Characterization of global transcriptomes using conventional short-read sequencing
is challenging due to the insensitivity of these platforms to transcripts isoforms,
multigenic RNA molecules, and transcriptional overlaps. Long-read sequencing (LRS)
can overcome these limitations by reading full-length transcripts. Employment of these
technologies has led to the redefinition of transcriptional complexities in reported
organisms. In this study, we applied LRS platforms from Pacific Biosciences and Oxford
Nanopore Technologies to profile the vaccinia virus (VACV) transcriptome. We performed
cDNA and direct RNA sequencing analyses and revealed an extremely complex transcriptional
landscape of this virus. In particular, VACV genes produce large numbers of transcript
isoforms that vary in their start and termination sites. A significant fraction of
VACV transcripts start or end within coding regions of neighbouring genes. This study
provides new insights into the transcriptomic profile of this viral pathogen.
