Figure 1
A: Position of the six lgr genes of P. amoebophila on the cumulative GC skew. B: on the G+C content curve (non-overlapping 1-kb windows). C: on the residual cumulative G+C content curve (5-kb windows sliding by 1-kb step). D: Values of the intragenic GC skew at the third position of the codons (GC3) versus the location of all 2031 ORFs of P. amoebophila encoded either by the leading (black +) or by the lagging strand (grey x), both strands defined by the origin and terminus of replication determined by the minimum and the maximum of the cumulative GC skew curve from Figure 1A; open red circles/squares highlight the lgr s located on the leading/lagging strand. E: Chromosome map of P. amoebophila showing by red circles the six lgr s encoded on the leading- (black), or the lagging strand (grey). F: Histogram of the GC3 values of all 2031 ORFs of P. amoebophila located on the leading (1065 ORFs) or lagging strand (988 ORFs). The values of the lgr s encoded by the leading/lagging strand are indicated by black +/grey x, and the median M of the leading/lagging strand values is labelled in black/grey. Since all six lgr s present higher G+C content than the rest of the genome (34.7%), they all exhibit steep slopes in the residual cumulative G+C content curve. The lgrE is located in Pam100G, a 100-kb genomic island presenting a particular GC skew profile whose boundaries are indicated by dashed lines in panels A to E. The GC3 values of all six lgr s is similar to that of the anti-orientated genes of P. amoebophila, although three lgr s are encoded by the leading strand (lgrB, lgrE and lgrF). Since GC3 values of the three latters (-0.08057 for lgrB, -0.05634 for lgrE, and -0.05228 for lgrF) are significantly lower than the median minus the standard deviation (0.129 ± 0.167) of all genes encoded on the leading strand (p = 0.005) and close to the median of the genes encoded by the lagging strand (median=-0.091 ± 0.171), it appears that an adaptation of the codon usage of these three lgr s is at work, due to a relatively recent re-orientation on the chromosome.