A comprehensive evolutionary classification of proteins encoded in complete eukaryotic genomes

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

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

*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.

ISSN: 1474-760X