Transcriptome-wide survey of pseudorabies virus using next- and third-generation sequencing platforms

Area of Science:

• Virology
• Genomics
• Bioinformatics

Background:

• Pseudorabies virus (PRV) is an alphaherpesvirus impacting swine populations.
• PRV possesses a large double-stranded DNA genome with a complex transcriptome.

Purpose of the Study:

• To present a large RNA-Seq dataset for Pseudorabies virus (PRV).
• To facilitate comparison of diverse sequencing approaches and library preparation methods.
• To support validation and testing of bioinformatics pipelines for viral transcriptomics.

Main Methods:

• Utilized both short-read (Illumina) and long-read (Pacific Biosciences, Oxford Nanopore) sequencing technologies.
• Employed various library preparation methods including random-primed, polyA-seq, non-amplified, amplified, direct RNA-sequencing, and Cap-selection.
• Aligned raw sequencing reads to the PRV reference genome (KJ717942.1).

Main Results:

• Generated a substantial dataset comprising millions of short reads and tens to hundreds of thousands of long reads.
• Obtained a significant number of PRV-specific reads across different sequencing platforms and protocols.
• Successfully aligned reads to the PRV genome, providing a basis for transcriptomic analysis.

Conclusions:

• The generated dataset is a valuable resource for studying the PRV transcriptome.
• The data allows for the evaluation and comparison of different sequencing and library preparation techniques.
• This resource aids in the development and validation of computational tools for viral genomics research.