FIG 2.

Nucleotide compositional bias toward G+C residues in repeat regions of herpesvirus genomes. (A) A line graph overlay of G+C versus A+T distribution in the HSV-1 genome (JN555585; human herpesvirus 1 [HHV-1]). A diagram beneath the line graph depicts the locations of UL and US (gray), as well as TRL/IRL and TRS/IRS (orange). SSRs are also marked in orange. (B) Another human alphaherpesvirus, VZV, is A+T rich in the UL and US regions (56%) but G+C rich in the inverted repeat regions (59% G+C). (C to E) Similar plots depict nucleotide distribution in unique versus repeated regions of human beta- (human cytomegalovirus [HCMV]) and gammaherpesviruses (Epstein-Barr virus [EBV] and Kaposi's sarcoma-associated herpesvirus [KSHV]). Note that each genome is drawn to an individual scale, as marked below each line graph. The KSHV genome has 35 to 45 copies of a terminal repeat (TR) on its termini; we show 40 here. The genome diagram follows the NCBI Refseq annotation in displaying the EBV and KSHV TRs only on the right-hand side. These TRs join together in circularized genomes. Nucleotide sequences and annotations of unique and repeated regions are derived from NCBI RefSeq records as follows: VZV strain Dumas (accession number NC_001348), HCMV strain Merlin (NC_006273), EBV strain B95-8 (NC_007605), and KSHV strain GK18 (NC_009333).