 and 5 | MSI4 | 2 | 1 | 1 (2) | 2 |
| Epigenetic gene regulation | CHR1/DDM1 | CHR1 | 1 | 2 | 1 (1) | 1 |
| Epigenetic gene regulation | CHR2 | CHR2 | 1 | 1 | 1 (1) | 2 |
| Epigenetic gene regulation | CHR3/SYD | SYD | 1 | 1 | 1 (1) | 1 |
| Epigenetic gene regulation | CHR4 | CHR4 | 1 | 1 | 1 (1) | 2 |
| Epigenetic gene regulation | CHR5 | CHR5 | 1 | 1 | 1 (1) | 2 |
| Epigenetic gene regulation | CHR6/GYM/PKL and CHR7 | CHR6 | 2 | 1 | 2 (3) | 2 |
| Epigenetic gene regulation | CHR8 | CHR8 | 1 | 1 | 1 (2) | 1 |
| Epigenetic gene regulation | CHR9 | CHR9 | 1 | 1 | 1 (2) | 1 |
| Epigenetic gene regulation | CHR10 | CHR10 | 1 | 1 | 0 | 1 |
| Epigenetic gene regulation | CHR11, 17 | CHR11 | 2 | 2 | 2 (4) | 2 |
| Epigenetic gene regulation | CHR12, 23 | CHR23 | 2 | 1 | 1 (1) | 1 |
| Epigenetic gene regulation | CHR13 | CHR13 | 1 | 1 | 1 (2) | 2 |
| Epigenetic gene regulation | CHR14 | CHR14 | 1 | 1 | 1 (2) | 1 |
| Epigenetic gene regulation | CHR15/MOM | CHR15 | 1 | 1 | 1 (2) | 0 |
| Epigenetic gene regulation | CHR18 | CHR18 | 1 | 1 | 1 (2) | 1 |
| Epigenetic gene regulation | CHR24 | CHR24 | 1 | 1 | 2 (4) | 2 |
| Epigenetic gene regulation | CHR25 | CHR25 | 1 | 1 | 1 (2) | 2 |
| Epigenetic gene regulation | CHR37 and 41 | CHR37 | 2 | 1 | 1 (2) | 0 |
| Epigenetic gene regulation | ATSWI3A and B | ATSWI3B | 2 | 2 | 1 (2) | 1 |
| Epigenetic gene regulation | ATSWI3C and D | ATSWI3C | 2 | 4 | 1 (2) | 3 |
| Epigenetic gene regulation | HIRA1 | HIRA1 | 1 | 1 | 1 (2) | 2 |
| Epigenetic gene regulation | RHL2 | RHL2 | 1 | 1 | 1 (2) | 1 |
| RISC complex | DCL1 | DCL4 | 1 | 1 | 1 (1) | 1 |
| RISC complex | DCL2 and 4 | DCL4 | 2 | 3 | 1 (2) | 1 |
| RISC complex | DCL3 | DCL4 | 1 | 2 | 2 (2) | 1 |
| RISC complex | AGO1 | AGO1 | 2 | 5 | 3(5) | 3 |
| RISC complex | AGO2, 3, and 7 | AGO7 | 3 | 3 | 1 (2) | 1 |
| RISC complex | AGO4, 6, 8, and 9 | AGO6 | 4 | 3 | 1 (2) | 3 |
| RISC complex | HEN1 | HEN1 | 2 | 1 | 1 (2) | 1 |
| RISC complex | RDR1 and 2 | RDR6 | 2 | 1 | 2 (4) | 1 |
| RISC complex | RDR3 to 5 | RDR4 | 3 | 2 | 1 (2) | 2 |
| RISC complex | RDR6 | RDR6 | 1 | 1 | 0 | 1 |
| RISC complex | HEN4 2) | HEN4 | 9 | 6 | 2 (3) | 1 |
| RISC complex | FLK | FLK | 2 | 5 | 1 (2) | 2 |
| Light signalling | PHYA to E | PHYA | 5 | 3 | 1 (1) | 8 |
| Light signalling | CRY1, 2 | CRY1 | 2 | 3 | 5 (9) | 2 |
| Light signalling | CRY3 | CRY3 | 1 | 1 | 1 (2) | 1 |
| Light signalling | PHOT1 and 2 | PHOT1 | 2 | 2 | 2 (4) | 6 |
| Light signalling | LKP2, FKF1, and ZTL/LKP1 | LKP2 | 3 | 2 | 1 (2) | 0 |
| Light signalling | HO1 to 4 | HO3 | 4 | 2 | 1 (2) | 5 |
| Light signalling | HY2 | HY2 | 1 | 1 | 1 (1) | 1 |
| Light signalling | PAT1 2) | PAT1 | 6 | 6 | 1 (1) | 2 |
| Light signalling | EID1 | EID1 | 1 | 1 | 1 (2) | 3 |
