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Table 5 Functional profiles of genes lost in different eukaryotic lineages

From: A comprehensive evolutionary classification of proteins encoded in complete eukaryotic genomes

Functional category Lost genes (KOGs)
  Hs* Dm* Coelomates/ Ecdysozoa Ce* Animals Sc Sp Yeasts Ec Fungi-Ec
Total 162/114 520/369 37/188 541/751 193 299 202 55 1,969 802
RNA processing and modification 2/3 9/8 1/2 10/11 4 15 7 1 88 32
Translation 3/3 16/11 0/5 13/10 9 9 6 3 122 10
Transcription 5/2 16/12 0/4 29/33 2 16 9 4 83 40
Replication and repair 4/5 28/14 1/15 29/14 2 9 7 3 60 16
Chromatin structure and dynamics 1/1 8/6 0/2 8/6 0 5 3 1 29 11
Energy production and conversion 7/10 9/10 5/4 12/10 7 6 13 1 110 37
Cell cycle control and mitosis 3/3 11/6 0/5 15/11 3 12 3 1 61 16
Amino acid metabolism and transport 5/6 16/9 1/8 15/7 38 6 9 0 110 18
Nucleotide metabolism and transport 3/3 6/3 0/3 8/5 5 0 3 1 38 9
Carbohydrate metabolism and transport 3/3 13/10 1/4 18/14 8 10 16 3 70 41
Coenzyme metabolism 0/2 5/5 2/2 14/12 11 1 1 0 51 12
Lipid metabolism 1/5 27/19 4/12 18/6 4 9 19 2 74 33
Membrane and cell wall structure and biogenesis 5/4 10/10 2/2 9/11 7 5 3 0 37 15
Post-translational modification, protein turnover, chaperone functions 3/5 22/15 2/9 44/40 8 29 21 4 167 69
Inorganic ion transport and metabolism 2/4 8/8 2/2 8/7 9 2 6 4 50 14
Secondary metabolites biosynthesis, transport and catabolism 1/2 6/5 1/2 5/3 2 4 1 0 23 5
Signal transduction 5/3 32/22 0/10 30/37 4 16 7 3 110 52
Intracellular trafficking and secretion 4/3 10/8 0/2 14/14 3 5 11 0 116 22
Nuclear structure 0/0 3/3 0/0 5/6 0 1 0 0 16 5
Cytoskeleton 0/0 2/2 0/0 6/8 0 9 0 3 44 6
General functional prediction only (typically, prediction of biochemical activity) 14/13 79/55 5/29 88/72 30 55 24 11 241 134
Function unknown 91/34 184/128 10/66 143/414 37 75 33 10 269 205
  1. *For each of the animals, the numerator indicates the number of genes lost under the coelomate topology of the species tree and the denominator indicates the number of genes lost under the ecdysozoan topology of the tree.