Measuring genome evolution

被引:329
作者
Huynen, MA
Bork, P
机构
[1] European Mol Biol Lab, D-69012 Heidelberg, Germany
[2] Max Delbruck Ctr Mol Med, D-13122 Berlin, Germany
关键词
ortholog; synteny; computer analysis; horizontal gene transfer;
D O I
10.1073/pnas.95.11.5849
中图分类号
O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];
学科分类号
07 ; 0710 ; 09 ;
摘要
The determination of complete genome sequences provides us with an opportunity to describe and analyze evolution at the comprehensive level of genomes. Here we compare nine genomes with respect to their protein coding genes at two levels: (i) we compare genomes as "bags of genes" and measure the fraction of orthologs shared between genomes and (ii) we quantify correlations between genes with respect to their relative positions in genomes. Distances between the genomes are related to their divergence times, measured as the number of amino acid substitutions per site in a set of 34 orthologous genes that are shared among all the genomes compared. We establish a hierarchy of rates at which genomes have changed during evolution. Protein sequence identity is the most conserved, followed by the complement of genes within the genome. Next is the degree of conservation of the order of genes, whereas gene regulation appears to evolve at the highest rate. Finally, we show that some genomes are more highly organized than others: they show a higher degree of the clustering of genes that have orthologs in other genomes.
引用
收藏
页码:5849 / 5856
页数:8
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