Table 6 Gene family assignment for retained and lost genes in Chiifu, turnip and rapid cycling
Chiifu | Turnip | Rapid cycling | |||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
TAIR gene family description | Class | Number of genes in common sets | Number of genes in unique and dispensable sets | TAIR gene family description | Class | Number of genes in common sets | Number of genes in unique and dispensable sets | TAIR gene family description | Class | Number of genes in common sets | Number of genes in unique and dispensable sets |
C2H2 transcription factor family | LOST | Acyl lipid metabolism family | LOST | C3H transcription factor family | LOST | ||||||
Core DNA replication machinery | LOST | C2H2 Transcription factor family | LOST | Cytochrome P450 | LOST | ||||||
Cytochrome P450 | LOST | Class III peroxidase | LOST | Cytoplasmic ribosomal protein gene family | LOST | ||||||
Cytoplasmic ribosomal protein gene family | LOST | Cytochrome P450 | LOST | Glutathione S-transferase family | LOST | ||||||
Cytoskeleton | LOST | Cytoplasmic ribosomal protein gene family | LOST | Glycoside hydrolase gene families | LOST | ||||||
EF-hand containing proteins | LOST | EF-hand containing proteins | LOST | Glycosyltransferase gene families | LOST | ||||||
Expansins | LOST | FH2 proteins | LOST | Homeobox transcription factor family | LOST | ||||||
Glutathione S-transferase family | LOST | Glycosyltransferase gene families | LOST | Inorganic solute cotransporters | LOST | ||||||
Glycosyltransferase gene families | LOST | MIP family | LOST | Lipid metabolism gene families | LOST | ||||||
Lateral organ boundaries gene family | LOST | Miscellaneous membrane protein families | LOST | MAP kinase kinase kinase kinase (MAPKKKK) family | LOST | ||||||
Miscellaneous membrane protein families | LOST | Monosaccharide transporter-like gene family | LOST | Miscellaneous membrane protein families | LOST | ||||||
MYB Transcription factor family | LOST | Trihelix transcription factor family | LOST | Primary pumps (ATPases) gene families | LOST | ||||||
Primary pumps (ATPases) gene family | LOST | ARF transcription factor family | RETAINED | 15 | 1 | Receptor kinase-like protein family | LOST | ||||
Acyl Lipid metabolism family | RETAINED | 587 | 3 | Carbohydrate esterase gene families | RETAINED | 75 | 1 | Acyl Lipid metabolism family | RETAINED | 587 | 4 |
AP2-EREBP transcription factor family | RETAINED | 170 | 1 | Chloroplast and mitochondria gene families | RETAINED | 53 | 1 | BZR transcription factor family | RETAINED | 6 | 1 |
ARF transcription factor family | RETAINED | 15 | 1 | Class III peroxidase | RETAINED | 71 | 1 | CBL-interacting serione-threonine Protein Kinases | RETAINED | 24 | 1 |
C2H2 transcription factor family | RETAINED | 215 | 1 | Cytochrome P450 | RETAINED | 144 | 2 | Core cell cycle genes | RETAINED | 65 | 1 |
C3H transcription factor family | RETAINED | 162 | 1 | Cytoplasmic ribosomal protein gene family | RETAINED | 221 | 1 | Cytochrome P450 | RETAINED | 144 | 3 |
CCAAT-HAP3 transcription factor family | RETAINED | 13 | 1 | GeBP transcription factor family | RETAINED | 10 | 1 | Glycoside hydrolase gene families | RETAINED | 335 | 1 |
Cytoplasmic ribosomal protein gene family | RETAINED | 221 | 2 | Glutathione S-transferase family | RETAINED | 37 | 2 | Glycosyltransferase gene families | RETAINED | 280 | 1 |
EF-hand containing proteins | RETAINED | 175 | 2 | Glycosyltransferase gene families | RETAINED | 280 | 1 | Histidine phosphotransfer proteins | RETAINED | 5 | 1 |
Eukaryotic initiation factor gene family | RETAINED | 101 | 1 | HSP70s | RETAINED | 4 | 1 | Inorganic solute cotransporters | RETAINED | 93 | 1 |
Glutathione S-transferase family | RETAINED | 37 | 1 | Lipid metabolism gene families | RETAINED | 106 | 2 | Lipid metabolism gene families | RETAINED | 106 | 1 |
Glycoside hydrolase gene families | RETAINED | 335 | 2 | MADS-box transcription factor family | RETAINED | 89 | 2 | Miscellaneous membrane protein families | RETAINED | 415 | 3 |
Glycosyltransferase gene families | RETAINED | 280 | 1 | Myosin | RETAINED | 17 | 1 | NAC transcription factor family | RETAINED | 97 | 1 |
Lateral organ boundaries gene family | RETAINED | 37 | 2 | Organic solute cotransporters | RETAINED | 272 | 1 | Nodulin-like protein family | RETAINED | 65 | 3 |
MAP kinase kinase kinase family | RETAINED | 74 | 1 | Receptor kinase-like protein family | RETAINED | 237 | 4 | Organic solute cotransporters | RETAINED | 272 | 2 |
MIP family | RETAINED | 37 | 1 | REM transcription factor family | RETAINED | 20 | 1 | Pollen coat proteome | RETAINED | 3 | 1 |
Miscellaneous membrane protein families | RETAINED | 415 | 2 | RCI2 gene family | RETAINED | 6 | 2 | ||||
MYB transcription factor family | RETAINED | 154 | 1 | SNAREs | RETAINED | 66 | 1 | ||||
Plant defensins superfamily | RETAINED | 6 | 1 | ||||||||
Plant U-box protein (PUB) | RETAINED | 66 | 1 | ||||||||
Primary pumps (ATPases) gene family | RETAINED | 31 | 1 | ||||||||
Receptor kinase-like protein family | RETAINED | 237 | 2 | ||||||||