Horizontal gene transfer in bacterial and archaeal complete genomes - PubMed (original) (raw)

Comparative Study

. 2000 Nov;10(11):1719-25.

doi: 10.1101/gr.130000.

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Comparative Study

Horizontal gene transfer in bacterial and archaeal complete genomes

S Garcia-Vallvé et al. Genome Res. 2000 Nov.

Abstract

There is growing evidence that horizontal gene transfer is a potent evolutionary force in prokaryotes, although exactly how potent is not known. We have developed a statistical procedure for predicting whether genes of a complete genome have been acquired by horizontal gene transfer. It is based on the analysis of G+C contents, codon usage, amino acid usage, and gene position. When we applied this procedure to 17 bacterial complete genomes and seven archaeal ones, we found that the percentage of horizontally transferred genes varied from 1.5% to 14.5%. Archaea and nonpathogenic bacteria had the highest percentages and pathogenic bacteria, except for Mycoplasma genitalium, had the lowest. As reported in the literature, we found that informational genes were less likely to be transferred than operational genes. Most of the horizontally transferred genes were only present in one or two lineages. Some of these transferred genes include genes that form part of prophages, pathogenecity islands, transposases, integrases, recombinases, genes present only in one of the two Helicobacter pylori strains, and regions of genes functionally related. All of these findings support the important role of horizontal gene transfer in the molecular evolution of microorganisms and speciation.

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Figure 1

Figure 1

Correspondence analysis of relative synonymous usage for genes of (A) Escherichia coli, (B) Bacillus subtilis, (C) Thermotoga maritima, and (D) Methanobacterium thermoautotrophicum. Triangles correspond to genes proposed as being acquired by horizontal gene transfer and included in regions with a low G+C content. Circles correspond to genes proposed as being acquired by HGT and included in regions with a high G+C content. Dots correspond to genes that are not proposed as being acquired by HGT. For the sake of clarity, genes proposed as being acquired by HGT that do not belong to a region that is high or low in the G+C content are not shown.

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