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Measuring genome evolution

M A Huynen¹, P Bork

¹European Molecular Biology Laboratory, Meyerhofstrasse 1, 69012 Heidelberg, Germany, and Max-Delbrück-Centrum for Molecular Medicine, 13122 Berlin-Buch, Germany. huynen@embl-heidelberg.de

Proceedings of the National Academy of Sciences of the United States of America

|May 30, 1998

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Genome evolution was analyzed by comparing gene content and order across nine species. Researchers found protein sequence identity is most conserved, while gene regulation evolves fastest, revealing varying genome organization.

Area of Science:

Comparative genomics
Evolutionary biology
Bioinformatics

Background:

Complete genome sequences offer a comprehensive view of evolutionary processes.
Analyzing genomes reveals insights into gene content, order, and regulation.

Purpose of the Study:

To compare nine genomes based on protein-coding genes.
To analyze gene orthology and positional correlations.
To establish a hierarchy of evolutionary rates for different genomic features.

Main Methods:

Comparative analysis of protein-coding genes across nine genomes.
Quantification of shared orthologs ('bags of genes' comparison).
Assessment of gene order correlations and relative positioning.
Calculation of divergence times using amino acid substitutions in 34 orthologous genes.

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Main Results:

Established a hierarchy of evolutionary rates: protein sequence identity (most conserved), gene complement, gene order, and gene regulation (fastest evolving).
Demonstrated that some genomes exhibit higher organization, characterized by increased clustering of orthologous genes.
Linked genomic distances to divergence times based on amino acid substitutions.

Conclusions:

Genome evolution proceeds at different rates for various features, with gene regulation being the most dynamic.
Genome organization and gene clustering vary significantly across species.
Comparative genomics provides a framework for understanding genome evolution and divergence.