| Light signalling | LAF3 | LAF3 | 1 | 1 | 2 (4) | 1 |
| Light signalling | FAR1, FRS1 to 12, and FHY3 3) | FAR1 | 14 | 56 | 0 | 0 |
| Light signalling | FHY1 | FHY1 | 1 | 2 | 1 (2) | 1 |
| Light signalling | PIF1/PIL5, PIF3 and 4, PIL1 to 4, and HFR/PIL6 2) | PIL6 | 14 | 10 | 3 (6) | 3 |
| Light signalling | NDPK1 | NDPK2 | 1 | 2 | 1 (2) | 2 |
| Light signalling | NDPK2 | NDPK2 | 1 | 1 | 1 (2) | 2 |
| Light signalling | PP5 | PP5 | 1 | 1 | 1 (1) | 2 |
| Light signalling | PP7 2) | PP7 | 3 | 1 | 3 (5) | 3 |
| Light signalling | ATFYPP3 | ATFYPP3 | 2 | 1 | 1 (2) | 2 |
| Light signalling | HRB1 3) | HRB1 | 7 | 7 | 4 (7) | 4 |
| Light signalling | SHL1 2) | SHL1 | 3 | 4 | 2 (3) | 6 |
| Light signalling | SUB1 2) | SUB1 | 3 | 3 | 2 (3) | 1 |
| Light signalling | NPH3 2) | NPH3 | 2 | 1 | 3 (6) | 15 |
| Light signalling | RPT2 2) | RPT2 | 8 | 5 | 2 (4) | 4 |
| Light signalling | JAC1 | JAC1 | 7 | 5 | 5 (7) | 4 |
| Light signalling | PKS1 | PKS1 | 4 | 1 | 0 | 0 |
| Light signalling | CDF1 | CDF1 | 7 | 6 | 3 (4) | 4 |
| Light signalling | SHB1 2) | SHB1 | 9 | 0 | 3(6) | 2 |
| Light signalling | COP1 2) | SPA1 | 1 | 1 | 1 (2) | 9 |
| Light signalling | COP10/FUS9 | COP10 | 1 | 1 | 1 (1) | 2 |
| Light signalling | CIP8 | CIP8 | 6 | 3 | 2 (4) | 0 |
| Light signalling | SPA1 to 4 | SPA1 | 4 | 2 | 1 (2) | 2 |
| Light signalling | CIP1 6) | CIP1 6) | 1 | 0 | 0 | 0 |
| Light signalling | CIP4 6) | CIP4 6) | 2 | 0 | 0 | 0 |
| Light signalling | CIP7 3) | CIP7 | 6 | 3 | 5 (9) | 2 |
| Light signalling | HY5 and HYH 2) | HY5 | 2 | 3 | 2 (4) | 2 |
| Light signalling | LAF1 1) | LAF1 | 3 | 3 | 0 | 0 |
| Light signalling | DET1/FUS2 | DET1 | 1 | 1 | 1 (2) | 3 |
| Light signalling | DDB1A | DDB1A | 2 | 1 | 1 (1) | 2 |
| Light signalling | COP11/FUS6 | COP11 | 1 | 1 | 1 (2) | 2 |
| Light signalling | COP12/FUS12 | FUS12 | 1 | 1 | 1 (2) | 3 |
| Light signalling | COP13/FUS11 | FUS11 | 1 | 1 | 1 (2) | 1 |
| Light signalling | COP8/FUS4/FUS8 | COP8 | 1 | 1 | 1 (2) | 1 |
| Light signalling | AJH1 and 2 | AJH2 | 2 | 1 | 1 (2) | 2 |
| Light signalling | CSN6A and B | CSN6A | 2 | 4 | 1 (2) | 2 |
| Light signalling | COP15/FUS5 | FUS5 | 1 | 1 | 1 (2) | 2 |
| Light signalling | COP9/FUS7 2) | COP9 | 1 | 2 | 1 (2) | 1 |
| Light signalling | AMP1 | AMP1 | 2 | 4 | 4 (7) | 2 |
| Light signalling | PFT1 3) | PFT1 | 1 | 1 | 2 (3) | 2 |
| Light signalling | TED3 | TED3 | 1 | 1 | 1 (2) | 1 |
| Light signalling | OBP3 1) | OBP3 | 13 | 4 | 0 | 0 |
| Light signalling | HLS1 2) | HLS1 | 4 | 4 | 1 (2) | 2 |
| Light signalling | CR88 | CR88 | 2 | 2 | 1 (1) | 2 |
| Light signalling | MIF1 | MIF1 | 3 | 3 | 0 | 0 |
| Light signalling | ZFP1 3) | ZFP1 | 27 | 27 | 6 (11) | 10 |
| Circadian clock | PRR3, 5, 7, and 9 2) | PRR7 | 5 | 2 | 3 (4) | 4 |
