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Due to divergence, genetic variation is generally believed to be high among distantly related strains, low among closely related ones and little or none within the same classified clonal groups. Several recent genome-wide studies, however, revealed that significant genetic variation resides in a considerable number of genes among strains with identical MLST (Multilocus sequence typing) types and much of the variation was introduced by homologous recombination. Recognizing and understanding genomic variation within clonal bacterial groups could shed new light on the evolutionary path of infectious agents and the emergence of particularly pathogenic or virulent variants. This commentary presents our recent contributions to this line of work. [ABSTRACT FROM AUTHOR]

Abstract: Methods for assessing gene presence and absence have been widely used to study bacterial genome evolution. A recent report by Zhaxybayeva et al. [Zhaxybayeva, O., Nesbo, C. L., and Doolittle, W. F., 2007. Systematic overestimation of gene gain through false diagnosis of gene absence. Genome. Biol. 8, 402] suggests that false diagnosis of gene absence or the presence of undetected truncated genes leads to a systematic overestimation of gene gain. Here (1) we argue that these annotation errors can cause more complicated effects and are not necessarily systematic, (2) we argue that current annotations (supplemented with BLAST searches) are the best way to consistently score gene presence/absence and (3) that genome wide estimates of gene gain/loss are not strongly affected by small differences in gene annotations but that the number of related gene families is strongly affected. We have estimated the rates of gene insertions/deletions using a variety of cutoff thresholds and match lengths as a way in which to alter the recognition of genes and gene fragments. The results reveal that different cutoffs for match length only cause a small variation of the estimated insertion/deletion rates. The rates of gene insertions/deletions on recent branches remain relatively high regardless of the thresholds for match length. Lastly (4), the dynamic process of gene truncation needs to be further considered in genome comparison studies. The data presented suggest that gene truncation tends to take place preferentially in recently transferred genes, which supports a fast turnover of recent laterally transferred genes. The presence of truncated genes or false diagnosis of gene absence therefore does not significantly affect the estimation of gene insertions/deletions rates, but there are several other factors that bias the results toward an under-estimation of the rate of gene insertion/deletion. All of these factors need to be considered. [Copyright &y& Elsevier]