High-throughput transcriptomic analysis of Pseudorabies virus

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The whole-genome sequence of PRV strain Ka was determined by cutting-edge long-read sequencing in order to facilitate accurate transcriptome mapping and further epigenetic studies of the virus. Illumina short-read, high-throughput sequencing was used for the first time on lytic-infection PRV samples in order to create a single-base resolution transcriptome map, along with the detailed polyadenylation landscape of the virus by PA-Seq. In accordance with expectations, most of the viral genome was transcribed, with the exception of several small intergenic repetitive sequences, and loci in the large internal and terminal repeats. Among the findings are a novel polyadenylated lncRNA near the OriL origin of replication, and the single-base resolution mapping of 3′ UTRs across the viral genome. A number of genes exhibited alternative polyadenylation sites, while previously described splice sites were confirmed and expanded with a novel alternative splicing event in the key regulator ep0 gene.

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