| Circadian clock | TOC1 | TOC1 | 1 | 1 | 1 (2) | 0 |
| Circadian clock | CCA1 and LHY 2) | LHY | 5 | 4 | 2 (3) | 2 |
| Circadian clock | COL3 | CO | 18 | 17 | 3 (5) | 6 |
| Circadian clock | ELF3 3) | ELF3 | 2 | 2 | 2 (4) | 4 |
| Circadian clock | ELF4 | ELF4 | 5 | 4 | 2 (3) | 1 |
| Circadian clock | SRR1 | SRR1 | 1 | 2 | 1 (2) | 2 |
| Circadian clock | LUX/PCL1 | PCL1 | 3 | 1 | 1 (2) | 3 |
| Circadian clock | CKB3 | CKB3 | 4 | 3 | 1 (2) | 4 |
| Circadian clock | TIC | TIC | 2 | 1 | 1 (2) | 0 |
| Auxin metabolism | YUCCA | YUCCA | 9 | 8 | 3 (6) | 6 |
| Auxin metabolism | CYP79B2 and B3 1) | CYP79B2 | 2 | 0 | 0 | 0 |
| Auxin metabolism | NIT1-3 | NIT1 | 3 | 0 | 0 | 0 |
| Auxin metabolism | CYP83B1/SUR2 1) | SUR2 | 2 | 0 | 0 | 0 |
| Auxin metabolism | GH3.6/DFL1 2) | DFL1 | 19 | 11 | 17 (29) | 2 |
| Auxin metabolism | AAO1 | AAO1 | 4 | 6 | 3 (5) | 2 |
| Auxin metabolism | TYDC1, 2 | TYDC2 | 2 | 1 | 5 (9) | 2 |
| Auxin metabolism | CYP79F1/SPS1 | SUPERSHOOT1 | 8 | 3 | 0 | 0 |
| Auxin signalling | TIR1 | TIR1 | 6 | 6 | 2 (4) | 4 |
| Auxin signalling | ABP1 | ABP1 | 1 | 1 | 2 (4) | 1 |
| Auxin signalling | IAA1 to 20, 26 to 34 2) | IAA31 | 29 | 30 | 4 (7) | 2 |
| Auxin signalling | ARF5/MP, NPH4/BIPOSTO, ARF6, 8, 16, and 19 2) | NPH4 | 5 | 8 | 3 (5) | 6 |
| Auxin signalling | ETT/ARF3, ARF1, 2, 4, 9, 11 to 15, 18, 20, and 21 | ETT | 15 | 9 | 2 (4) | 4 |
| Auxin signalling | ARF10, ARF16 | ARF16 | 2 | 4 | 2 (4) | 2 |
| Auxin signalling | ARF17 | ARF16 | 1 | 1 | 0 | 0 |
| Auxin signalling | AXR1 2) | AXR1 | 3 | 1 | 1 (2) | 2 |
| Auxin signalling | SKP1/ASK1 | SKP1 | 17 | 12 | 1 (2) | 3 |
| Auxin signalling | AXR6/ATCUL1 | ATCUL1 | 2 | 3 | 1 (2) | 3 |
| Auxin signalling | RCE1 | RCE1 | 2 | 3 | 3 (5) | 5 |
| Auxin carriers | AUX1 | AUX1 | 4 | 4 | 2 (4) | 4 |
| Auxin carriers | PIN1 to 8 2) | PIN5 | 9 | 11 | 5 (7) | 3 |
| Auxin carriers | MDR/PGP1 | PGP1 | 1 | 1 | 0 | 0 |
| Auxin carriers | PGP19 | PGP1 | 1 | 2 | 2 (4) | 2 |
| Auxin carriers | MDR4/PGP4 | PGP1 | 8 | 8 | 5 (9) | 1 |
| Auxin carriers | PID | PID | 3 | 3 | 0 | 0 |
| Auxin carriers | BIG1 | BIG1 | 1 | 1 | 1 (2) | 2 |
| Jasmonic acid biosynthesis | OPR3 | OPR3 | 1 | 1 | 1 (2) | 2 |
| Jasmonic acid signalling | COI1 9) | COI1 | 1 | 3 | 4 (8) | 3 |
| Cytokinin metabolism | CKX1 to 7 | CKX7 | 7 | 11 | 2 (4) | 6 |
| Cytokinin biosynthesis | CYP735A1 and CYP735A2 | CYP735A1 | 2 | 2 | 0 | 0 |
| Cytokinin signalling | AHK2, 3, and CRE1/WOL/AHK4 | CRE1 | 3 | 5 | 2 (3) | 3 |
| Cytokinin signalling | AHP1 to 6 | AHP2 | 7 | 4 | 2 (4) | 3 |
| Cytokinin signalling | ARR3 to 9, 15 to 17 2) | ARR5 | 11 | 15 | 2 (4) | 7 |
| Cytokinin signalling | ARR1, 2, 10 to 14, and 18 to 211) | ARR1 | 12 | 9 | 5 (9) | 5 |
| Gibberellic acid biosynthesis | GA1/KSA/CPS and GA2/KSB 3) | GA2 | 11 | 13 | 9 (13) | 2 |
