RNA-seq characterization of an infection of Mycobacterium smegmatis by a cluster A4 mycobacteriophage

We present transcriptomic analysis of an infection by a cluster A4 mycobacteriophage of its host, Mycobacterium smegmatis, at six time points (n = 2). Viral transcription is detectable 5 minutes into infection, and viral mRNA makes up the vast majority of all transcription by 30 minutes. Kampy, like many phages, has a genome organized into two arms bearing early- and late-phase genes. We identify two transcriptional start sites (TSS’s) consistent with an early promoter driving expression of half of the genome, along with a second, late-stage promoter that becomes active around 30 minutes after the start of infection. Overall design: One timepoint before and five timepoints during infection were analyzed using an Ion Torrent PGM. Two biological replicates were sequenced for each timepoint.