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Study Underscores Importance of Horizontal Transfer in Prokaryote Gene Family Expansion

By a GenomeWeb staff reporter

NEW YORK (GenomeWeb News) – Horizontal gene transfer plays a larger role than gene duplication in bacterial and archaeal gene family expansion, a new study suggests.

French researchers looked at gene family, sequence, and location patterns in more than 100 prokaryote genomes, ranging in size from small to large. Their analyses suggest horizontal gene transfer is likely the driving force behind protein family evolution in prokaryotes, while duplication is more apt to contribute to gene dosage. The study appeared online last night in PLoS Genetics.

"Prokaryotes invented most of life's biochemical diversity," co-authors Todd Treangen and Eduardo Rocha wrote. "Therefore, the study of the evolution of biology systems should explicitly account for the predominant role of horizontal gene transfer in the diversification of protein families."

Both authors participated in the study while affiliated with the Institut Pasteur, Centre National de la Recherche Scientifique, and Université Pierre et Marie Curie. Treangen is currently a post-doctoral researcher at the University of Maryland's Center for Bioinformatics and Computational Biology.

Despite their relatively small sizes, archaeal and bacterial genomes can code for between a few hundred and several thousand genes, the researchers explained. The mechanisms by which these prokaryotic genomes evolve and adapt to specific environments and growth strategies is poorly understood, they added, though horizontal gene transfer — the movement of genes from one organism to another — is thought to contribute to this process.

"While there is ample evidence of adaptive gene duplication in prokaryotes, it is not clear whether duplication outweighs the contribution of horizontal gene transfer in the expansion of protein families," they wrote.

Using information from Genbank, Treangen and Rocha scrutinized genome data for Helicobacter, Neisseria, Streptococcus, and Sulfolobus species known to have particularly puny genomes. They then compared these to average-sized genomes of some Bacillus and Enterobacteriaceae species and to several large genomes, including those of species in the Pseudomonas genera and Bradyrhizobiaceae family.

Overall, the analysis encompassed 110 prokaryote genomes representing organisms from eight different clades.

All told, the pair identified 419,035 proteins in 59,541 families. After tossing out unrelated sequences and gene families containing only one member, the researchers characterized gene expansion patterns in a set of 3,190 gene families.

From sequence data, the number of genes in each family, the locations of these genes, and more, the researchers concluded that some 88 to 98 percent of protein family expansions are a consequence of horizontal gene transfer rather than duplication.

"After removing the effects of transposable elements and phages, we show that the vast majority of expansions of protein families are due to transfer, even among large genomes," Treangen and Rocha wrote.

The xenologs that result from these horizontal transfers also seem to stick around longer than paralogs produced by duplication events, they noted.

On the other hand, the duo found that duplicated genes tend to evolve more slowly in prokaryote genomes but are often expressed at relatively high levels.

Based on the patterns detected, they argue that "gene transfer and gene duplication have very different roles in shaping the evolution of biological systems: transfer allows the acquisition of new functions and duplication leads to higher gene dosage."

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