| Gibberellic acid biosynthesis | GA4 | GA4 | 4 | 2 | 1 (1) | 1 |
| Gibberellic acid signalling | GID1L1 to 3 | GID1 4) | 3 | 1 | 2(4) | 0 |
| Gibberellic acid signalling | GAI, RGA, and RGL1 to 3 4) | GAI | 5 | 1 | 1 (2) | 2 |
| Gibberellic acid signalling | SPY | SPY | 1 | 1 | 1 (2) | 2 |
| Abscisic acid biosynthesis | ABA1/ZEP | ABA1 | 1 | 2 | 1 (2) | 2 |
| Abscisic acid biosynthesis | NCED3 | NCED3 | 5 | 4 | 1 (2) | 2 |
| Abscisic acid biosynthesis | ABA2 and ATA1 | ABA2 | 11 | 20 | 5 (10) | 2 |
| Abscisic acid biosynthesis | AAO3 | AAO3 | 4 | 6 | 3 (6) | 2 |
| Abscisic acid signalling | PYR1 | PYR1 | 7 | 6 | 4 (8) | 4 |
| Abscisic acid signalling | GTG1 | GTG1 | 2 | 1 | 1 (2) | 0 |
| Abscisic acid signalling | CHLH | CHLH | 1 | 1 | 1 (2) | 1 |
| Abscisic acid signalling | ABH1 | ABH1 | 1 | 1 | 1 (2) | 2 |
| Abscisic acid signalling | ABI1 | ABI1 | 9 | 10 | 3 (6) | 2 |
| Ethylene biosynthesis | ACS1 to 9, and 11 | ACS2 | 10 | 5 | 0 | 0 |
| Ethylene biosynthesis | ACO1 and 2 | ACO2 | 5 | 7 | 0 | 0 |
| Ethylene biosynthesis | RCN1 | RCN1 | 3 | 1 | 2 (4) | 4 |
| Ethylen signalling | ETR1 and ERS1 | ETR1 | 2 | 2 | 3 (6) | 4 |
| Ethylen signalling | ETR2, ERS2, and EIN4 1) | ETR1 | 3 | 3 | 0 | 1 |
| Ethylen signalling | CTR1 | CTR1 | 6 | 8 | 4 (6) | 0 |
| Ethylen signalling | EIN2 | EIN2 | 1 | 3 | 1 | 1 |
| Ethylen signalling | EBF1 and 2 | EBF1 | 2 | 2 | 2 (2) | 2 |
| Brassinosteroid biosynthesis | SMT1 | SMT1 | 1 | 3 | 1 (2) | 1 |
| Brassinosteroid biosynthesis | FK | FK | 1 | 1 | 1 (2) | 1 |
| Brassinosteroid biosynthesis | HYD1 | HYD1 | 1 | 1 | 2 (4) | 1 |
| Brassinosteroid biosynthesis | DWF5 7) | DWF5 | 1 | 1 | 1 (2) | 2 |
| Brassinosteroid biosynthesis | DET2 | DET2 | 1 | 2 | 2 (4) | 1 |
| Brassinosteroid biosynthesis | CPD, DWF4, ROT3, and BR6ox1 and 2 | CPD | 19 | 16 | 4 (8) | 3 |
| Brassinosteroid signalling | BRI1 and BRL1 | BRI1 | 4 | 4 | 0 | 0 |
| Brassinosteroid signalling | BAK1, SERK1, 2, and 9 | SERK2 | 5 | 3 | 2 (2) | 3 |
| Brassinosteroid signalling | BIN2, AT1G06390, and AT2G30980 2) | AT1G06390 | 10 | 9 | 2 (4) | 6 |
| Brassinosteroid signalling | BSU1 | BSU1 | 1 | 0 | 0 | 0 |
| Brassinosteroid signalling | BIM1 to 3 2) | BIM1 | 3 | 3 | 1 (2) | 3 |
| Brassinosteroid signalling | BES1 3) | BES1 | 6 | 4 | 5 (9) | 6 |
| Brassinosteroid signalling | TRIP1 | TRIP1 | 2 | 2 | 1 (2) | 3 |
| Seed | LEC1 | LEC1 | 2 | 2 | 1 (2) | 0 |
| Seed | ABI3, FUS3, and LEC2 2) | FUS3 | 3 | 5 | 3 (6) | 11 |
| Seed | HSI2 | HSI2 | 3 | 2 | 1 (2) | 2 |
| Seed | ABI4 1) | ABI4 | 9 | 5 | 4 (6) | 7 |
| Seed | ABI5 7) | ABI5 | 7 | 5 | 4 (8) | 1 |
| Embryo | EMB1417 and 2748 2) | AT1G04590 | 2 | 3 | 2 (3) | 1 |
| Embryo | EMB3001 | AT1G08910 | 2 | 1 | 2 (3) | 0 |
