Mapping of Marek's disease virus genome: identification of junction sequences between unique and inverted repeat regions.

Polymerase chain reaction (PCR) to amplify MDV DNA and subsequent sequencing identified the junction of TRL/UL, UL/IRL, IRS/US, and US/TRS. The TRL/UL junction is located 192 bp downstream of the last EcoRI site in the TRL region, while the UL/IRL junction is located 192 bp upstream of the first EcoRI restriction enzyme site in the IRL region. The IRS/US junction is located 950 bp downstream of the second EcoRI site in the IRS region, while the US/TRS junction is located 950 bp upstream of the first EcoRI restriction enzyme site in the TRS region. BamHI restriction enzyme mapping of one of the PCR products identified two novel DNA subfragments, BamHI-U2 and -P4, upstream of the US/TRS junction of the MDV genome. Sequencing of the BamHI-D fragment revealed a novel open reading frame (ORF) encoding a 155 amino acid protein. The TRL/UL junction is located in this ORF. The N-terminal 65 amino acids of this protein is homologous to the N-terminal region of the previously reported pp38, which is located in the UL/IRL region. Computer-assisted analysis indicated that both are transmembrane proteins and that they share an antigenic domain.