Figure 1

Overall comparison of M. agalactiae genomes from the PG2 and 5632 strains. (A) VISTA comparison [61]. The graph represents the sequence nucleotide identity (in %) using a sliding window of 100 bp and the 5632 genome as a reference. Colored boxes represent gene families or ICE (orange for the drp genes, yellow for the vpma, green for the spmas, and purple for the ICEs); blue triangles insertion sequence (IS) (dark blue for ISMag1, light blue for ISMag2). Filled orange and blue circles represent respectively the p48 lipoprotein gene and CDSs related to restriction-modification systems. Boxes or triangles surrounded with dotted lines indicate pseudogenes or ICE vestiges. (B) Comparison of CDSs using the MolliGen dot plot alignment [58]. Each dot represents a blastp hit (threshold 10^-8) between a CDS of 5632 (ordinates) and a CDS of PG2 (abscises). On axes, the length between two large marks corresponds to 100 kbp. (C) Circular representation of 5632 genome using the Artemis suite DNAplot [63]. Outer to inner circles correspond to: circle1, 5632 mobilome with IS in red and ICEs in purple (the position of the unique vestigial ICE of strain PG2 is also indicated); circle 2, CDS predicted as implicated in HGT with mycoplasmas of the "mycoides" group; circle 3, positive strand annotated CDSs; circle 4, negative strand annotated CDSs; circle 5, CDS of interest discussed in the text (color code as in panel 1); circle 6, CDS predicted as lipoproteins; circle 7, percent G+C content (high G+C content in dark grey and low G+C content in light grey); circle 8, GC skew.