| Embryo | EMB1273 | AT1G49510 | 1 | 0 | 1 (2) | 2 |
| Embryo | EMB2423 | AT3G48470 | 1 | 1 | 1 (2) | 1 |
| Embryo | EMB1703 | AT3G61780 | 2 | 0 | 1 (2) | 2 |
| Embryo | EMB2739 | AT4G14590 | 1 | 1 | 2 (3) | 1 |
| Embryo | EMB1895 | AT4G20060 | 1 | 2 | 2 (4) | 2 |
| Embryo | EMB1027 | AT4G26300 | 2 | 3 | 1 (1) | 1 |
| Embryo | EMB2735 | AT5G06240 | 1 | 2 | 1 (2) | 1 |
| Embryo | EMB2196 | AT5G10330 | 1 | 1 | 1 (2) | 1 |
| Embryo | EMB2024 2) | AT5G24400 | 5 | 4 | 2 (4) | 2 |
| Embryo | EMB3012 | AT5G40480 | 1 | 0 | 2 (3) | 1 |
| Embryo | EMB1875 | AT5G40600 | 1 | 0 | 0 | 0 |
| Embryo | EMB1187 | AT2G26830 | 1 | 1 | 1 (2) | 2 |
| Root | PLT1 and 2 | ANT | 8 | 11 | 1 (2) | 3 |
| Root | SHR | SHR | 1 | 2 | 3 (6) | 2 |
| Root | SCR | SCR | 1 | 2 | 2 (4) | 3 |
| Root | WOX5 3) | WUS | 16 | 10 | 9 (16) | 3 |
| Lateral root | NAC1 | NAC1 | 3 | 10 | 0 | 0 |
| Lateral root | SINAT5 2) | SINAT5 | 6 | 5 | 4 (8) | 4 |
| Lateral root | AIR3 | AIR3 | 3 | 5 | 10 (10) | 1 |
| Lateral root | PAS2 | PAS2 | 1 | 5 | 1 (2) | 1 |
| Lateral root | ATNRT2.1/LIN1 7) | ATNRT2.1 | 7 | 4 | 2 (4) | 8 |
| Lateral root | ALF4 | ALF4 | 1 | 1 | 1 (1) | 2 |
| Lateral root | RPD1 2) | RPD1 | 15 | 17 | 10 (20) | 4 |
| Shoot meristem | WUS and WOX1 to 14 3) | WUS | 16 | 10 | 9 (16) | 3 |
| Shoot meristem | CLV1 | CLV1 | 4 | 6 | 3 (3) | 0 |
| Shoot meristem | CLV2 | CLV2 | 2 | 3 | 2 (2) | 0 |
| Shoot meristem | STM, BP, KNAT1, and 6 | KNAT1 | 4 | 9 | 3 (3) | 3 |
| Shoot meristem | KNAT3 to 5, and 7 | KNAT3 | 4 | 4 | 2 (2) | 2 |
| Shoot meristem | AS1 1) | AS1 | 1 | 1 | 1 (2) | 0 |
| Shoot meristem | AS2 | AS2 | 1 | 2 | 0 | 0 |
| Shoot meristem | BOP1 and 2 | BOP1 | 2 | 2 | 2 (3) | 3 |
| Shoot meristem | CUC1, 2, and 3 | CUC1 | 11 | 12 | 3 (6) | 8 |
| Shoot meristem/Gynoecium | BEL1, BLR, PNF, and PNY 2) | BLR | 13 | 13 | 2 (2) | 4 |
| Shoot meristem | TPL | TPL | 5 | 2 | 3 (6) | 2 |
| Shoot meristem | HAN 1) | HAN | 3 | 2 | 2 (3) | 4 |
| Shoot meristem | ULT1 | ULT1 | 2 | 1 | 0 | 0 |
| Shoot meristem | BBM1 | ANT | 8 | 11 | 1 (2) | 3 |
| Axillary meristem | MAX1 | MAX1 | 1 | 5 | 1 (2) | 0 |
| Axillary meristem | MAX2 | MAX2 | 1 | 1 | 1 (2) | 1 |
| Axillary meristem | MAX3 | MAX3 | 1 | 1 | 1 (2) | 3 |
| Axillary meristem | MAX4 | MAX4 | 1 | 2 | 1 (2) | 1 |
| Axillary meristem | RAX1 1) | RAX1 | 6 | 8 | 1 (2) | 0 |
| Axillary meristem | LAS | LAS | 1 | 2 | 1 (2) | 2 |
| Leaf | PHB, PHV, REV, COR, and ATHB8 | PHV | 5 | 4 | 3 (6) | 5 |
| Leaf | CRC, FIL, and INO | INO | 6 | 7 | 0 | 0 |
| Leaf | KAN 2) | KAN | 4 | 6 | 3 (6) | 3 |
| Leaf | AN | AN | 1 | 2 | 1 (2) | 5 |
| Leaf | ANT | ANT | 8 | 11 | 1 (2) | 3 |
| Leaf | ARGOS and ARL | ARGOS | 2 | 2 | 0 | 0 |
| Leaf | TCP3 and 4 2) | TCP3 | 8 | 8 | 3 (6) | 2 |
| Leaf | TSL | TSL | 1 | 1 | 1 (2) | 1 |
