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A comprehensive evolutionary classification of proteins encoded in complete eukaryotic genomes
Eugene V Koonin1, Natalie D Fedorova, John D Jackson
1National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA. koonin@ncbi.nlm.nih.gov
Genome Biology
|February 5, 2004
Summary
Comparative genomics reveals a core set of essential eukaryotic genes and highlights gene loss and innovation in eukaryotic genome evolution. This study reconstructs ancestral eukaryotic genomes and predicts functions for uncharacterized genes.
Area of Science:
- Genomics
- Evolutionary Biology
- Bioinformatics
Background:
- Comparative genomic analysis of diverse eukaryotes aids in reconstructing ancestral genomes and understanding eukaryotic evolution.
- Functional predictions for uncharacterized conserved genes can be made through this approach.
Purpose of the Study:
- To examine functional and evolutionary patterns in eukaryotic orthologous groups (KOGs) across seven diverse eukaryotic genomes.
- To reconstruct ancestral eukaryotic genomes and predict functions for uncharacterized genes.
Main Methods:
- Analysis of 5,873 eukaryotic orthologous groups (KOGs) from seven eukaryotic genomes.
- Correlation of KOG conservation with function and gene knockout effects.
- Prediction of functions for uncharacterized KOGs using sequence analysis and genomic context.
- Reconstruction of gene sets for ancestral eukaryotic forms.
Main Results:
- KOG conservation correlates with function and essentiality; ~40% of KOGs are highly conserved and enriched in housekeeping functions.
- Identified 131 pan-eukaryotic KOGs, with functions predicted for ~20 uncharacterized proteins, often part of multiprotein complexes.
- Phyletic patterns indicate significant lineage-specific gene loss and gene invention.
- Reconstructed the gene set of the last common ancestor (3,413 KOGs), with only 44% having prokaryotic homologs.
Conclusions:
- KOG analysis reveals a conserved core of essential eukaryotic genes and significant diversification/innovation during eukaryotic genome evolution.
- Provides quantitative support for major eukaryotic evolutionary trends and a basis for reconstructing ancestral eukaryotic biology.