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Table 6 Gene family assignment for retained and lost genes in Chiifu, turnip and rapid cycling

From: Beyond genomic variation - comparison and functional annotation of three Brassica rapagenomes: a turnip, a rapid cycling and a Chinese cabbage

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         
  1. Overview of lost and retained genes assigned to A. thaliana gene families. The “LOST” gene family has no value in the dispensable and unique gene set because the inconsistency of counts in the other two genotypes.