Going the Distance: Optimizing RNA-Seq Strategies for Transcriptomic Analysis of Complex Viral Genomes

J Virol. 2018 Dec 10;93(1):e01342-18. doi: 10.1128/JVI.01342-18. Print 2019 Jan 1.

Abstract

Transcriptome profiling has become routine in studies of many biological processes. However, the favored approaches such as short-read Illumina RNA sequencing are giving way to long-read sequencing platforms better suited to interrogating the complex transcriptomes typical of many RNA and DNA viruses. Here, we provide a guide-tailored to molecular virologists-to the ins and outs of viral transcriptome sequencing and discuss the strengths and weaknesses of the major RNA sequencing technologies as tools to analyze the abundance and diversity of the viral transcripts made during infection.

Keywords: PacBio; RNA sequencing; minION; nanopore sequencing; next-generation sequencing; single-cell RNA-seq; transcriptome; virus.

Publication types

  • Research Support, N.I.H., Extramural
  • Review

MeSH terms

  • Computational Biology / methods
  • Gene Expression Profiling / instrumentation
  • Gene Expression Profiling / methods*
  • Gene Expression Regulation, Viral
  • Genome, Viral
  • High-Throughput Nucleotide Sequencing
  • Nanopores
  • RNA Viruses / genetics*
  • Sequence Analysis, RNA / instrumentation*
  • Sequence Analysis, RNA / methods
  • Single-Cell Analysis