| Epidermal cell differentiation | ANL2, AtML1, GL2, and PDF2 1) | GL2 | 17 | 10 | 5 (9) | 4 |
| Epidermal cell differentiation | TTG1 | TTG1 | 1 | 1 | 0 | 0 |
| Epidermal cell differentiation | ATAN11 | TTG1 | 2 | 1 | 1 (2) | 4 |
| Epidermal cell differentiation | MYB23, GL1, and WER 1) | MYB23 | 3 | 0 | 0 | 0 |
| Epidermal cell differentiation | EGL3, GL3, and TT8 | GL3 | 4 | 7 | 1 (2) | 1 |
| Epidermal cell differentiation | CPC, ETC1, ETC2, and TRY | CPC | 6 | 1 | 0 | 0 |
| Epidermal cell differentiation | RHD3 | RHD3 | 3 | 3 | 1 (1) | 3 |
| Epidermal cell differentiation | IRE 2) | IRE | 4 | 2 | 2 (4) | 5 |
| Epidermal cell differentiation | AKT1 and SPIK | AKT1 | 7 | 9 | 0 | 4 |
| Epidermal cell differentiation | RHD2 2) | RHD2 | 10 | 9 | 11 (20) | 4 |
| Epidermal cell differentiation | RIC1 to RIC10 2) | RIC1 | 10 | 10 | 1 (2) | 1 |
| Epidermal cell differentiation | RIC2 3) | RIC2 | 9 | 7 | 1 (2) | 0 |
| Epidermal cell differentiation | SUB | SUB | 3 | 4 | 0 | 0 |
| stomata opening | GPA1 | GPA1 | 1 | 1 | 1 (2) | 0 |
| stomata opening | AGB1 | AGB1 | 1 | 1 | 1 (2) | 1 |
| stomata opening | AGG1 and 2 | AGG1 | 2 | 2 | 0 | 0 |
| stomata opening | GCR1 | GCR1 | 1 | 1 | 1 (2) | 2 |
| stomata opening | GORK | GORK | 2 | 2 | 1 (2) | 0 |
| Stomata development | SDD1 | SDD1 | 3 | 13 | 0 | 0 |
| Vascular system | VAN3 | VAN3 | 2 | 1 | 1 (2) | 3 |
| Vascular system | DRP1A | DRP1A | 2 | 2 | 0 | 0 |
| Vascular system | CVP2 | CVP2 | 7 | 11 | 2 (4) | 6 |
| Vascular system | VND1 to 7 and NST1 and 2 | VND7 | 13 | 10 | 4 (7) | 8 |
| Vascular system | COV1 2) | COV1 | 4 | 5 | 1 (2) | 4 |
| Vascular system | APL | APL | 4 | 3 | 2 (4) | 7 |
| Lignin synthesis | PAL | PAL | 4 | 10 | 2 (3) | 11 |
| Lignin synthesis | C4H | C4H | 1 | 2 | 1 (2) | 6 |
| Lignin synthesis | 4CL1 2) | 4CL1 | 4 | 5 | 2 (3) | 4 |
| Lignin synthesis | HCT 7) | HCT | 2 | 2 | 1 (2) | 1 |
| Lignin synthesis | C3H | C3H | 1 | 2 | 1 (2) | 1 |
| Lignin synthesis | CCOAOMT1 2) | CCOAOMT1 | 1 | 1 | 3 (6) | 1 |
| Lignin synthesis | CCR1 and 2 | CCR2 | 2 | 13 | 3 (5) | 1 |
| Lignin synthesis | CAD1 to 9 | CAD9 | 9 | 8 | 5 (7) | 2 |
| Lignin synthesis | FAH1 1) | FAH1 | 2 | 2 | 0 | 0 |
| Lignin synthesis | COMT 2) | COMT | 13 | 11 | 16 (28) | 3 |
| Phase transition | CLF and SWN | MEA | 2 | 2 | 1 (2) | 1 |
| Phase transition | MEA | MEA | 1 | 0 | 0 | 0 |
| Phase transition | FIE 2) | FIE | 1 | 2 | 1 (2) | 1 |
| Phase transition | EMF2, FIS2, and VRN2/VEF1 | EMF2 | 4 | 2 | 1 (2) | 3 |
| Phase transition | MSI1 | MSI1 | 1 | 1 | 1 (2) | 1 |
| Flowering | CO 2) | CO | 18 | 17 | 3 (5) | 6 |
| Flowering | FCA | FCA | 2 | 1 | 1 (2) | 2 |
| Flowering | FY | FY | 1 | 1 | 1 (2) | 1 |
| Flowering | FT and TFL1 | FT | 5 | 14 | 0 | 0 |
| Flowering | FD | FD | 2 | 1 | 0 | 0 |
