Supplemental text

Restriction modification systems

As shown in Table S15, H. somnus 129Pt had genes encoding components of type I and the BcgI restriction-modification systems. H. ducreyi 35000HP had one gene encoding a possible type I methytransferase protein(HD0914), as well as genes encoding a type III system and possibly the BcgI system. H. influenzae Rd had genes encoding components of type I, II and III systems, but not BcgI. In terms of type I systems, H. somnus 129Pt had hsdS (HS_0556) and an hsdR gene (HS_0559) that was also present in H. influenzae Rd (HI1285). H. somnus 129Pt had a second hsdS (HS_0560), but not hsdM. H. influenzae Rd had one complete type I system composed of the genes HI1285 – HI1287 (hsdR, hsdS and hsdM). Another type I system in H. influenzae Rd consisted of HI0215 (hsdM, which contained a frameshift), HI0216 (hsdS) and hsdR (HI0218). Neither H. somnus 129Pt nor H. ducreyi 35000HP had any type II system genes. H. influenzae Rd had three complete type II systems, encoded by HI0512 and HI0513, HI1040 and HI1041, HI1393 and HI1392. H. somnus 129Pt did not have any type III restriction-modification system genes. H. influenzae Rd had a type III methylase gene (HI1056), while H. ducreyi 35000HP had a complete type III system (HD1690 to HD1693).

There is evidence supporting the hypothesis that restriction modification systems may move between and within genomes and may cause evolutionary changes in genomes (25). This evidence includes observations of the proximity of mobile genetic elements to restriction modification gene complexes. Our results indicated that all of the restriction modification system gene complexes in H. somnus 129Pt were in the vicinity of mobile elements, including putative prophage regions and transposases (Table 15). Also, as the H. influenzae DNA uptake signal sequence is overrepresented in H. somnus (2), mobile elements may not be necessary for the movement of restriction modification gene complexes. Several of the restriction-modification genes either contain the H. influenzae DNA uptake signal sequence or are close to H. influenzae DNA uptake signal sequences, so they may have been acquired by DNA uptake.

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Table S1. Candidate prophages and phage-related genes

Gene