Comparison and sharing of Genomic Islands within the strains
The coding regions of the predicted GIs of each genome were sorted out. The sequences of the proteins present in the predicted GIs of each strain of M. haemolytica under study retrieved on local system and were used as query for an organism-specific BLASTP (http://blast.ncbi.nlm.nih.gov) search against each of the other strains of under study. This was done in order to identify their homologues in the each other strains to understand the relatedness of GIs between these strains. This revealed that M. haemolytica USMARC-183 sharing 79.09% of its ORFs of GIs with M. haemolytica M42548 and noted as highest relatedness while only ...view middle of the document...
These unique GIs are mainly coding for putative proteins and ABC transporters. Especially the parts of ORFs of GI-17 coding for aminoglycoside transferases (MHH_c22540 to MHH_c22570) and lipidA (MHH_c22090), outermembrane proteins (MHH_c22100) are unique and indicating this strain become more virulent and obtained acquired antibiotic resistance through HGT. The part of M-GI-3 this is unique for M42548 strain and coding for β-lactamase (MHH_c02670, MHH_c02680) evident that this strain evolved recently and obtained resistance against lactam inhibiting antibiotics.
Only one Genomic Island (M-GI-10) of M42548 strain was completely homologous to all other strains under study except with M. haemolytica D171 in which it was absent. This homologue was observed to be in reverse orientation in USMARC-183 strain, and in same orientation in other strain genomes. It was interesting to note that one whole GI coded as M-GI-7 was homologous to M. haemolytica strains namely D174, USMARC-183 and USMARC-2286. But it was observed in opposite orientation in all three strains when comparing with M42548 (Supplementary Table 1).
Oligopeptide ABC transporter (MHH_c15100, MHH_c15110) of M-GI-11 present in two copies of all strain Genomes except D171strain having one ORF. Two sets of Carbonic anhydrase proteins (MHH_c15120, MHH_c15130) present in this GI flanked by Oligopeptide ABC transporter set, this combination is absent D171 and D174 strains. A group of six hypothetical proteins flanked by integrating conjugative element protein present in this M-GI-11, but this stretch is completely absent in D171 strain. While complete stretch of these ORFs was homologous in the two strains of this study i.e. USMARC-183 and SAM-185 but observed in opposite orientation. For surprise this combination was absent in strain USMARC-2286 except for flanking proteins on each side but only three middle hypothetical proteins were absent in case of D174. In Strain D153 only one hypothetical protein that was flanked by integrating conjugative element protein was absent and rest of stretch was homologous and in the same orientation as of M42548 strain.
Figure 5: The diagram representing the percentage of genes present in the putative GIs of M. haemolytica strains shared with M. haemolytica M42548 strain (M.h = Mannheimia haemolytica)
Earlier it was thought that essential genes, like those encoding ribosomal RNA, are unlikely to be transferred successfully since recipient taxa would already bear functional orthologues, however it was proved that rRNA operons also can be transferred by Horizontal transfer in Thermomonospora chromogena (Yap et.al, 1999). There was another study showed there is a chance for the horizontal transfer of segments of 16S rRNA genes between Streptococcus anginosus group (Schouls et al, 2003). In this study predicted GI of M42458 strain M-GI-7 found to be coding for large and small sub units of ribosomal proteins (MHH_c07540 - MHH_c07700). This entire GI was also...