| Flowering | VRN1 | VRN1 | 1 | 2 | 1 (2) | 6 |
| Flowering | VIP2 | VIP2 | 2 | 3 | 1 (2) | 3 |
| Flowering | VIP3 | VIP3 | 1 | 1 | 1 (2) | 2 |
| Flowering | VIP4 | VIP4 | 1 | 2 | 1 (2) | 1 |
| Flowering | TFL2/LHP1 | TFL2 | 1 | 1 | 1 (2) | 0 |
| Flowering | VIN3 | VIN3 | 4 | 4 | 2 (3) | 0 |
| Flowering | FLD 2) | FLD | 3 | 3 | 1 (2) | 2 |
| Flowering | FPA 2) | FPA | 2 | 2 | 1 (2) | 2 |
| Flowering | FRI 2) | FRI | 8 | 5 | 3 (6) | 2 |
| Flowering | EMF1 | EMF1 | 1 | 1 | 0 | 0 |
| Flowering | ESD4 | ESD4 | 3 | 2 | 1 (2) | 2 |
| Flowering | GI | GI | 1 | 1 | 1 (2) | 0 |
| Flowering | LD | LD | 1 | 1 | 1 (2) | 1 |
| Flowering | LFY | LFY | 1 | 1 | 1 (1) | 2 |
| Floral organ | HUA1 | HUA1 | 1 | 1 | 0 | 0 |
| Floral organ | HUA2 2) | HUA2 | 4 | 2 | 4 (8) | 2 |
| Floral organ | RBE and SUP | SUP | 5 | 4 | 2 (4) | 8 |
| Floral organ | JAG and NUB | NUB | 2 | 1 | 2 (4) | 2 |
| Floral organ | AP2 | ANT | 2 | 5 | 2 (4) | 0 |
| Floral organ | PTL | PTL | 5 | 4 | 2 (4) | 4 |
| Floral organ | SPL8 2) | SPL8 | 1 | 3 | 4 (8) | 6 |
| Floral organ | UFO | UFO | 1 | 1 | 1 (1) | 0 |
| Floral organ | AG, PI, AP3, AP1, SHP1 and 2, SEP1-3 | MIKCc-type MADS-box genes 5) | 38 | 34 | 3 (5) | 6 |
| Floral organ | LUG | LUG | 1 | 3 | 3 (6) | 3 |
| Gynoecium | STY2 | STY2 | 10 | 5 | 3 (5) | 2 |
| Gynoecium | IND | IND | 5 | 5 | 2(4) | 6 |
| Gynoecium | ALC | ALC | 2 | 3 | 3 (6) | 3 |
| Endosperm | TTN9 | TTN9 | 1 | 1 | 1 (2) | 1 |
| pollen | AGL30, AGL65, AGL66, AGL94, and AGL104 | MIKC*-type MADS-box genes 5) | 6 | 3 | 3 (6) | 11 |
| Pollen | EMS1/EXS | EMS1 | 1 | 2 | 2 (2) | 6 |
| Pollen | SPL/NZZ | SPL | 1 | 1 | 2 (4) | 3 |
| Pollen | TPD1 3) | TPD1 | 4 | 14 | 5 (9) | 9 |
| Pollen | GPAT1 2) | GPAT1 | 8 | 15 | 10 (20) | 7 |
| Pollen | MEI1 | MEI1 | 1 | 1 | 1 (2) | 1 |
| pollen | ASK1, ASK2, and OST1 2) | ASK1 | 10 | 10 | 3 (6) | 4 |
| Pollen | CDC45 | CDC45 | 1 | 2 | 1 (2) | 1 |
| Pollen | ATK1 | ATK1 | 4 | 3 | 2 (4) | 2 |
| Pollen | TES/STD | TES | 2 | 1 | 1 (2) | 3 |
| Pollen | MRE11 | MRE11 | 1 | 1 | 1 (2) | 1 |
| Pollen | ATRAD50 | ATRAD50 | 1 | 1 | 1 (2) | 1 |
| Pollen | MMD1/DUET 7) | MMD1 | 4 | 2 | 1 (2) | 2 |
| Pollen | MS5 3) | MS5 | 5 | 4 | 2 (4) | 7 |
| Pollen | SYN1 | SYN1 | 1 | 1 | 1 (2) | 1 |
| Pollen | NEF1 | NEF1 | 1 | 1 | 1 (2) | 1 |
| Pollen | AMS | AMS | 1 | 1 | 1 (2) | 2 |
| Pollen | YRE/FLP1/WAX2 | CER1 | 1 | 3 | 3 (6) | 2 |
| Pollen | DEX1 | DEX1 | 1 | 1 | 2 (4) | 1 |
| Pollen | MS2 | MS2 | 2 | 1 | 2 (4) | 2 |
| Pollen | ADL1C | ADL1C | 3 | 3 | 3 (6) | 5 |
| Pollen | DUO1 | DUO1 | 1 | 1 | 2 (4) | 2 |
| Pollen | BCP1 | BCP16) | 2 | 0 | 0 | 0 |
| Pollen | CER1 | CER1 | 3 | 5 | 1 (2) | 2 |
| Pollen | MYB4 and 32 | MYB4 | 6 | 6 | 2 (4) | 0 |
| Pollen | QRT3 | QRT3 | 2 | 1 | 0 | 2 |
