Poxviruses are large DNA viruses infecting humans and animals. Vaccinia virus (VACV)
has been applied as a live vaccine for immunization against smallpox, which was eradicated
by 1980 as a result of worldwide vaccination. VACV is the prototype of poxviruses
in the investigation of the molecular pathogenesis of the virus. Short-read sequencing
methods have revolutionized transcriptomics; but, they are not efficient in distinguishing
between the RNA isoforms and transcript overlaps. Long-read sequencing (LRS) is much
better suited to solve these problems, and also allow direct RNA sequencing. Despite
the scientific relevance of VACV, no LRS data have been generated for the viral transcriptome
so far.For the deep characterization of the VACV RNA profile, various LRS platforms
and library preparation approaches were applied. The raw reads were mapped to the
VACV reference genome and also to the host (Chlorocebus sabaeus) genome. In this study,
we applied the Pacific Biosciences RSII and Sequel platforms, which altogether resulted
in 937,531 mapped reads of inserts (1.42 Gb), while we obtained 2,160,348 aligned
reads (1.75 Gb) from the different library preparation methods, using the MinION device
from Oxford Nanopore Technologies.By applying cutting-edge technologies, we were able
to generate a large dataset that can serve as a valuable resource for the investigation
of the dynamic VACV transcriptome, the virus-host interactions and RNA base modifications.
These data can provide useful information for novel gene annotations in the VACV genome.
Our dataset can also be applied for analyzing the currently available LRS platforms,
library preparation methods and bioinformatics pipelines.
