An Integrated Sequencing Approach for Updating the Pseudorabies Virus Transcriptome

Area of Science:

• Virology
• Genomics
• Molecular Biology

Background:

• Long-read sequencing (LRS) technologies have recently unveiled significant complexity in viral gene expression.
• Previous studies on the pseudorabies virus (PRV) transcriptome were limited by available sequencing technologies.

Purpose of the Study:

• To conduct a comprehensive analysis of the PRV transcriptome.
• To identify novel viral genes, transcripts, and isoforms using integrated sequencing data.

Main Methods:

• Systematic analysis of PRV transcriptome data.
• Integration of data from Pacific Biosciences Sequel and Oxford Nanopore Technologies MinION LRS.
• Combination with previously generated LRS and short-read sequencing data.

Main Results:

• Identification of numerous novel genes, transcripts, and transcript isoforms, including splice and length variants.
• Discovery of many 5'-truncated putative mRNAs co-terminal with canonical PRV mRNAs, some containing in-frame ATGs.
• Observation that the CTO-S RNA molecule is expressed at exceptionally high levels.

Conclusions:

• The PRV transcriptome is significantly more complex than previously understood.
• LRS technologies are crucial for uncovering the full extent of viral RNA diversity.
• The identified truncated transcripts may represent a novel source of functional viral proteins.