| Pollen | AT2G19620 | AT2G19620 | 3 | 4 | 1 (2) | 7 |
| Pollen | AT5G56200 2) | AT5G56200 | 9 | 8 | 2 (3) | 4 |
| Pollen | SEC8 | SEC8 | 1 | 1 | 1 (2) | 3 |
| Pollen | POK | POK | 2 | 1 | 1 (2) | 1 |
| Pollen | NPG1 2) | NPG1 | 3 | 3 | 2 (4) | 2 |
| Pollen | ACA9 7) | ACA9 | 6 | 4 | 2 (4) | 3 |
| Pollen | ATAPY2 | ATAPY2 | 2 | 8 | 1 (2) | 3 |
| Pollen | KIP | KIP | 2 | 1 | 1 (2) | 1 |
| Pollen | GCS1 | GCS1 | 1 | 2 | 1 (2) | 1 |
| Other factors | ACC1 | ACC1 | 2 | 1 | 1 (2) | 2 |
| Other factors | ACX4 | ACX4 | 1 | 2 | 1 (2) | 2 |
| Other factors | EMB1187 | EMB1187 | 1 | 1 | 1 (2) | 2 |
| Other factors | RPE | RPE | 1 | 1 | 1 (2) | 3 |
| Other factors | TPC1 | TPC1 | 1 | 1 | 0 | 2 |
| Other factors | MEE63/AT1G02140 | MEE63 | 1 | 1 | 1 (2) | 2 |
| Other factors | ATNAP6 | ATNAP6 | 1 | 1 | 1 (2) | 2 |
| Other factors | CPN60A and EMB3007 7) | CPN60A | 2 | 2 | 2 (4) | 3 |
| Other factors | VAM3 2) | VAM3 | 4 | 3 | 2 (4) | 4 |
| Other factors | NIT4 | NIT1 | 1 | 2 | 1 (2) | 1 |
| Other factors | ATHB1, 3, 5 to 7, 12, 13, and 16 1) | ATHB7 | 17 | 12 | 4 (8) | 1 |
| Other factors (Type C response regulator) | ARR22 | ARR22 | 2 | 1 | 2 (3) | 3 |
| Cell wall | CESA1 | CESA1 | 3 | 3 | 4 (8) | 8 |
| Cell wall | Porphyra CESA1 | PorphyraCESA | 0 | 0 | 4(8) | 1 |
1) When genes are involved in a gene family that is divided into subgroups based on a domain structure, an amino acid similarity for a most coding region, or functions, a minimum land plant clade is defined in the subgroup.
2) When genes are involved in a gene family defined as a domain structure or amino acid similarity for a most coding region and when bootstrap supports of the inter gene relationships were low, all members in the gene family were counted as potential land plant orthologues.
3) When genes are involved in a gene family defined as a domain structure or amino acid similarity for a most coding region and when a root is hard to identify because of the lack of outgroup taxa, all members in the family were counted as potential land plant orthologues.
4) Angiosperm gene other than A. thaliana was used as a query.
5) Homologues of A. thaliana MADS-box genes were collected from NCBI protein database. Homologues of O. sativa MADS-box genes were collected from the Database of Rice Transcription Factors (http://drtf.cbi.pku.edu.cn/). S. moellendorffii MADS-box genes were collected using a Selaginella remotifolia SrMADS1 MADS-box gene as a query. The sequences of P. patens MADS-box genes, which we have already cloned, were used and we confirmed that there are no more MADS-box genes in P. patens genome.
6) Homologues were only found in A. thaliana and no phylogenetic tree was constructed.
7) The number of potential orthologs was counted with the maximum-likelihood tree.