Prophage genes with no expression level in RNA-seq analysis are likely to be true phage genes

Bacteriophages could elect to undergo lysogeny in the infected bacterial cell during unfavourable circumstances. During this process, the entire phage genome would be integrated into the host genome at appropriate genomic locus. After integration, the phage genome remains transcriptionally silent given that phage genes do not contribute to cellular maintenance and fitness. However, transposase activity could introduce transposons that may randomly disrupt phage genes in the host genome through integration of entire open reading frames and associated promoter. Through this process, original phage gene locus would be transformed into one carrying genes from the host genome with host transcriptional control elements such as promoters. Hence, these transformed phage genes would be transcriptionally active, and could be detected by modern high throughput RNA-seq transcriptome analysis. Extending this logic, putative phage genes integrated into the host genome that register low or no expression level in RNA-seq transcriptome analysis of host cells may thus qualify for classification as true phage genes that have not been disrupted or affected by transposon activity. Knowledge of these true phage genes may hold important implications for our understanding of prophage evolution in the context of the host cell environment, as well as providing critical reference genes useful for probing the provenance and evolution of the prophage prior to genome integration.