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Table 6 Groups of functionally linked genes co-eliminated during evolution of different eukaryotic lineages

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

Functional group/ complex Lost KOGs*
  Hs Dm Ce Coelomates/ Ecdysozoa Animals Yeasts Fungi-Ec
Mitochondrial ribosomal proteins 3331, 3435/ 3331, 3435 3505, 4600, 4612/ None 3505, 4122, 4600, 4612/ 4122 None/ 3505, 4600, 4612 0899, 0938, 1740, 3254, 3278, 4844   0408,1686, 1708, 4707
Spliceosome, including putative associated proteins   1847, 1960/ 1847 1902, 1960, 2991, 3414 None/ 1960    0105, 0107, 0117, 1365, 1588, 1676, 1847, 1996, 2191, 2242, 2548, 2991, 4207, 4211
Exosome   1004, 1613      
Replication origin-recognition complex    2228, 2538, 4557     4557
Mismatch repair system   0218, 0220, 221, 1977 0218, 1977, 4120 None/ 0218, 1977    
Ubiquitin system/ proteasome-signalosome components   0170, 0428, 1814, 4116, 4185, 4412 0168, 0170, 0320, 0421, 0423, 1364, 1571, 1645, 1871, 1873, 1887, 2561, 2932, 3061, 3250, 3268, 4146, 4159, 4275, 4412, 4413, 4414, 4692, 4761 None/ 0170, 4412   0823, 1645, 1734 0311, 0423, 0427, 0827, 0895, 1100, 1139, 1464, 1571, 1812, 1887, 2561, 2932, 3011, 3050, 3268, 4185, 4248, 4265, 4275, 4413, 4414, 4427, 4642, 4692, 4761
NADH-ubiquinone oxido-reductase/ NADH dehydro-genase        2865, 2870, 3256, 3300, 3365, 3382, 3389, 3426, 3446, 3456, 3458, 3466, 3468, 4009, 4662, 4668, 4669, 4770, 4845
  1. *For each of the animals, the numerator indicates the KOGs lost under the coelomate topology of the species tree, and the denominator indicates KOGs lost under the ecdysozoan topology.