Mutational pressure is a cause of inter- and intragenomic differences in GC-content of simplex and varicello viruses

Total GC-content (G + C), GC-content in codon positions and 0-fold, 2-fold and 4-fold degenerated sites in all coding districts from 10 completely sequenced genomes of simplex and varicello viruses have been calculated by the original “Coding Genome Scanner” algorithm. The low coefficient of correlation (R < 0.5) between 3GC and G + C in all coding districts from unique regions (UL and US) of alphaherpesvirus genome is a new criterion of the strong mutational pressure that is the process of increasing the rates of nonsynonymous mutations because of the extreme saturation (GC-pressure) or desaturation (AT-pressure) of third (liberal) codon positions with G and C. Unique regions of HSV1, HSV2, CeHV1, CeHV2, CeHV16 and BoHV5 are under the influence of strong GC-pressure caused mostly by AT to GC transversions. Unique regions of EqHV1 are under the influence of weak GC-pressure. In unique regions of CeHV9 AT-pressure is strong; in EqHV4 and VZV unique regions AT-pressure is weak. Mutational AT-pressure in CeHV9 and VZV is caused mostly by transitions, while in EqHV4 it is caused mostly by transversions. The level of 3GC in coding districts situated in long terminal inverted repeats (LTR) of all these viruses is much higher than in coding districts from UL and US. Higher GC-content does not seem to depend on the gene itself, but it does depend on its location. V67 gene of EqHV1 is situated in LTR (3GC = 0.853), while V67 gene of EqHV4 is situated in US (3GC = 0.397). Higher rates of AT to GC transversions in coding districts situated in LTR should be due to the “anatomy” of long terminal inverted repeats. The process of AT to GC transversions is thought to take place only in doublestranded DNA. Indeed, in the potential secondary structure formed by singlestranded genomic DNA of alphaherpesviruses only joined inverted repeats should be doublestranded.