A comprehensive evolutionary classification of proteins encoded in complete eukaryotic genomes was conducted by analyzing 5,873 clusters of predicted orthologs (KOGs) from seven eukaryotic genomes. These KOGs were used to identify conserved genes and their evolutionary patterns. The study revealed that approximately 40% of KOGs are conserved across six or seven species and are involved in essential functions such as translation and RNA processing. The analysis also identified I31 single-member, pan-eukaryotic KOGs, which were examined in detail. For around 20 of these KOGs, functions were predicted through sequence analysis and genomic context. These proteins are often subunits of known or predicted multiprotein complexes, supporting the balance hypothesis of gene copy number evolution. The study also examined the phyletic patterns of KOGs, which revealed a conserved eukaryotic gene core and substantial diversity. The pan-eukaryotic genes, represented in all seven analyzed genomes, account for around 20% of the KOGs. The analysis showed that the majority of KOGs are involved in functions such as RNA processing, transcription, and chromatin dynamics. The study also identified lineage-specific gene loss and the 'invention' of new genes in eukaryotic evolution. The results provided quantitative support for major trends in eukaryotic evolution and a basis for detailed reconstruction of eukaryotic genome evolution. The study also examined the evolutionary rates of KOGs and found that the fastest-evolving KOGs are involved in cellular trafficking and transport, while the slowest-evolving KOGs are involved in translation and RNA processing. The analysis of gene loss and emergence in eukaryotic evolution revealed that the fungal clade experienced massive gene loss, while the animal clade emerged with a large set of new genes. The study also identified that the common ancestor of the crown group had a gene set of 3,413 KOGs, which largely included proteins involved in genome replication and expression, and central metabolism. The study also examined the evolutionary relationships between eukaryotic and prokaryotic orthologous gene sets and found that a significant fraction of eukaryotic KOGs have prokaryotic counterparts. The analysis of gene dispensability in yeast and worm genes showed that essential genes are more conserved across species, while non-essential genes are less conserved. The study also identified domain accretion in orthologous sets of eukaryotic proteins, which reflects the increasing complexity of domain architecture in multicellular organisms. The results of this study provide a comprehensive evolutionary classification of proteins encoded in complete eukaryotic genomes and highlight the importance of conserved genes and their evolutionary patterns in eukaryotic evolution.A comprehensive evolutionary classification of proteins encoded in complete eukaryotic genomes was conducted by analyzing 5,873 clusters of predicted orthologs (KOGs) from seven eukaryotic genomes. These KOGs were used to identify conserved genes and their evolutionary patterns. The study revealed that approximately 40% of KOGs are conserved across six or seven species and are involved in essential functions such as translation and RNA processing. The analysis also identified I31 single-member, pan-eukaryotic KOGs, which were examined in detail. For around 20 of these KOGs, functions were predicted through sequence analysis and genomic context. These proteins are often subunits of known or predicted multiprotein complexes, supporting the balance hypothesis of gene copy number evolution. The study also examined the phyletic patterns of KOGs, which revealed a conserved eukaryotic gene core and substantial diversity. The pan-eukaryotic genes, represented in all seven analyzed genomes, account for around 20% of the KOGs. The analysis showed that the majority of KOGs are involved in functions such as RNA processing, transcription, and chromatin dynamics. The study also identified lineage-specific gene loss and the 'invention' of new genes in eukaryotic evolution. The results provided quantitative support for major trends in eukaryotic evolution and a basis for detailed reconstruction of eukaryotic genome evolution. The study also examined the evolutionary rates of KOGs and found that the fastest-evolving KOGs are involved in cellular trafficking and transport, while the slowest-evolving KOGs are involved in translation and RNA processing. The analysis of gene loss and emergence in eukaryotic evolution revealed that the fungal clade experienced massive gene loss, while the animal clade emerged with a large set of new genes. The study also identified that the common ancestor of the crown group had a gene set of 3,413 KOGs, which largely included proteins involved in genome replication and expression, and central metabolism. The study also examined the evolutionary relationships between eukaryotic and prokaryotic orthologous gene sets and found that a significant fraction of eukaryotic KOGs have prokaryotic counterparts. The analysis of gene dispensability in yeast and worm genes showed that essential genes are more conserved across species, while non-essential genes are less conserved. The study also identified domain accretion in orthologous sets of eukaryotic proteins, which reflects the increasing complexity of domain architecture in multicellular organisms. The results of this study provide a comprehensive evolutionary classification of proteins encoded in complete eukaryotic genomes and highlight the importance of conserved genes and their evolutionary patterns in eukaryotic evolution.