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Chapter 3 : Genomes of Streptococcus mitis, Streptococcus oralis, and Streptococcus infantis
This chapter talks about the closest relatives of Streptococcus mitis that are the commensals S. oralis, S. infantis, and, in particular, the important pathogen Streptococcus pneumoniae and the still relatively unknown Streptococcus pseudopneumoniae. The genetic diversity among S. mitis strains may have important consequences in the oral cavity. Draft genomes display an artificially high total number of genes and number of paralogs due to sequencing errors and gaps leading to gene fragmentation, as well as low-quality redundant sequences at contig ends. The verification results in the conclusion that this observation is not due to the fact that (i) all but one of the non-S. pneumoniae genomes studied are draft genomes, and (ii) gene prediction standards differ among sequencing centers. First, the closed S. mitis B6 genome displays a higher coding percentage. Second, the coding density was measured in three unpublished draft S. pneumoniae genomes obtained from three different sequencing centers, and the average coding percentage was 84.9%. The previous observation that virtually every independent isolate of S. mitis represents a distinct species according to traditional taxonomic principles is supported by our multigenome analysis. The significant sharing of core genes between S. mitis and S. pneumoniae reinforces the conclusion that S. pneumoniae is one lineage of the S. mitis complex.