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As expected, no protein level similarity was observed between the type specific modification genes of the six bacteriophages.
The CC11 genomes and N1568 shared an IS1655 insertion (also identical in sequence) between the restriction and modification genes of Nme18ORF295P (fig. 6 A).
It is striking that phylogenetic incongruence was found between the restriction and modification genes of the same RMS (see fig. 6 for examples), which suggests that the restriction and modification genes of the same RMS in the same strain could be of different origins.
To further explore whether ASHM genes could lead to differences in histone modification, we analyzed the differential modification genes of H3K27me3 or H3K36me3 modifications between the F1 hybrid and the parents.
Phylogenetic incongruence between the restriction and modification genes of each RMS was examined by the approximately unbiased (AU) test (Shimodaira 2002) implemented in the CONSEL program (Shimodaira and Hasegawa 2001).
ATCC13091 and alpha14 shared identical modification genes of NmeAI, the restriction gene in ATCC13091 differed from alpha14 by 47 nucleotides, and the short patch repair genes only differed by one nucleotide between ATCC13091 and alpha14.
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For example, a 1,025-nucleotide 1,025-nucleotidemodeletionon gene of the Nme53442ORF1140 system was found in botheNmodification8187.
Together with the modification gene of EcoPI-ModD1 only present in three of the five CC41/44 strains, we determined whether these clade-specific genes contained the recognition sites of any RMSs present in the clade.
For instance, the modification gene of the Nme18ORF295P system in N1568 is identical with M01-240355, whereas the restriction gene of Nme18ORF295P in N1568 is identical with genomes in CC11 (from K1207 to FAM18 in fig. 6).
These results suggest that the serological differences between the members of these seven groups have been generated by acquisition of modification genes outside of the O-AGC as shown for O17 and O44 of Gp9.
Grosjean, H., Gaspin, C., Marck, C. & Decatur, W.A. & de Crecy-Lagard, V. RNomics and Modomics in the halophilic archaea Haloferax volcanii: identification of RNA modification genes.
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