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Abstract: The evolution of influenza viruses is remarkably dynamic. Influenza viruses evolve rapidly in sequence and undergo frequent reassortment of different gene segments. Homologous recombination, although commonly seen as an important component of dynamic genome evolution in many other organisms, is believed to be rare in influenza. In this study, 256 gene segments from 32 influenza A genomes were examined for homologous recombination, three recombinant H1N1 strains were detected and they most likely resulted from one recombination event between two closely rated parental sequences. These findings suggest that homologous recombination in influenza viruses tends to take place between strains sharing high sequence similarity. The three recombinant strains were isolated at different time periods and they form a clade, indicating that recombinant strains could circulate. In addition, the simulation results showed that many recombinant sequences might not be detectable by currently existing recombinant detection programs when the parental sequences are of high sequence similarity. Finally, possible ways were discussed to improve the accuracy of the detection for recombinant sequences in influenza. [Copyright &y& Elsevier]

Meningococcal disease is a widely distributed complex disease affecting all age categories. It can cause severe meningitis and septicemia, especially in unvaccinated infants and young children. The causative agent, Neisseria meningitidis (Nm), can be phenotypically and genetically differentiated into serogroups and sequence types (STs) and has a highly dynamic population structure. To obtain a deeper understanding of the epidemiology of Nm, we sequenced seven Nm genomes. Large-scale genomic analysis was conducted with these 7 Nm genomes, 27 additional Nm genomes from GenBank, and 4 other Neisseria genomes. We observed extensive homologous recombination in all gene functional categories among different Nm genomes. Homologous recombination is so frequent that it has resulted in numerous chimeric open reading frames, including genes in the capsule biosynthesis cluster and loci targeted by commercial vaccines. Our results reveal that, despite widespread use, evolutionary relationships inferred from the standard seven-gene multilocus sequence typing (MLST) method could not predict virulence gene content or strain phenotype. In fact, up to 28% of the virulence-associated genes could differ between strains of identical STs. Consistent with previous studies, we found that allelic recombination is also associated with alterations in antibiotic susceptibility. Overall, these findings emphasize the extensive genomic plasticity of Nm and the limitations of standard molecular methods to quantify this genotypic and phenotypic diversity. [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]