Lineage-specific gene expansions in bacterial and archaeal genomes

Gene duplication is an important mechanistic antecedent to the evolution of new genes and novel biochemical functions. In an attempt to assess the con tribution of gene duplication to genome evolution in archaea and bacteria, clusters of related genes that appear to have expanded subsequent to the di versification of the major prokaryotic lineages (lineage-specific expansion s) were analyzed. Analysis of 21 completely sequenced prokaryotic genomes s hows that lineage-specific expansions comprise a substantial fraction (simi lar to5%-33%) of their coding capacities. A positive correlation exists bet ween the fraction of the genes taken up by lineage-specific expansions and the total number of genes in a genome. Consistent with the notion that line age-specific expansions are made up of relatively recently duplicated genes , >90% of the detected clusters consists of only two to four genes. The mor e common smaller clusters tend to include genes with higher pairwise simila rity (as reflected by average score density) than larger clusters. Regardle ss of size, cluster members tend to be located more closely on bacterial ch romosomes than expected by chance, which could reflect a history of tandem gene duplication. In addition to the small clusters, almost all genomes als o contain rare large clusters of size greater than or equal to 20. Several examples of the potential adaptive significance of these large clusters are explored. The presence or absence of clusters and their related genes was used as the basis for the construction of a similarity graph for completely sequenced prokaryotic genomes. The topology of the resulting graph seems t o reflect a combined effect of common ancestry, horizontal transfer,and lin eage-specific gene loss.