Base composition analysis supports gene transfer

Both our results and those recently published by another group suggest that uptake sequences are less common in genes that don't have homologs in related genomes.  I'm using 'related' loosely here, as our analysis searched for homologs in genes from other families of bacteria whereas the other group searched in members of the same genus.  But both results are best explained by the hypothesis that genes lacking uptake sequences are often those that a genome has recently acquired by lateral transfer from genomes that don't share that species' uptake sequence. 

To test this, we looked at gene properties that might give evidence of lateral transfer.  The simplest such property is base composition (%G+C), a property that differs widely between different bacterial groups and changes only slowly after a sequence has been transferred to a different genome.  My bioinformatics collaborator had already tabulated the %G+C of all the genes in the H. influenzae and N. meningitidis genomes, noting whether each gene had (1) uptake sequences and (2) homologs in the test genomes (see previous two posts for more explanation).  She'd then calculated the means and standard deviations of the base compositions of genes in each of the four classes.  

This analysis showed that, on average, the genes with no uptake sequences and no homologs also had anomalously low base compositions and larger standard deviations.  But I thought the effect might be clearer with a graphical presentation, so I plotted the actual %G+C for each gene as a function of which class it is in (presence/absence of uptake sequence and homologs).  I also noted sample sizes, as some classes have a lot more genes than others.  This gave a nice visualization of the effects, showing, not surprisingly, that genes with homologs in the control genomes have more homogeneous base compositions than those without homologs, and that the effect is quite a bit stronger for those genes that don't have uptake sequences.